computational science and engineering (cse) · zu¨rich, december 15, 2016 ralf hiptmair, director...
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Computational Science and Engineering (CSE) Annual Report 2015/2016
.
CSEComputational Science and Engineering
Annual Report
2015 / 2016
July 2015 to July 2016
Impressum:
© 2016
ETH Zürich
Editors:
Vasile Gradinaru, Ralf Hiptmair, Markus Reiher
ETH Zürich
PDF files of this report are available from:
Dr. Vasile Gradinaru
Seminar for Applied Mathematics
Tel.: 41 44 632 3448
E-mail: [email protected]
or may be downloaded from:
www.rw.ethz.ch
CSE curricula at ETH Zürich on the internet:
www.rw.ethz.ch or www.cse.ethz.ch
Cover:
Simulation steps for electron emission from a tungsten tip illuminated by a focused
laser beam
Groups having contributed to this report
Research Group Institute Projects Publs.
P. Arbenz Computer Science 40 96
K. Boulouchos Engines and Combustion Laboratory 41 97
C. Coperet Inorganic Chemistry 46 98
C. Hafner Electromagnetic Fields 47 100
H. Herrmann Building Materials 48 101
R. Hiptmair Seminar for Applied Mathematics 49
P. Hora Virtual Manufacturing 55 104
P. H6nenberger Physical Chemistry 56 105
P. Jenny Fluid Kynamics 57 106
A. Jentzen Seminar for Applied Mathematics 108
M. Kröger Polymer Physics 58 110
M. Luisier Integrated Systems Laboratory 59 112
S. Mishra Seminar for Applied Mathematics 60 114
R. M6ller Biomechanics 61 116
M. Parrinello Computational Science & USI 62 117
M. Quack Physical Chemistry 75 119
M. Reiher Physical Chemistry 76 122
S. Riniker Physikal Chemistry 77 124
C. Schär Atmospheric and Climate Science 78 125
C. Schwab Seminar for Applied Mathematics 79 128
P. Tackley Geophysics 86 131
M. Troyer Theoretical Physics 87 133
W. van Gunsteren Physical Chemistry 88 138
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Table of Contents
1 Introduction 9
2 Education 15
3 CSE Case Studies Seminar 23
4 Computational Highlight 27
5 CSE Research Projects 39
6 High Performance Hardware 91
7 Publications in 2015/2016 95
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1
Introduction
9
Preface to CSE Report 2016
R. Hiptmair1
December 14, 2016
1 Editorial
The “E” in CSDE stands for Egineering and a core engineering discipline is electricalengineering, whose home at ETH Zurich is D-ITET (Departement fur Informationstech-nik und Elektrotechnik). It goes without saying that researchers and engineers in thisfield both in academia and industry have always been early adopters of and even keycontributors to computer simulation technology. Nowadays, design and optimization ofcircuits, antennas, electronic and optical devices, electrical machines, and most othergifts of electrical engineering is inconceivable without the aid of computer simulation.
No doubt, electrical engineering plays an important role as a driver of developmentsin CSE. Therefore I met three prominent ETH scientists from D-ITET to learn abouttheir views of the role of CSE in the field and in their research.
L. Novotny D-ITET
Lukas Novotny graduated from ETH Zurich in 1992 witha Diploma in Electrical Engineering and in 1996 with a PhDin physics on “Light Propagation and Light Confinement inNear-field Optics”. He spent three years at the Pacific North-west National Laboratory in Richland (Washington, USA),before he continued his academic career as a professor foroptics, physics, and biomedical technology at the Universityof Rochester (NY, USA). In 2012 he joined D-ITET of ETHZurich as professor for photonics and head of the PhotonicsLaboratory.
1SAM, ETH Zurich, CH-8092 Zurich, [email protected]
10
Jurg Leuthold has a PhD degree in physics from ETH Zrichfor work in the field of integrated optics and all-optical com-munications. From 1999 to 2004 he has been affiliated withBell Labs, Lucent Technologies in Holmdel, USA, where hehas been performing device and system research with III/Vsemiconductor and silicon optical bench materials for applica-tions in high-speed telecommunications. From 2004 through2013 he was a full Professor at Karlsruhe Institute of Tech-nology (KIT), where he headed the Institute of Photonics andQuantum Electronics (IPQ) and the Helmholtz Institute ofMicrotechnology (IMT). Since March 2013 he is a full Pro-fessor at ETH Zurich and head of the Electromagnetic FieldsLaboratory (IEF).
J. Leuthold, D-ITET
Ch. Hafner, D-ITET
Christian Hafner was a student at the Department of Elec-trical Engineering of ETH Zurich. In 1980 he got his PhDunder the direction of Prof. H. Baggenstos at the IFH with aproposition of a new method for computational electromagnet-ics, the Multiple Multipole Program (MMP). This method wasalso the main part of his habilitation in 1987 and obtained aSeymour Cray award for scientific computing in 1990. In 1999he was given the title of Professor and currently he is a groupleader in the field of Computational Electromagnetics at theIEF of ETH. He has been the lead developer of several elec-tromagnetic simulation codes, some of which are now availablethrough the open-source project OpenMaxwell.
I would like to thank the three colleagues for taking the time to meet me. I haveextracted main points addressed in our conversation, which was in German, of course,and I am going to present them in the form of a fictitious interview:
1. The role of numerical simulation in your research projects?
L.N.: In my research there is a clear focus on experiments and modelling, becausemy goal is to understand physical effects and exploit them for the design of newdevices. In fact, numerical simulation plays an important role in testing models,but it is considered a mere tool; the results are important, not methods or codes.
J.L.: My PhD students spend a lot of their time doing simulations, but, again,it is considered a tool to supplement theory and measurements. Simulation hasbecome indispensable for testing ideas and optimizing designs of devices, becauseit can give us feedback fast.
2. Use of commercial codes versus own code development?
L.N.: We mainly use commercial codes like Lumerical2, Comsol3, and others foreveryday simulations. Sometimes we also rely on open source codes, but we never
2https://www.lumerical.com/3https://www.comsol.com/
11
delve into substantial implementation, let alone pursue projects with the goal of
developing simulation software. In fact, we regularly “outsource” simulation in
collaborative projects.
J.L.: In my team there is hardly any expertise in the development of advanced
simulation software and, in light of the pivotal role of simulation, we are forced to
use commercial codes. These codes are well suited for standard tasks and settings,
but more and more often their limitations become apparent, as research in devices
explores and exploits effects on smaller and smaller scales, down to the size of
atoms. Commercial software is not yet ready for these regimes.
In this situation we try to join forces with experts in numerical simulation to expand
our simulation capabilities. We seek advice on numerical modelling and enter into
cooperations with academic developers of simulation software.
C.H.: Academic efforts to create simulation codes are in crisis, because software
companies can rely on overwhelming manpower to add extensive pre- and postpro-
cessing facilities to their products and make them easy to use. No research code
can compete in this respect. Moreover, as numerical methods increase in sophisti-
cation, implementation becomes more and more time-consuming, beyond what can
be done in a regular research project. However, scientists should be more aware
that commercial codes are usually not tested or even not applicable for cutting-edge
research problems.
3. Validity and validation of numerical results?
C.H.: The situation is bleak: Numerical results are often published without proper
documentation and, thus, are by no means reproducible. The use of commercial
codes leaves scientists in the dark about the computational methods and they often
trust the results with gullible blindness. Basic checks for convergence and accuracy
are skipped frequently. Making matters worse, software vendors usually will not
admit limitations of their codes and this provokes use beyond their scope.
J.L.: For standard situations modern simulation has become fairly reliable. Never-
theless, we hesitate to publish results based on simulation alone. If possible, there
should be experimental underpinning and measured data matching what was ob-
served in the simulation. Simulation results usually support an observation or help
understand the physics behind an experiment.
L.N.: We carefully scrutinize numerical results assessing them in light of experi-
ments and our experience. This provides some kind of external validation for the
numbers generated by the computer.
4. Appreciation of CSE-oriented research in your community?
J.L.: The electrical engineering community is dominated by experimentalists and
designers, the majority of whom is not interested in numerical methods. Reviewers
often have a bias in favor of experimental work, conference audiences are deterred
by numerical topics, and simulation techniques are considered opaque. You get little
credit and attention for devising new numerical methods, and even if used, your
work may not be cited. This is not inevitable; if numerical papers were written in a
more accessible style and gave relevant examples, they would receive due attention.
12
C.H.: The community is not really aware of the effort and ingenuity required to
develop methods for fast, reliable, and accurate numerical simulations for nano-
optics. Codes are viewed as convenience tools that can be bought off the shelf.
5. Training of engineers in numerical simulation?
J.L.: Engineering education is still dominated by computing analytic solution in
simple cases, whereas all relevant solutions, for instance of electromagnetic field
problems, are nowadays obtained by numerical methods, both in academia and
industry. This should be reflected in engineering curricula in order to prepare
graduates for wisely using simulation codes.
Zurich, December 15, 2016
Ralf Hiptmair,
Director of Studies CSE, member of the CSE Committee
Post-Preface. This report is the first in a new format, in which groups are asked to
give an overview of their CSE-related research instead of presenting individual projects.
Ideas of what is a proper “overview” differ and this accounts for the large diversity in
appearance, style, and level of detail of the contributions in this volume.
13
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14
2
Education
15
In September 2015, 27 new students started their CSE Bachelor studies, 16 in the first
semester and 11 in the third semester. From outside ETH 8 students entered the CSE Master
curriculum.
The total number of CSE students enrolled at 4th November 2015 was 157 (headcount: 99 in
the BSc program and 58 in the MSc programh.
In the past academic year 38 students have successfully finished a CSE curriculum, 16
Bachelor students and 22 Master students, and have received a CSE degree, some with very
good scores. In the following list we give the name of the student, the title of the
Bachelor/Master thesis and the name and the department of the advisor.
The Willi Studer Preis 2016 for the best CSE Master Diploma in the past academic year was
awarded to Thomas Häner.
Number of CSE students in the curriculum; dark = number of new students
Number of CSE graduates
06/07 07/08 08/09 09/10 10/11 11/12 12/13 13/14 14/15 15/160
10
20
30
40
50
60
70
80
90
100
BSc
MSc
06/07 07/08 08/09 09/10 10/11 11/12 12/13 13/14 14/15 15/160
5
10
15
20
25
BSc
MSc
16
Bachelor Theses
Mark Ballandies An Implicit High-Resolution Scheme for Systems of
Hyperbolic Conservation Laws with Multiple Time Scales
(Siddhartha Mishra, D-MATHh
Stefan Beyeler Development of a High-Resolution Spatio-Temporal Model for
Predicting Urban Air Pollution
(Andreas Krause, D-INFKh
Michaja Bösch Efficient Implementation of Hagedorn Wavepackets in C++
(Ralf Hiptmair, D-MATHh
Luzius Brogli Kinect Sensor Interference Measurement
(Andreas Kunz, D-MAVTh
Daphne Chopard Data-Driven Assessment of Mathematical Abilities in a Computer-
Based Training Environment
(Markus Gross, D-INFKh
Carlo Del Don N-tem Approximation for Ridgelet Packets and Phantom
Reconstruction
(Phillip Grohs, D-MATHh
Simon Frasch The Reaction Field Method and Possible Improvements for Systems
with Liquid-Liquid Interfaces
(Sereina Riniker, D-CHABh
Thomas Graf On Bohmian Mechanics
(Siddhartha Mishra, D-MATHh
Linus Groner Multi-Agent Pathfinding on Graphs
(Torsten Hoefler, D-INKFh
David Haldimann Influence of Elastic Compressibility on Impact Simulations
(Taras Gerya, D-ERDWh
Andreas Hug Impact of Highly Non-Affine, 3D, Hybrid Meshes on the
Convergence of Iterative Methods
(Ralf Hiptmair, D-MATHh
Sarah Jetzer Virtual Reality System for Improved Hand-Eye Coordination
(Andreas Kunz, D-MAVTh
Julia Pfund Explosive Percolation Through Pdf Based Merger Control
(Hans Hermann, D-BAUGh
17
Lukas Strebel Soil Water Transport in a Stand-Alone Version of the Land-Surface
Model TERRA ML
(Christoph Schär, D-USISh
Benjamin Ulmer A Fault-Tolerant In-Memory Routine For The One Dimensional Heat
Equation
(Matthias Troyer, D-PHYSh
Tobias Wicky Communication-Avoiding Parallel Algorithms for Solving Triangular
Matrix Equations
(Torsten Höfler, D-INFKh
Master Theses
Leonardo Echeverria Numerical Modeling of Human Population Dynamics
(Anthony Patt, D-USYSh
Matthias Frey Matched Distributions in Cyclotrons with Higher Order Moments of
the Charge Distributions
(Andreas Adelmann, PSIh
Maurice Gonzenbach Sentiment Classification and Medical Health Record Analysis using
Convolutional Neural Networks
(Thomas Hofmann, D-INFKh
Thomas Häner Theory, Implementation, and Efficiency of Quantum Algorithms
(Matthias Troyer, D-PHYSh
Rico Häuselmann Automated Workflows for Maximally Loacalized Wannier Functions
via VASP and Wannier90 using AiiDA
(Matthyas Troyer, D-PHYSh
Stefan Hegglin Simulating Collective Effects on GPUs
(Peter Arbenz, D-INFKh
Samuel Keusch Detecting and Tracking of Sperms Using Machine Learning
(Anton Gunzinger, D-ITETh
Lionel Miserez Improving Single Core Performance in OPAL
(Peter Arbenz, D-INFKh
Lukas Mosimann Towards Online Cloud Tracking with the COSMO-Model
(Heini Wernli, D-USYSh
An Phi Nguyen Watlets: Computational Design of Water Surfaces
(Markus Gross, D-INFKh
18
Seonwook Park Dense Visual SLAM for RGB-D Cameras in Project Tango
(Marc Pollefeys, D-INFKh
Sandro Sgier Parallel STL. Prototype Implementation and Evaluation on
Algorithmic Motifs Found in Scientific Computing
(Torsten Höfler, D-INFKh
Kelly Steich Tree Cavity Inspection Using Aerial Robots
(Roland Siegwart, D-MAVTh
Benjamin Ulmer The P3M Model on Emerging Computer Architectures With
Application to Microbunching
(Andreas Adelmann, PSIh
Ann-Christine Straw Development of Seeding Algorithms in CUDA for the CMS
Experiment at CERN
(Günther Dissertori, D-PHYSh
Roger Walt Divergence-Free Wind Downscaling using Numerical Weather
Prediction Data
(Christoph Schär, D-USYSh
Christian Zeman An Isentropic Mountain Flow Model with Iterative Synchronous Flux
Correction
(Christoph Schär, D-USYSh
Dzmitry Zhyhadla Numerical Modeling Of Meteorite Impacts With Continuum-Based
Approach
(Taras Gerya, D-ERDWh
Listed below are term papers written by the CSE Master students in the past two semesters.
Term Papers
Gabriele Abbati Reinforcement Learning for Optimal Motion of Interacting Swimmers
(Petros Koumoutsakos, D-MAVTh
Dominik Eugster The Water Drop Stereo Camera: From Wide Field of View Macro
Imaging to 3D Reconstruction
(Markus Gross, D-INFKh
Xiaolin Guo Exploit Automatic Overlap and Concurrency of Stencils of the
Dycore of COSMO for GPUs using STELLA
(Ulrike Lohmann, D-USYSh
19
Maurice Gonzenbach Predict Seizures in Intracranial EEG Recordings
(Gabor Székely, D-ITETh
Lionel Miserez Porting WaveBlocksND Matrix Potential Functionality to C++
(Vasile Gradinaru, D-MATHh
Benedek Vartok Implementation of WaveBlocksNDs Quadrature and
Inner Products in C++
(Vasile Gradinaru, D-MATHh
Ann-Christine Straw On the collapse of Molecular Clouds using Formulations of the SPH
equations
(Lucio Mayer, UZHh
Kevin Wallimann Advanced Mixed-Integer Solver for Field-Guided Parameterization
(Olga Sorkine-Hornung, D-INFKh
Daniel Wählhli Implementation of Multi-Asset Spread Option Pricing Methods
(Walter Farkas, D-MATHh
Baranidharan Mohan Two Dimensional Concurrent Start for Scalable Parallelism
(Torsten Hoefler, D-INFKh
Felix Thaler Adaptive MPI for Automatic Load-Balancing of GPU-based High
Performance Applications
(Petros Koumoutsakos, D-MAVTh
Thijs Vogels Webpage Main Story Extraction using Structured Support Vector
Machines
(Thomas Hofmann, D-INFKh
Alessio Zanchettin Robust Vision Based Automatic Takeoff and Landing for UAVs
(Roland Siegwart, D-MAVTh
Raphael Stadler RoboCup: Ball Dribbling
(John Lygeros, D-ITETh
Rico Häuselmann Generic Implementation of a Monte Carlo Simulation of the
Heisenberg model
(Mattyas Troyer, D-PHYSh
Cattaneo Roman Porting FLake to GPU
(Oliver Fuhrer, Meteo Swissh
Xiaolin Guo Feasibility Study for Achieving Performance Portable Global Weather
and Climate Models on Icosahedral Grids using DSL Libraries
(Oliver Fuhrer, Meteo Swissh
20
Zürich, November 6, 2016
Vasile Gradinaru,
Advisor of Student Studies CSE and member of the CSE Committee
(Fachberater RW und Mitglied des Ausschusses Rechnergestützte Wissenschaftenh
For detailed information on the RW/CSE curricula at ETH Zürich see:
www.rw.ethz.ch or www.cse.ethz.ch
21
.
22
3
CSE Case Studies Seminar
23
The CSE Case Studies Seminar takes place each semester on Thursdays, 15 - 17
hours. Speakers from ETH, from other universities as well as from industry are
invited to give a 2x45 minutes talk on an applied topic. The idea is to show the
students a case study of an application problem containing the problem setting, the
modelling, the mathematical approach and the simulation on a computer. In addition,
such a case study should show what is going on in the field of CSE and what are the
job perspectives for a CSE engineer. The seminars of the past academic year are given
in the two following lists.
Case Studies Seminar HS15
01.10.15 Rémi Abgrall, Mathematics & Computational Science, Univ. Zürich
Computing Compressible Flows: What are the Issues, How is it
Possible?
08.10.15 Will Sawyer, CSCS, Lugano
GPGPUs: Fad or Fundament? Use Cases from Applications Running
at CSCS
29.10.15 Sereina Riniker, Physical Chemistry
Multiscaling in Biomolecular Simulations
19.11.15 Perry Bartelt, WSL, Inst. for Snow and Avalanche Research, Davos
Snow Avalanche Dynamics: Physics, Modelling and Applications
26.11.15 Tomas Zimmermann, Seminar for Applied Mathematics (SAM)
Electron Ionization with Ultra-Short Laser Pulses:
Quantum and Classical Dynamics
03.12.15 Rudiyanto Gunawan, Chemical and Bioengineering
Mitochondrial DNA Mutations and Ageing: Insights from in Silico
Modelling and Analysis
17.12.15 Andreas Adelmann, Paul Scherrer Institut (PSI)
Particle Accelerator Modelling: from Lie Algebra to GPUs
24
Case Studies Seminar FS16
25.02.16 Vasile Gradinaru, Seminar for Applied Mathematics (SAM)
Numerical Methods for Semi-classical and Quantum Dynamics of Nuclei
03.03.16 Petros Koumoutsakos and Diego Rossinelli, Mechanical Engineering
The in Silico Lab on a Chip: HPC for Circulating Tumor Cells
10.03.16 Markus Püschel, Computer Science
How to Give Strong Technical Presentations
07.04.16 Beat Müller, Swisstom AG, Landquart
Real-time Monitoring of Mechanical Ventilated Lungs Based on Electrical
Impedance Tomography (EIT): From Research Towards a Medical Device
12.05.16 Arnulf Jentzen, Seminar for Applied Mathematics (SAM)
An Introduction to the Approximative Pricing of Financial Derivatives
02.06.16 Dagmar Iber, Computational Biology
Computational Studies of Organogenesis
25
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26
4
Computational Highlight
27
Advanced Electromagnetic Simulations
Ch. Hafner1, J. Leuthold
1, J. Smajic
1,2, A. Emboras
1, H. Yanagisawa
3
1Institute of Electromagnetic Fields (IEF), ETH Zurich
2Institute of Energy Technology, University of Applied Sciences of Eastern Switzerland, Rapperswil
3Ludwig-Maximilians University and Max-Plank Institute of Quantum Optics, Garching, Germany
Introduction
After the pioneering experiments of Faraday, his discovery of electromagnetic induction in1831, and
based on his conception of fields (lines of force), Maxwell published a set of coupled partial differential
equations that are considered to be the theoretical fundament of electromagnetics. These equations
were brought into a more user-friendly form by Heaviside and build the core of computational
ouPv]X &Ç[ oÁ ( ]vµ]v o Z Àouv ( o]uU PvU
v(u X v Z( ÁoÁ] o] Á µoÇU DÆÁoo[ µ]ons also
demonstrated the possibility of electromagnetic waves and the conception of light as an
electromagnetic wave. Finally, these waves led to worldwide data communication.
Before Faraday, it was not clear that the various observations of electric and magnetic effects have a
common basis and these effects were neither well understood nor exploited for practical applications.
Lightning, the most impressive and scaring natural demonstration of electromagnetism was hitting
churches with tall towers more frequently than other buildings and this must have troubled people at
that time. In 1749, Franklin studied lightning and this led to the protection by means of a lightning rod,
i.e., a metallic wire connected to earth with a sharp tip Z^_~u]ts) lightning. Today, the
lightning rod effect is not only exploited to protect tall buildings, such as antenna towers (containing
sensitive electronic parts) that are hit by many lightning events par year, but also in high voltage
applications down to nano- and even atomic scale configurations.
Since sharp metallic tips lead to Z]PZo](]ovZ]UZÇuZÁ^(]ouo](]_
and they may act as sources of sparcs, which are desirable in sparc plugs for petrol engines but should
be avoided in many other applications. In 1887, Hertz noticed that that electric sparks are created more
easily when the metallic electrode is not only under high voltage, but also illuminated by ultraviolet
light. This photoeffect was not also important for the ignition of sparcs and for the development of
sensors, its explanation by Einstein in 1905 also led to quantum mechanics, i.e., also electromagnetic
fields and light are involved, the effect cannot be explained by Maxwell theory alone. Thus, one can
correctly simulate structures containing sharp metallic tips using Maxwell solvers alone only when no
sparks and not even electrons are emitted and when the radius of curvature is large enough for using
bulk material models.
28
In 1981 Binning and Rohrer built the Scanning Tunneling Microscope (STM) that exploited a sharp metallic tip
over a conducting surface and measured the tunneling current as a function of the tip position in order to
visualize atomic-scale features that could not be observed with microscopes. The tunneling of electrons is
also a quantum effect that cannot be understood by Maxwell theory. Soon after, the configuration was
slightly modified and mechanical forces were measured instead of tunneling currents in Atomic Force
Microscopes (AFM), and various other effects were exploited in Scanning Probe Microscopy (SPM), e.g., in
Scanning Nearfield Optical Microscopes (SNOM). The most successful SNOMs are modified STMs or AFMs
with a sharp metallic tip, illuminated, e.g., by a focused laser beam. Unlike classical optical microscopes,
SNOMs are not limited by the Abbé limit, i.e., they can resolve objects that are considerably smaller than half
of the applied wavelength because their resolution is mainly limited by the radius of curvature of the tip.
Utilizing light allows one to gather much more information than by observing tunneling currents and forces.
Finally, one can do spectroscopy and this leads to Tip Enhanced Raman Specroscopy (TERS).
Microscopy is essential for observing small structures, but setups with a high resolution also may be exploited
for high-density data storage. This may be again based on various physical effects and many of them belong
to the area of electromagnetics, e.g., magnetic and optical disks and more recent memristor memory that
essentially consists of an array of ultra-thin metallic filaments connecting two tiny electrodes. Essentially,
each of these filaments is a nano- or even atomic-scale electric switch. For the same reason as mentioned
above, memristors and similar structures cannot be modeled by Maxwell solvers alone.
It is important to note that even configurations with sharp metallic tips that could be explained sufficiently
well with Maxwell theory may be crucial for Maxwell solvers because they include very small parts causing
strong effects in rather large structures. As soon as the electric field near a tip is strong enough, electrons
may be emitted and then Maxwell solvers are no longer sufficient to study the structure. This may happen on
a large scale at very high voltage but also at very small scales at moderate voltages. In all cases, one can still
benefit from Maxwell solvers but one has to add other software. This will be detailed in the following.
Design of high voltage switches (Jasmin Smajic)
Despite of its primitive concept, electric current interruption by separating electric conductors is a difficult
task. However, the processes behind current breakers are very complicated. At the moment of time prior to
the contact separation, an electric current flows through the connected conductors. This current has a
considerable magnetic energy stored in all the inductive components of the system before interrupting the
contact. The stored magnetic energy does not tolerate the tendency of current reduction as soon as the
process of contact separation begins. The counter action of the stored magnetic energy is measurable as an
induced voltage (the so-called interrupter return voltage) acting between the contacts of the interrupting.
The return voltage increases the electric field between the separated contacts causing an ionization process
of the gas between the contacts thus making the gas electrically conductive and establishing a volume of high
temperature plasma or an electric arc. At moderate voltages, the resulting sparcs may be almost invisible but
they may lead to a corrosion of the contacts in the long term. At high voltages, the stored magnetic energy is
rather big and impressive (and destructive) sparcs are observed, as illustrated in Fig. 1. Due to its own
pressure buildup and due to the magnetic Lorenz force the plasma can move in the surrounding space and
have a very complicated shape.
29
For fast and efficient interruptions of currents a special gas (SF6) with pronounced high voltage withstand
capabilities is presently used in modern high voltage circuit breakers. The gas is pressurized in large switching
compartments that include circuit breakers, busbars, connecting elements, disconnectors, insulators and
measuring equipment. The entire system is called Gas Insulated Switchgear (GIS) and a prominent example of
it is shown in Fig. 2.
Fig. 1. Interruption of current with a simple open-air-contact between two conductors of a high voltage
system resulted in a permanently burning electric arc that cannot be extinguished (from
teslamania.delete.org).
Fig. 2. '/^]voo]v(Zí[íììlsÇu]vZ]v~www.abb.com).
The described ionization process due to the induced return voltage happens also inside of modern circuit
breakers. The breaker however has advanced systems to efficiently extinguish the burning electric plasma
30
between its contacts at the zero-crossing ( Z µvX Z µv[ Ì-crossing the hot and
electrically conductive plasma between the contacts is usually blown away and replaced by a cold gas in such
a way that Zv[]vµo]v]o]] are fully recovered.
Every GIS installation is evidently a large encapsulated volume. This gives rise to additional problems of
electromagnetic wave nature, the so-called very fast transients (VFT) that can be analyzed by solving Maxwell
equations in time domain. The VFT problem is presented in Fig. 3. By separating the contact of the high
voltage disconnector shown in Fig. 3 (left) one side of it follows the AC grid potential and the other side
retains the potential value of the separation moment. The contacts move at a finite speed away from each
other. The potential difference, however, steeply increases and the electric field quickly reaches the
ionization level yielding an electric spark. This steep discharge generates high frequency electromagnetic
waves that exist for considerably long time in GIS due to its encapsulated nature. Being permanently
reflected and transmitted in the GIS volume, the electromagnetic waves lead to a very complicated dynamic
voltage distribution with peak values that could reach 2.5 times the nominal voltage, which is a considerable
design challenge.
To mitigate this problem 3D full-Maxwell time domain simulations are required. A 3D simulation model of a
GIS-section along with the discharge modeling function are presented in Fig. 4. The obtained results in form
of the electric field (Fig. 5) show the wave nature of the transients. They cover the frequency range up to
100MHz. The simulations results were verified by comparison against the dynamic voltage measurements
given in Fig. 6. The comparison revealed the accuracy level acceptable for daily design purposes.
Fig. 3. Origin of very fast electromagnetic transients in GIS [1].
31
Fig. 4. 3D simulation model of the GIS [1]. The insulation collapse between the contacts is modeled as a time
dependent electric conductivity function defined according to the available measured data.
Fig. 5. Electric field distributions as a result of the full-Maxwell simulation in time domain at different
uuv ( ]u ( Z ]ZP :X ^ui]U tX ,oµU :X <À]U hX Z]ZU ^ï &µoo-Maxwell
^]uµo]v(sÇ &dv]v ]v'/^_U /dv]vvDPv]UsoXðóUEXñUXíñíð-1517,
May 2011.].
32
Fig. 6. Verification of the results by comparison against measurements (left) and the measurement setup [1].
Electron emission of sharp tips stimulated by optical pulses (Hirofumi Yanagisawa, Christian Hafner)
It is well known, that electrons may exit negatively charged metallic electrodes when the electric field on the
surface is strong enough. This should not be possible according to pure electromagnetic theory because of
oo]vP(µÇ^u]ZP_, which form a surface barrier, in other words a work function, as
indicated by dashed lines in Fig. 7(a). When strong electric fields are applied to the metallic surface, the
surface barrier becomes bent and prompt electron emission by tunnelling through the thinned surface
barrier as shown in Fig. 7(a) is obtained. This is a quantaum mechanical phenomenon. The photoeffect
suggests that the electron emission may be triggered by pulses of light and this is indeed exploited in electron
guns, e.g., in the huge Swiss Light Source (SLS) facility. Since the tip effect or lightning rod effect leads to a
strong concentration of the electric field near a negatively charged metallic tip, electron excitation can be
confined around the apex of the sharp tip. . In contrast to relatively large, flat electrodes in electron guns one
then may have a very small area - ranging from a couple of tens of nanometers to the atomic level - where
the electrons are generated and one may even trigger a single electron by an ultra-short optical pulse with
down to attosecond temporal confinement. Thus this has the advantage that one rather precisely knows
both location and time of the electron emission. In order to clarify the electron emission mecahnism and
ultrafast electron dynamics under laser irradiation, we have simulated electron dynamics from inside of
metal up to counter electrode, and reproduced energy spectra which will then be compared with the
observed energy spectra. As mentioned before, the electron emission is a quantum effect that cannot be
]uµoµ]vPDÆÁoo[µ]vX Quantum mechanical simulation tools that might simulate the entire
structure, however, demand huge computer resorces. Since some process can be treated as classical, we
separate the entire process to four steps as shown in Fig. 7. Here, we use Maxwell solvers for almost all the
involved processes, namely step 1-3.
.
33
In a first step one therefore must compute both the electrostatic high-voltage field of the configuration and
the electrodynamic field of the laser pulse interacting with the tip. The electrostatic computation must take
the entire configuration of the tip with the flat counter electrode into account and this computation must he
highly accurate. This excludes Finite Element Methods (FEM) from being applied. Instead, we applied the
electrostatic Multiple Multipole Program (MMP) that is contained in the OpenMaXwell software [2,3]. MMP
ooÁvÆ]uZ](]oÀǵoÇÁ]ZZuoovµu(^(]]]µZP_
placed along the axis of the tip. These charges are static and need to be computed only once. Furthermore,
they simplify tracing moving electrons which left the tip and are accelerated by the electric field. The
electrodynamic computation is more demanding because the excitation is a pulsed laser that is focused on
the tip and that excites surface plasmons surrounding the tip. For electromagnetic pulse propagation one
often uses the Finite Difference Time Domain (FDTD) technique, but this is not appropriate here, because of
the geometry of the configuration and because metals are strongly frequency dependent at optical
frequencies, which either leads to substantial numerical errors or extremely high computational costs. A
much better time domain solver is Discontinuous Galerkin FEM [4]. Another alternative is to apply the
dynamic MMP solver of OpenMaXwell together with Fourier transform since MMP is a frequency domain
solver. We tried both strategies and obtained good agreement of the results.
In the second step, the probability of the electron emission for each point on the surface of the tip can be
computed from an experimentally obtained work function and the normal component of the electric field
extracted from OpenMaXwell [3]. Here we can also choose the emission mechanism. As soon as an electron
has been emitted, it is accelerated by the electric field and it can be traced by algoriths that are used for the
simulation of electron guns in the step 3. In this process, excited electrons may interact with other excited
electrons and also with the image charges in the tip. Furthermore, because of the statistic nature caused by
quantum effects, one has to cary out many electron tracing simulations and consider the statistics of all of
them. From this, one finally obtains the energy distribution of electrons which go through a pinhole on the
counter electrode as indicated by a white circle that is measured in the experiment [5].
34
Fig. 7. Simulation steps for electron emission from a tungsten tip illuminated by a focused laser beam.
35
Atomic-scale optical switch (Alexandros Emboras)
Modulating and switching waveguide modes by changing the geometry of the waveguide is a fundamental
and very old concept. Essentially, this concept was mostly replaced when electronics came in, but RF-MEMS
technology brought a revival and numerous publications can be considered as a further miniaturization step.
When thinking towards the maximum possible miniaturization, one comes to a mechanical movement of a
single atom. The mechanical or electrically induced movement of an atom is possible and has been exploited
for creating ultra-small electrical switches for memory applications (so-called memristors). If we want to have
an observable impact of the movement of an atom on an optical wave propagating in an optical waveguide,
Ávu(^uo](]]v_uZv]uZulZÀ]Z]PZoÇv]]ÀZuÀuv(
an atom. We exploit two mechanisms: the field enhancement by tips and the shift of a plasmonic resonance.
Recently we were able to show the first integrated atomic scale plasmonic switch. Fig. 8(a) shows a SEM
picture of the fabricated device. An optical signal can be launched into the device through optical Si
waveguides. This signal is first converted into an SPP (surface plasmon polariton) mode of a MIM (metal
insulator metal) waveguide, i.e., a plasmonic slot consisting of Ag-aSi-Pt. The slot, in which the SPP is
propagating, is tapered down and forms a junction with a minimum gap width of only 20 nm. At the edge
where the gap width is smallest, a tiny Ag filament is grown by applying a modest voltage between the Ag
and Pt electrodes. Depending on the polarity of the applied voltage, this growth process can reversibly form
or destruct the atomic scale nanofilament which shunts or opens the two metallic electrodes through the aSi
insulator. The underling switching mechanism of our device is based on an electrical manipulation of a few
atoms that reside in either of two resonance states. The resonance states can be controlled by the polarity of
the applied voltage in the plasmonic cavity. By moving only a few atoms the resonance condition of the
plasmonic cavity is altered. The optical transmission can thus be electrically controlled by moving back and
forth only a few atoms.
In order to understand the working principles and to design an appropriate structure, appropriate
simulations are desirable. On one hand side, the entire structure is far too big for brute-force simulations
based on quantum mechanics. On the other hand side one cannot expect accurate results from Maxwell
solvers in the core are of the switch, where one or a few atoms are moved. Therefore, we performed
Maxwell simulations of the entire structure without expecting precise quantitative results but these
simulations showed that plasmonic resonances occur and must be shifted by the change of the filament in
such a way that the transmitted light will be affected sufficiently for being observed. This simulation was
complemented by an ab-initio quantum transport simulation of the tip of the filament.
Experimental results show digital switching of up to 10 dB when electrically relocating a single (or at least a
few) atom(s) in a plasmonic cavity Fig. 8(c). The experiments have shown a reproducible and reliable
operation for days. The structure is CMOS compatible and is derived from a standard memrestive technology
known from electronics. Finally the demonstrated power consumption at the fJ level for a single switch
operation is orders of magnitude smaller than what was known in optics before.
The proof of atomic scale operation is clearly demonstrated by the quantized conductance levels in current
voltage measurement Fig 8(b). Three distinct levels of conductance close to the quantum conductance unit
G0 can be seen. This is confirmed by the ab-initio quantum transport calculations (dashed blue lines). The
plotted atomic structures have been simulated: the red atoms have been gradually added to the filament,
36
37
[4] Josip Mihaljevic, Jens Niegemann, Sascha M. Schnepp, and Christian Hafner, On the Numerical Modeling
of Sharp Metallic Tips, Quantum matter, (2014) Valencia, CA: American Scientific Publishers.
[5] Hirofumi Yanagisawa, Matthias Hengsberger, Dominik Leuenberger, Martin Klöckner, Christian Hafner,
Thomas Greber, Jürg Osterwalder, Energy Distribution Curves of Ultrafast Laser-Induced Field Emission and
Their Implications for Electron Dynamics, Physical review letters, Vol. 107, No. 8, pp. 087601, 2011.
38
5
CSE Research Projects
39
Title: Parallelization of the time integration for time-periodic flow problems
Researchers: Peter Arbenz⋆
Daniel Hupp⋆
Dominik Obrist†
Institute/ ⋆Computer Science Department, ETH ZurichGroup: †ARTORG Center, University of Bern
Description:We investigate parallel algorithms for the solution of flow problems that are periodic intime. Finite difference approximations on a mesh in space-time are used. For periodicsolutions, the discretized problem can be written as a large non-linear system of equations.This system of equations is solved by a Newton-Krylov method, using a preconditionedGMRES solver. The parallel performance of this algorithm is illustrated by a number ofnumerical experiments in one and two space dimensions.
References:
D. Hupp, P. Arbenz, and D. Obrist. A parallel Navier–Stokes solver using spectral dis-
cretization in time. Int. J. Comput. Fluid Dyn., 2016. doi:10.1080/10618562.2016.
1242725.
P. Benedusi, D. Hupp, P. Arbenz, R. Krause: A parallel multigrid solver for time-periodic
incompressible Navier–Stokes equations in 3D. In: Numerical Mathematics and AdvancedApplications - ENUMATH 2015. B. Karasozen, M. Manguoglu, M. Tezer–Sezgin, S.Goktepe, O. Ugur (eds.). To appear 2016.
D. Hupp, D. Obrist, P. Arbenz: Multigrid preconditioning for time-periodic Navier–Stokes
problems. Proc. Appl. Math. Mech. (PAMM) 15, 595–596 (2015).
P. Arbenz, D. Hupp, D. Obrist: A parallel solver for the time-periodic Navier–Stokes
equations. In: Parallel Processing and Applied Mathematics (PPAM 13), Part II. R.Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski (eds.). Lecture Notes in Com-puter Science 8385, pp. 291–300. Springer, Berlin, 2014.
40
Title: Three-dimensional direct numerical simulations of turbulent fuel-
lean H2/air hetero-/homogeneous combustion over Pt with detailed
chemistry
Institute/
Group:
B.O. Arani1, C.E. Frouzakis1, J. Mantzaras2, K. Boulouchos1
1Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Combustion Fundamentals Group, Paul Scherrer Institute, CH-
5232 Villigen PSI, Switzerland
Three-dimensional direct numerical simulations with detailed heterogeneous and homoge-
neous chemistry and transport were carried out to investigate the turbulent combustion of fuel-
lean hydrogen/air mixtures (equivalence ratios φ = 0.16 and 0.18) in a Pt-coated channel with
prescribed wall temperatures of 1250 K and 1270 K and an incoming bulk Reynolds number
of 5700. Over the channel domain where only catalytic reactions were present, temporally
and spatially segregated islands with increased concentration of the limiting hydrogen reactant
formed on the walls, a manifestation of finite-rate surface chemistry effects. Fluctuations of
either gaseous or surface species were significant (up to 34%) at the upstream channel locations
and dropped farther downstream due to the flow laminarization induced by the heat transfer
from the hot walls and the growth of the turbulent boundary layer, exemplifying the necessity
of appropriate catalytic chemistry turbulence closures similar to those used for gas-phase reac-
tions. Downstream of homogeneous ignition, gas-phase combustion was concentrated in elon-
gated streamwise stripes confined close to the walls. Hydrogen was incompletely converted
within the gaseous combustion zones, and the leaking fuel reacted on the catalytic walls leading
to combined hetero-/homogeneous combustion over the entire post-ignition domain. Local ex-
tinction of gaseous combustion was finally observed in spatially isolated regions characterized
by high streamwise vorticity.
(a, b) Instantaneous profiles of catalytic (C) and gaseous (G) fuel conversion rates on the lower wall
at (a) x = 0.7, (b) x = 0.7. (c) Instantaneous map of gaseous fuel conversion rates [kg/m2s] and of
quasi-streamwise streak vorticity structures ωz = ±0.4 (black and white isolines) on the zx -plane at
y = 0.95.
References:
• B.O. Arani, C.E. Frouzakis, J. Mantzaras, K. Boulouchos Three-dimensional direct numerical
simulations of turbulent fuel-lean H2/air hetero-/homogeneous combustion over Pt with detailed
chemistry, Proc. Combust. Inst., 36 (in press)
41
Title: Direct numerical simulation of the compression stroke under engine
relevant conditions: Local wall heat flux distribution
Institute/
Group:
M. Schmitt1, C.E. Frouzakis1, Y.M. Wright1, A.G. Tomboulides2,
K. Boulouchos1
1Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Department of Mechanical Engineering, University of Western
Macedonia, 50100 Kozani, Greece
The distribution of the heat flux on the walls in a closed cylinder during the compression
of a non-reactive hydrogenair mixture is investigated by direct numerical simulation of a com-
pression stroke under engine-relevant conditions. The temperature field relation with the local
heat flux distribution is found to depend strongly on the distance from the wall. The strong
correlation within the viscous sublayer deteriorates with increasing distance from the wall. The
flow in the wall-normal direction transports hot gases towards and cold gases away from the
wall and the velocity in the wall-normal direction is correlated to the heat flux distribution also
further away from the wall. A local flow away from the wall results in a lower and more uniform
heat flux while flow towards the wall result in significantly higher and strongly fluctuating heat
fluxes. Ejection streams localized in the near-wall region are found to be responsible for the
highly fluctuating heat flux distributions. The joint PDF distributions of wall-normal velocity
and temperature with the heat flux collapse when scaled by density-weighted wall-normal units,
which can be used to model the heat flux distribution within coarser RANS and LES cells and
may therefore provide a promising basis for future engine wall heat transfer models.
Velocity components at 346 crank angle degrees in the (a) azimuthal, (b) radial and (c) axial direction at
a horizontal slice at 0.375 mm below the cylinder head; (d) heat flux distribution on the cylinder head.
References:
• M. Schmitt, C.E. Frouzakis, Y.M. Wright, A.G. Tomboulides, K. Boulouchos, Direct numeri-
cal simulation of the compression stroke under engine relevant conditions: Local wall heat flux
distribution, Int. J. Heat Mass Transfer, 92, 718-731, 2016.
42
Title: Towards Direct Numerical Simulations of realistic IC Engine ge-
ometries
Institute/
Group:
G.K. Giannakopoulos1, C.E. Frouzakis1, P.F. Fischer3, A.G.
Tomboulides2, K. Boulouchos1
1Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Mechanical Eng. Dept., Aristotle U. Thessaloniki, Greece3Computer Science Dept., U. Illinois Urbana-Champaign, U.S.A.
Incompressible direct numerical simulations were performed in the intake pipe of a labora-
tory scale internal combustion engine at Reynolds numbers corresponding to realistic operating
conditions. Flow features were identified as the fluid passes through the intake pipe and in-
teracts with the cylindrical valve stem before entering the cylinder. The sensitivity of the flow
development on the velocity profile imposed at the inflow boundary was assessed. It was found
that the flow becomes turbulent very quickly as it passes around the valve stem, even though no
noise was added at the inflow boundary to mimic turbulent velocity fluctuations. The transition
to turbulence is a result of competing and interacting instability mechanisms both at the inner
curved part of the intake pipe and at the valve stem’s wake. Subsequently, the flow in the intake
pipe was coupled with the engine cylinder, in a configuration where the valve is fixed at its
half-lift position and the piston moves from the top to the bottom dead center. The asymmetry
in the mass flux generated at the intake pipe due to the presence of the valve stem, as well as
the non-central placement of the intake valve, were found to have an important impact on the
charging motion inside the cylinder by inducing a swirling motion that affects all subsequent
processes such as mixing, flame propagation, heat transfer, and eventually the overall engine
performance.
(a) (b)
Iso-surfaces of λ2 colored with the flow velocity magnitude during the simulation of the (a) intake pipe
and (b) intake pipe coupled with the cylinder of an IC engine.
References:
• G.K. Giannakopoulos, C.E. Frouzakis, P.F. Fischer, A.G. Tomboulides, K. Boulouchos, DNS
of the flow in the intake pipe of an internal combustion engine, ETMM11, 21-23 Sept. 2016,
Palermo, Italy.
• G.K. Giannakopoulos, C.E. Frouzakis, P.F. Fischer, A.G. Tomboulides, K. Boulouchos, To-
wards DNS of realistic ICE geometries: flow in the intake pipe of the TCC-III engine test bench,
LES4ICE 2016, 30 Nov.-1 Dec. 2016, Paris, France.
43
Title: Spectral Quasi-Equilibrium Manifold for Chemical Kinetics
Institute/
Group:
M. Kooshkbaghi1, C.E. Frouzakis1, K. Boulouchos1, I.V. Karlin1
1Aerothermochemistry and Combustion Systems Laboratory,
ETHZ
The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique
for chemical kinetics based on entropy maximization under constraints built by the slowest
eigenvectors at equilibrium. The method is revisited here and discussed and validated through
the MichaelisMenten kinetic scheme, and the quality of the reduction is related to the temporal
evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mech-
anisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air
in adiabatic constant pressure reactors. The system states computed using SQEM are compared
with those obtained by direct integration of the detailed mechanism, and good agreement be-
tween the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of
hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled
Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is
found to provide a more accurate description.
References:
• M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. Karlin, Spectral Quasi-Equilibrium
Manifold for Chemical Kinetics, J. Phys. Chem. A, 34063413, 120(20), 2016.
44
Title: Unstructured LES-CMC modelling of turbulent premixed bluff body
flames close to blow-off
Institute/
Group:
D. Farrace1, K. Chung1, S.S. Pandurangi1, Y. M Wright1, K.
Boulouchos1, N. Swaminathan2
1Aerothermochemistry and Combustion Systems Laboratory, ETHZ2 Department of Engineering, University of Cambridge, Cambridge,
U.K.
A finite volume Large Eddy Simulation-Conditional Moment Closure (LES-CMC) formu-
lation is applied to turbulent premixed bluff body methane-air flames at conditions far from
(A1) and close to (A4) blow-off. The unstructured topology of the CMC grid allows refinement
in regions where turbulence inhomogeneity is expected, providing an improved description of
the turbulence-chemistry interaction phenomenon, non-negligible at conditions investigated in
this study. Subgrid scale (SGS) progress variable variance and scalar dissipation rate are closed
with models associated with the SGS combustion, turbulence and molecular diffusion processes
of premixed flames using detailed kinetics. The simulations effectively reproduce the general
trends: the characteristic ‘M’-shaped morphology of flame A4 and the significant increase in
flame brush thickness compared to flame A1 is accurately replicated, although overall flame
heights are under-predicted. For flame A4 close to blow-off, the calculation generally shows
appreciable quantities of CH2O throughout the recirculation zone with isolated pockets of OH,
surrounded by high heat release, in agreement with experimental findings. The simulation fur-
ther evidences that in regions experimentally void of both CH2O and OH, large quantities of
partially reacted fluid are present which entered the recirculation zone from the top.
Comparison between experimental mean OH-PLIF (top) and computed OH mean mass fraction (bottom)
for A1 (left) and A4 (right) - (arbitrary units).
References:
• D. Farrace, K. Chung, S.S. Pandurangi, Y. M Wright, K. Boulouchos, N. Swaminathan, Un-
structured LES-CMC modelling of turbulent premixed bluff body flames close to blow-off,
Proc. Combust. Inst., 36 (in press).
45
CSE group research description
Institute/Group: Department of Chemistrt and Applied Biosciences, Laboratort of
Inorganic Chemistrt. Comas-Vives and Copéret Groups.
Researchers: Lucas Foppa, Aleix Comas-Vives and Christophe Copéret
Description:
Our research activities in the field of computational chemistrt aim at providing ket
information in order to understand at molecular level how heterogeneous cataltsts
work. One intensive area of research is the use of ab initio calculations in
combination with spectroscopic techniques, in particular IR and NMR, in order to
assign the active sites of heterogeneous cataltsts. We studt bt means of first
principles the reactivitt of catalttic processes taking place on the surface of metal
oxides, on single site cataltsts oxides, single-site cataltsts and of metallic
nanoparticles supported on oxides. We combine different techniques adapted to the
ststem of interest and the time-scale: static calculations, ab initio molecular dtnamics
(including metadtnamics) and microkinetic modeling.
46
Title: Design and optimization of electromagnetic structures and devices
Researchers: Jürg Leuthold
Christian Hafner
Jasmin Smajic
Pascal Leuchtmann
Alexandros Emboras
Alexander Dorodnyy
Sahar Sargheini
Pegah Souzanghar
Uli Koch
Christian Haffner
Institute Institute of Electromagnetic Fields
Description:
We develop various numerical methods and software packages for computational
electromagnetics and optimal design with applications ranging from very low up to optical
frequencies. These codes, free software (freeFEM++, NGsolve, Concepts) and commercial
packages (Comsol, CST, HFSS, etc.) are applied to 1) metamaterials for magnetic field shielding,
radar absorption, thermal protection, and efficient solar cells; 2) photonic crystals, dielectric and
plasmonic waveguide structures for optical frequencies and for fast interconnects in the mm
wave range; 3) ultra-compact plasmonic devices for optical communication such as modulators,
switches, etc., 4) design of antenna structures ranging from radio frequencies up to optical
frequencies, e.g., plasmonic nano antennas for bio sensing; 5) analysis and design of scanning
probe tips for microwaves, optics, and electron emission; etc.
Currently we develop and combine various field solvers based on boundary discretization
methods such as the Multiple Multipole Program (MMP) as well as domain discretization
methods in frequency and time domain, namely Finite Elements Methods (FEM), Discontinuous
Galerkin (DG), Fourier Modal Method (FMM), etc.
Our MMP and FDTD codes are contained in the OpenMaXwell platform, which is an
OpenSource project (see http://openmax.ethz.ch/).
We link our electromagnetic field simulation codes with other software, e.g., for handling
quantum effects and for optimizing structures and devices. We use freely available optimizers
but we also develop our own codes for increasing the efficiency.
References:
From fall 2015 till fall 2016, 9 papers on various topics of computational electromagnetics were
published in reviewed journals.
47
Institute/Group: Computational Physics for Engineering Materials - Institute for
Building Materials, ETH Zurich
Researchers: Prof. Dr. Herrmann, Hans J.; Dr. Lukovic, Mirko; Dr. Mendoza Jimenez,
Miller; Dr. Mora Mendez, Diego; Dr. Nagler, Jan; Dr. Wittel, Falk; Alonso Amor,
Tatiana; Berger, Damian; Bianchi, Filippo; Bottcher, Lucas; Castro, Caio; Debus, Jens-
Daniel; Flouris, Kyriakos; Furtmaier, Oliver; Giordanelli, Ilario; Iliev, Pavel; Jaeger,
Robin; Melnikov, Konstantin; Michiels van Kessenich, Laurens; Munglani, Gautam; Ser-
gio Solorzano Rocha; Stager, Dominik; Verma, Trivik; Yoshimatsu, Ryuta;
Description:
The group’s main focus areas lie in the study of granular flow and fluid-particle interac-
tion, dynamics on complex networks, the packing of space filling spheres, and statistical
properties of random surfaces.
Granular Flow With the help of the Lattice Boltzmann Method, re-
search is being done on the granular front formation in free-surface flow of
concentrated suspensions and the impact of debris flow on flexible barriers.
The group also deals with micro-mechanical failure analysis of wet granular
matter and the analysis of the velocity field of granular hopper flow. In
the context of active particle flow, we are engaged in understanding how
asymmetrically shaped walls influence the flow of pedestrians in corridors.
Network Dynamics Research in this area mainly focuses on understand-
ing epidemic spreading over community networks and properties of neural
network avalanches - their temporal correlations and scaling behaviour. The
former has led us to the development of a model for the growth of the World
Airline Network and a general model for failure and recovery in dynamical
networks. We are also studying the relationship between network connec-
tivity disruption and explosive epidemic spreading.
Sphere Packing In the context of sphere packing, our group stud-
ies complex networks of space-filling bearings, properties of self-similar
space-filling sphere packings in three and four dimensions, and the
prediction and control of slip-free rotation states in sphere assem-
blies.
Random Surfaces The group primarily investigates the conformal in-
variance of random surfaces and in particular graphene sheets. The iso-
height lines of correlated random surfaces are analysed in the context of the
stochastic Loewner evolution, which is also shown to relate anomalous dif-
fusion and anisotropic percolation. We also study the influence of statistical
properties of Fourier coefficients on random surfaces.
48
Group of Prof. Ralf Hiptmair
(Seminar for Applied Mathematics, D-MATH)
HyDi – A C++ Finite Element Framework
From 2013 through 2016 a modern, highly modular, general, 3D finite element codehas been developed as part of the CTI-funded project “Simulation of Arc-Extinction inSwitching Chambers” jointly with ABB corporate research in Baden-Dattwil. This codeadheres to object-oriented and generic-programming software design paradigms and hasthe following features:
• Can handle unstructured 3D hybrid meshes comprising tetrahedra, hexahedra,prisms, and pyramids.
• Complies with the DUNE mesh interface specification.
• Implements hierarchic Lagrangian (nodal), edge, and face finite elements of arbi-trary polynomial degree.
• Accommodates non-matching meshes across interfaces.
• Offers full support for Discontinuous Galerkin (DG) methods.
• Provides shared-memory parallelization.
Comprehensive unit tests and a thorough and current documentation are supplied.
In his thesis project R. Casagrande has used the HyDi code as a basis for the implemen-tation of an eddy current simulation tool that features
• the treatment of non-conforming interfaces by means of DG coupling,
• an extended finite element scheme for the resolution of skin layers and edge singu-larities.
The HyDi code is also used by the industrial partner ABB for electromagnetic fieldcomputations in the context of plasma arc simulations.
The development of HyDi supported by CTI grant 15183.1 and ABB Schweiz AG, Corporate
Research.
49
Publications
[1] R. Casagrande, Discontinuous Finite Element Methods for Eddy Current Simulation, ethdissertation, SAM, ETH Zurich, Switzerland, 2016. Submitted.
[2] R. Casagrande, R. Hiptmair, and J. Ostrowski, An a priori error estimate for inte-
rior penalty discretizations of the curl-curl operator on non-conforming meshes, Journal ofMathematics in Industry, 6 (2016), pp. 1–25.
[3] R. Casagrande, C. Winkelmann, R. Hiptmair, and J. Ostrowski, DG treatment
of non-conforming interfaces in 3D curl-curl problems, Tech. Rep. 2014-32, Seminar forApplied Mathematics, ETH Zurich, Switzerland, 2014.
BETL – A C++ Boundary Element Template Library
BETL is a header-only template library mainly intended for the Galerkin boundaryelement discretization of 3D boundary integral operators as they arise in various physicaland engineering applications. Prominent examples are, e.g., electrostatic or thermalmodels as well as the scattering of acoustic and electromagnetic waves. Fully continuous,tangentially continuous, and discontinuous boundary element functions are supported,but extension to other approximation spaces is easy. BETL relies on transformation-based adaptive quadrature to deal with singular integral kernels. Integration of 3rdparty libraries for local low-rank matrix compression is available. BETL also offerscomprehensive support for low-order polynomial Galerkin finite element methods (nodaland edge finite elements).
BETL has been developed by Dr. Lars Kielhorn as part of the project “Edyson 2020:Entwicklung eines effizienten C++ Simulationscodes zur Berechnung elektromagnetischerFelder auf der Grundlage von FEM-BEM Kopplung” jointly with Robert-Bosch GmbH,Germany. It is used for eddy current and electromechanical simulations at Bosch Corpo-rate Research.
BETL’s development was funded by Robert Bosch GmbH as part of the project “Edyson 2010:
Entwicklung eines effizienten C++ Simulationscodes zur Berechnung elektromagnetischer Felder
auf der Grundlage von FEM-BEM Kopplung”.
Publications
[1] R. Hiptmair and L. Kielhorn, BETL – a generic boundary element template library,Report 2012-36, SAM, ETH Zurich, Switzerland, 2012.
Second-Kind Boundary Integral Equation Methods for Scattering at Com-
posite Objects
We target frequency-domain acoustic and electromagnetic scattering of incident wavesat objects that consist of several homogeneous, isotropic materials. The behavior of thefields can be modelled using boundary integral equations (BIE) for unknown traces on the
50
interfaces between material domains. The BIE are amenable to Galerkin discretizationby means of boundary element methods (BEM).
In this project we investigate so-called 2nd-kind boundary integral equations, which arisefrom new multi-potential representation formulas. These BIE are set in L
2-type spacesand, thus, no continuity constraints have to be imposed on the boundary elements. inaddition, natural choices for local basis functions will lead to well-conditioned linearsystem, for which iterative solvers converge fast.
The new formulations have been implemented both in 2D and 3D and their excellentperformance has been demonstrated in numerical tests. The 3D implementation wasbased on the finite element template library BETL.
This research was supported by SNF under grant 200021 137873/1 “Well-conditioned Boundary
Integral Formulations for Scattering”
0 200 400 600 800 1000
10−5
100
number of iterations
2−
norm
of re
sid
uum
second−kind, 140
second−kind, 560
second−kind, 2240
second−kind, 8960
first−kind, 140
first−kind, 560
first−kind, 2240
first−kind, 8960
Figure 1: 2nd-kind BIE/BEM for EM scattering at compisite object: trace of electricfield (left) and convergence history of GMRES
Publications
[1] X. Claeys, R. Hiptmair, and E. Spindler, Second-kind boundary integral equations
for scattering at composite partly impenetrable objects, Tech. Rep. 2015-19, Seminar forApplied Mathematics, ETH Zurich, Switzerland, 2015. Submitted to Communications inComputational Physics.
[2] X. Claeys, R. Hiptmair, and E. Spindler, A second-kind Galerkin boundary element
method for scattering at composite objects, BIT Numerical Mathematics, 55 (2015), pp. 33–57.
[3] X. Claeys, R. Hiptmair, and E. Spindler, Second kind boundary integral equation for
multi-subdomain diffusion problems, Tech. Rep. 2016-44, Seminar for Applied Mathematics,ETH Zurich, Switzerland, 2016. Submitted to Adv. Cmput. Math.
51
[4] , Second-kind boundary integral equations for electromagnetic scattering at composite
objects, Preprint 2016-43, SAM, ETH Zurich, Switzerland, 2016. Submitted to Computers& Mathematics with Applications.
[5] E. Spindler, Second Kind Single-Trace Boundary Integral Formulations for Scattering at
Composite Objects, eth dissertation no. 23620, ETH Zurich, Switzerland, 2016.
Multi-Trace Boundary Integral Equations
We consider scalar or vectorial 2nd-order diffusion or scattering transmission problems in
the exterior of a bounded domain ΩZ ⊂ Rd. The coefficients are assumed to be piecewise
constant with respect to a partition of Rd \ ΩZ into subdomains. Dirichlet boundary
conditions are imposed on ∂ΩZ .
In the spirit of domain decomposition, we recast the transmission problems into two novel
well-posed multi-trace boundary integral equations. Their unknowns are functions on the
product of subdomain boundaries. Compared to conventional single-trace formulations
they offer the big benefit of being amenable to operator preconditioning. We could achieve
a comprehensive numerical analysis of the new formulations. Moreover, numerical tests
have confirmed the efficacy of operator preconditioning.
This project was funded by Thales SA, France, with grant “Preconditioned Boundary Element
Methods for Electromagnetic Scattering at Dielectric Objects”
Publications
[1] X. Claeys, R. Hiptmair, and C. Jerez-Hanckes, Multi-trace boundary integral equa-
tions, in Direct and Inverse Problems in Wave Propagation and Applications, I. Graham,U. Langer, J. Melenk, and M. Sini, eds., vol. 14 of Radon Series on Computational andApplied Mathematics, De Gruyter, Berlin/Boston, 2013, pp. 51–100.
[2] X. Claeys, R. Hiptmair, C. Jerez-Hanckes, and S. Pintarelli, Novel multi-trace
boundary integral equations for transmission boundary value problems, in Unified Transformfor Boundary Value Problems: Applications and Advances, A. Fokas and B. Pelloni, eds.,SIAM, Philadelphia, 2014, pp. 227–258.
[3] R. Hiptmair and C. Jerez-Hanckes, Multiple traces boundary integral formulation for
Helmholtz transmission problems, Adv. Comput. Math., 37 (2012), pp. 39–91.
[4] R. Hiptmair, C. Jerez-Hanckes, J.-F. Lee, and Z. Peng, Domain decomposition for
boundary integral equations via local multi-trace formulations, in Domain DecompositionMethods in Science and Engineering XXI., J. Erhel, M. Gander, L. Halpern, G. Pichot,T. Sassi, and O. Widlund, eds., vol. 98 of Lecture Notes in Computational Science andEngineering, Springer, Berlin, 2014, Proceedings of the XXI. International Conference onDomain Decomposition Methods, Rennes, France, June 25-29, 2012 I, pp. 43–58.
Shape Sensitivity and Shape Optimization
52
For a functional F that depend on the solution u of a boundary value problem on a domainΩ we study the impact of small perturbations of Ω on f(u). This can be quantified by thedirectional shape gradient, the “derivative” of F (u) in a “direction of deformation” of Ω.For second order elliptic boundary value problems formulas for shape gradients involveboth the solution of the boundary value problem (state problem) and the solution of arelated adjoint boundary value problem. Equivalent formulas based either on integrationover Ω or its boundary ∂Ω can be derived. However, in the case of finite element ap-proximation of both state and adjoint problem the volume formulas provide significantlymore accurate approximations of shape gradients. We could give a rigorous justificationfor this observation.
(a) (b)
Figure 2: Shape optimization of microlenses [4]: An incoming plane wave hits (fromthe left) a cylindrical lens with semi-circular cross section (a). The shape of the lens isoptimized to maximize the focused light in the thing rectangle on the backside of the lens(b).
Shape gradients are a key building block for descent methods for shape optimization.The other is a suitable representation of shape deformations. We use a volume basedencoding of shape distortions by means of tensor product splines. In this space we expressthe shape gradient through its H1-representative. Line search along this direction is usedfor the iterative minimization of the objective functional. This techniques has successfullybeen employed for shape optimization of nano-lenses, see Figure 2.
The project “Computational Nano-Optics: Shape Calculus and Inverse Problems” was funded
by ETH Zurich under CHIRP grant CH1-02 11-1.
Publications
[1] R. Hiptmair and A. Paganini, Shape optimization by pursuing diffeomorphisms, Comput.Methods Appl. Math., 15 (2015), pp. 291–305.
[2] R. Hiptmair, A. Paganini, and S. Sargheini, Comparison of approximate shape gradi-
ents, BIT Numerical Mathematics, 55 (2014), pp. 459–485.
[3] A. Paganini, Numerical shape optimization with finite elements, eth dissertation 23212,ETH Zurich, 2016.
53
[4] A. Paganini, S. Sargheini, R. Hiptmair, and C. Hafner, Shape optimization of mi-
crolenses, Opt. Express, 23 (2015), pp. 13099–13107.
[5] S. Sargheini, Shape Sensitivity Analysis of Electromagnetic Scattering Problems, eth dis-sertation, ETH Zurich, 2016.
54
Group: Institute of Virtual Manufacturing
Description:
1. Efficient simulation of industrial sheet metal forming processes under non-
proportional loading conditions
State of the art numerical simulations of sheet metal forming processes are mostly based
on the assumption of monotonic deformation paths. However real industrial processes
often experience load reversal as well as load path changes even if the forming process is
executed in a single step. The project investigates the effective implementation of
numerical models able of capturing Bauschinger as well as latent hardening effects for
industrial scale applications. The results are validated against optically measures strain
fields obtained from deep drawing experiments.[1]
2. A Fourier series based new class of generalized yield surfaces for the computationally
efficient numerical modelling of hcp-metals
As most of the hcp- metals, commercially pure titanium exhibits strong yield asymmetry
as well as anisotropy and distortional hardening. The computational modelling of these
materials therefore requires mathematically complex yield surface models in order to be
able to capture all the mentioned effects. In the scope of this project, a novel yield surface
model is proposed which is based on a fourier series, greatly reducing the required
computational complexity in metal forming simulations. The model is validated against
optically measured cup drawing experiments, and feature a superior accuracy than well-
established alternatives.[2]
3. Computational modelling of fracture in multi-layer aluminum alloys
Multi-layer aluminum alloys combine excellent bendability with very high tensile
strengths and are thus ideal for use in crash relevant components in automotive industry.
The numerical modelling of these materials is challenging, especially concerning the
definition of fracture limits. The project proposes a novel methodology for characterizing
fracture strains in multi-layered materials, as well as a tailored numerical strategy
implemented into LS-Dyna as a user subroutine. [3]
4. Efficient stress integration algorithms for non-associated flow rule based constitutive
models
Constitutive modelling approaches based on a non-associated flow rule represent an
additional challenge for stress integration algorithms, as the overall nonlinearity of the
problem is increased. The present work aims to comparatively analyze explicit and
implicit return mapping algorithms for their performance with respect to deep-drawing
applications computed using a non-associated material model. The results indicate that
explicit integration schemes are very accurate and effective for problems with limited
geometrical complexity, whereas implicit methods take the upper hand when more
challenging forming processes are simulated.[4]
55
Group: Prof P.H. Hunenberger - Computer Simulation of Molecular Systems (CSMS)
Researchers: Prof P.H. Hunenberger / Pavel Oborsky / David Hahn / Marina Pereira
Description: The research of our group focuses on the development and application of meth-ods for the classical computer simulation of molecular systems, namely in terms of method
development :
• Treatment of electrostatic interactions
• Force-field parametrization (GROMOS)
• Thermodynamic boundary conditions
• Enhanced conformational sampling
• Extended-system methods
• Free-energy calculations
• Development of simulation algorithms
• Development of trajectory analysis methods
and in terms of applications :
• Single-ion solvation (book: www.csms.ethz.ch/publications/book)
• Properties of ionic systems (electrolyte solutions, crystals)
• Simulation of biomolecular systems (with a main focus on carbohydrates and lipids)
• Role of electrostatic interactions (hydrogen bonding, salt bridges) in (bio)molecular sys-tems
56
Institute of Fluid Dynamics / Computational Fluid Dynamics and Multi-Scale Modeling
published [1-3][4-12], in press [13-15], submitted [16-22]
Researchers: Prof. Dr. Patrick Jenny, Nemanja Andric, Dr. Davide Cortinovis, Rajdeep
Deb, Valentin Giddey, Dr. Hossein Gorji, Dr. Karim Khayrat, Thomas Kummer, Stephan
Küchlin, Adrien Lücker, PD Dr. Daniel W. Meyer, Arthur Moncorgé*, Daniel Oppliger*,
Franca Schmid, Ran Sui*, Dr. Karol Swiderski*, Philipp Weiss *) external project staff
Description:
Most of our current research projects are grouped into the following four major directions:
(1) Flow and transport in porous and fractured media: This is a collaborative research
effort with researchers from Chevron, Total, Imperial College London, and Stanford
University. Subsurface flows of water or oil are determined by the permeability distribution
K(x), which is typically a very heterogeneous quantity. For fast flow and transport simulations
with K(x) given, we have been generalizing our multiscale finite-volume method (MSFV).
Moreover, with K(x) being a highly uncertain quantity, we are developing numerical methods
that translate given statistics for K(x) to flow and transport statistics. In the context of
geothermal energy production, we are developing numerical solution methods for the coupled
flow/geomechanics problem. Lastly, we have been working on models for single- and multi-
phase transport that enable a simplified representation of pore-scale effects at larger scales.
(2) Fluid dynamics in biomedical systems: We are collaborating with researchers from the
Universities of Arizona, Berlin, Bern, San Diego, and Zürich. In a first research area, we have
been devising a computational modeling framework that sheds light on the rheological
influence of red blood cells (RBCs) on cerebral blood flow in capillary networks. Moreover,
we have been developing a numerical model for oxygen transport from capillaries to tissue.
These models allow us to investigate the heterogeneity of capillary transit times of RBCs or
the so-called neurovascular coupling linking neuronal activity to cerebral blood flow. Our
second focus deals with the development of a numerical model of the human hearth that
accounts for electrophysiology as well as structure mechanics. We intend to use this model for
the investigation of novel heart assist device concepts.
(3) Turbulence modeling and turbulent reactive flow: The combustion of fuel sprays is
central in aircraft turbines and Diesel engines. We are developing codes to conduct direct
numerical simulation (DNS) studies to investigate the dynamics of fuel droplets in turbulent
reactive flows. We intend to use the DNS results to inform a model development effort in the
context of relatively inexpensive RANS and PDF methods for spray combustion simulations.
(4) Rarefied gas dynamics: This research area is relevant for the simulation of flows in, e.g.,
nano-scale devices, during re-entry of a space vehicle, or of plasma. In a first subproject, we
have been developing a general-purpose algorithm that encompasses all Knudsen number
(Kn) regimes and that is applicable for practically relevant geometries (Kn characterizes the
degree of gas rarefaction). This approach is based on our inexpensive Fokker-Planck collision
operator for small and intermediate Kn. To reduce statistical errors, we have developed a
novel variance reduction scheme. A second subproject deals with the study of gas-surface and
gas-gas interactions for species separation at high Knudsen numbers. This work benefits from
detailed molecular dynamics simulations of gas molecules interacting with solid walls.
57
Group: Computational Polymer Physics, D-MATL, ETH Zurich
Researchers: Prof. Martin Kroger 1
Prof. Ying Li 2
Prof. Avraham Halperin 3
Prof. Andreas Bausch 4
Prof. Nic Spencer 5
Affiliations: 1 Polymer Physics, D-MATL, ETH Zurich2 University of Connecticut, USA3 CEA Grenoble, France4 TU Munich, Germany4 Surface Science, D-MATL, ETH Zurich
Description:
Computational Polymer Physics @ ETH recently focused its attention on the simulation
of the self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles [1], es-
tablished equilibration protocols for polymeric systems [2], developed molecular simula-
tion guided constitutive modeling [3], performed a topological analysis of entangled lin-
ear, long- and short-chain branched polyethylene melts [4], studied the rheology and pack-
ing of dendronized polymers [5], the influence of chain stiffness, grafting density and nor-
mal load on the tribological and structural behavior of polymer brushes [6] and the effect
of crosslinking on the microtribological behavior of model polymer brushes [7]. We ad-
dressed the question on how boundaries steer the contraction of active gels [8], and studied
the shape effect in cellular uptake of PEGylated nanoparticles via dissipative particle dy-
namics and self-consistent field theory [9]. The internal organization of macromonomers
and dendronized polymers based on thiophene dendrons had been investigated in collab-
oration with Carlos Aleman [10]. Details available at www.complexfluids.ethz.ch
[1] Z. Shen, D.T. Loe, J.K. Awino, M. Kroger, J.L. Rouge, Y. Li, Nanoscale 8 (2016) 14821-14835.
[2] Y.R. Sliozberg, M. Kroger, T.L. Chantawansri, J. Chem. Phys. 144 (2016) 154901.
[3] Y. Li, S. Tang, M. Kroger, W.K. Liu, J. Mech. Phys. Solids 88 (2016) 204-226.
[4] S.H. Jeong, J.M. Kim, J. Yoon, C. Tzoumanekas, M. Kroger, C. Baig, Soft Matter 12 (2016)
3770-3786.
[5] S. Costanzo, L.F. Scherz, T. Schweizer, M. Kroger, G. Floudas, A.D. Schluter, D. Vlassopoulos,
Macromolecules 49 (2016) 7054-7068.
[6] M.K. Singh, P. Ilg, R.M. Espinosa-Marzal, N.D. Spencer, M. Kroger, Polymers 8 (2016) 254.
[7] M.K. Singh, P. Ilg, R.M. Espinosa-Marzal, M. Kroger, N.D. Spencer, Tribol. Lett. 63 (2016) 17.
[8] M. Schuppler, F.C. Keber, M. Kroger, A.R. Bausch, Nat. Commun. 7 (2016) 13120.
[9] Y. Li, M. Kroger, W.K. Liu, Nanoscale 7 (2015) 16631-16646.
[10] E. Cordova-Mateo, O. Bertran, A.D. Schluter, M. Kroger, C. Aleman, Soft Matter 11 (2015)
1116-1126.
58
Title: Ab-initio simulation of 2-D materials: from mobility to I-V characteristics
Researchers: Aron Szabo
Christian Stieger
Mathieu Luisier
Institute/ Integrated Systems Laboratory/
Group: Nano-TCAD Group
Description:
Following the initial discovery of graphene in 2004 several other two-dimensional (2-D) sem-
iconductors have received a wide attention from the scientific community. This is the case, for
example, of transition metal dichalcogenides (TMDs), based either on Molybdenum (MoX2),
Tungsten (WX2), or Tin (SnX2), but also of black phosphorus (BP). Different crystal struc-
tures exist for these 2-D materials such as trigonal prismatic (2H) or octahedral (1T) for
TMDs and orthorhombic for BP. When used in logic applications 2-D monolayers exhibit at-
tractive mobility values (>100 cm2/Vs at room temperature), while the ON/OFF current ratio
of transistors with a 2-D channel can reach 106 or more. Although already impressive these
results could be further improved if the quality of the underlying 2-D crystals would increase
through a reduction of the defect concentration and of charged impurity scattering.
The technology is currently not mature enough to fully determine the potential of 2-D materi-
als. To better assess their maximum achievable performance in logic applications (transistors),
we have computed the intrinsic, phonon limited mobility and I-V characteristics of selected
components with a state-of-the-art ab-initio simulation approach. The latter combines the
VASP density-functional theory (DFT) tool, the Wannier90 basis converter, and the OMEN
quantum transport solver. Both VASP and OMEN heavily rely on high performance compu-
ting resources to rapidly deliver accurate results. Results are shown below for 8 materials and
device configurations (MoS2, MoSe2, MoTe2, WS2, WSe2, SnS2, and black phosphorus with
transport along the armchair and zigzag crystal orientations). GPU acceleration was used to
reduce the computational time of all presented simulations.
Left plot: Phonon-limited electron mobility of selected single-layer 2-D materials
Right plot: Transfer characteristics of the same 2-D materials as on the left when used as channel of next-
generation n-type logic switches with a gate length of 10.7 nm.
59
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
density , sample 51, t = 4
x
y
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
1 1.2 1.4 1.6 1.8 20
50
100
150
200
250
Insitute: Research group of S. Mishra, SAM, ETH Zurich.
Researchers: S. Mishra, R. Kappeli, F. Leonardi, K. Lye, F. Weber,C. Pares Pulido, S. Gurjar.
Description: Research in the group of S. Mishra is focussed on the de-sign, analysis and implementation of efficient numerical methods for non-linear hyperbolic and convection-dominated partial differential equationsand their application in fluid dynamics and astrophysics. In 2016, one ofthe major research projects in the group has been the development of anovel solution concept, that of statistical solutions, for compressible as wellas incompressible Euler equations of fluid dynamics. This solution conceptis promising in terms of the possibility of proving global well-posedness.It also appears to be a natural paradigm for uncertainty quantification inturbulent fluid flows. Statistical sampling techniques such as Monte Carloand Multi-level Monte Carlo are combined with efficient arbitrary high-order finite volume, DG and spectral (viscosity) methods to compute the(multi-point) statistics for turbulent flows.
Among other projects pursued in the group in 2015, notable examplesinclude the design of well-balanced schemes for simulating astrophysicalflows and their application to supernova core collapse and simulation ofclimate of exo-planets. Another project of interest is the design of arbi-trary high-order WENO schemes for discretizing the primitive equationsof climate dynamics within a LES framework.
60
Institute/Group: Institute for Biomechanics / Laboratory for Bone Biomechanics
Researchers: Nicholas Ohs
Sandro D. Badilatti
Patrik Christen
Peter Arbenz (collaborator at the Computer Science Department)
Ralph Müller
Description:
The Laboratory for Bone Biomechanics aims at providing a bridge between biologists, who
have brought molecular and cellular components within the realm of engineering, and
engineers, who have brought the methods of measurement, analysis, synthesis, and control
within the realm of molecular and cell biology. More specifically, new developments in
biomechanical research are aimed at the quantification and modelling of bone at the molecular,
cellular, and organ level incorporating novel principles and techniques of mechanics, imaging,
and computational modelling applied to the areas of tissue engineering, regenerative medicine,
systems medicine and mechanobiology.
One of our recent computational modelling contributions is the simulation of cement
augmentation in human vertebrae (vertebroplasty). Cement augmentation is usually used to
restore mechanical strength after fractures, but could also be used as a prophylactic treatment.
So far, the mechanical competence has been determined immediately post-treatment, without
considering long-term effects of bone adaptation. In this work, we investigated such long-term
effects of vertebroplasty on the stiffness of the augmented bone by means of computer
simulation of bone adaptation. Using the highly parallel micro-finite element solver ParOSol
on the Cray XC40 system at CSCS, we determined sites of increased mechanical stress and
stress-shielding as well as regions with increased or decreased bone loss due to augmentation.
Cement volumes connecting the endplates led to increased stress-shielding and bone loss. The
increased stiffness due to the augmentation, however, remained constant over the simulation
time of 30 years. If the intervention was performed at an earlier time point, it did lead to more
bone loss but did not affect long-term stability. In particular, around the augmentation cement,
bone structures were preserved, suggesting a long-term integration of the cement in the
augmented bone. The impact of vertebroplasty on bone at the microstructural level, therefore,
seems less detrimental than previously thought.
We also contributed to the emerging fields of big data and personalised medicine by proposing
an integrative computer simulation approach to connect diverse clinical big data and use them
to predict disease development and treatment outcomes as well as improve our disease
understanding. It employs a cellular automaton (CA) to represent structural data such as medical
images, micro-finite element analysis to calculate loading, and Boolean networks to integrate
molecular and cellular interactions. A first prototype has been used to investigate the complex
and not well understood disease adolescent idiopathic scoliosis where the mainly adolescent
female patients suffer from a spinal deformity. Medical images of the distal tibia, physical
activity scores, and vitamin D and parathyroid hormone levels were successfully integrated as
measured clinically while the time development of bone density was realistically simulated.
The highly parallel GPU implementation enabled very fast CA and Boolean network
computation even on a desktop computer making the approach suitable for usage in the clinic.
61
Title: Variationally Optimized Free-Energy Flooding for Rate Calculation
Researchers: J. McCarty1
O. Valsson1,2
P. Tiwary3
M. Parrinello1,2
Institute/Group: 1 Department of Chemistry and Applied Biosciences, ETH Zurich and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900 Lugano,
Switzerland 3 Department of Chemistry, Columbia University, New York, New York
10027, USA
Description:
We propose a new method to obtain kinetic properties of infrequent events from molecular
dynamics simulation. The procedure employs a recently introduced variational approach [Valsson
and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of
several collective variables that is designed to flood the associated free energy surface up to a
predefined level. The resulting bias potential effectively accelerates transitions between metastable
free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates
to be obtained. We test the method on a few illustrative systems for which we obtain an order of
magnitude improvement in efficiency relative to previous approaches and several orders of
magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in
more complex systems. This and the ability of the variational approach to deal efficiently with a
large number of collective variables will greatly enhance the scope of these calculations. This work
is a vindication of the potential that the variational principle has if applied in innovative ways.
References: Phys. Rev. Lett., 115 (7), 2015, 070601
DOI: 10.1103/PhysRevLett.115.070601
62
Title: de Broglie Swapping Metadynamics for Quantum and Classical Sampling
Researchers: M. Nava1
R. Quhe2
F. Palazzesi1
P. Tiwary3
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, ETH Zurich, and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 State Key Laboratory of Information Photonics and Optical
Communications & School of Science, Beijing University of Posts and
Telecommunications, Beijing 100876, China 3 Department of Chemistry, Columbia University, 3000 Broadway, New
York, New York 10027, United States
Description:
This paper builds on our previous work on Path Integral Metadynamics [Ruge et al. J. Chem.
Theory Comput. 2015, 11, 1383] in which we have accelerated sampling in quantum systems
described by Feynman’s Path Integrals using Metadynamics. We extend the scope of Path
Integral Metadynamics by combining it with a replica exchange scheme in which artificially
enhanced quantum effects play the same role as temperature does in parallel tempering. Our
scheme can be adapted so as to be used in an ancillary way to sample systems described by
classical statistical mechanics. Contrary to Metadynamics and many other sampling methods no
collective variables need to be defined. The method in its two variants, quantum and classical, is
tested in a number of examples.
References: J. Chem. Theory Comput., 11 (11), 2015, pages 5114-5119
DOI: 10.1021/acs.jctc.5b00818
63
Title: A Perturbative Solution to Metadynamics Ordinary Differential Equation
Researchers: P. Tiwary1
J. Dama2
M. Parrinello3
Institute/Group: 1 Department of Chemistry, Columbia University, New York, NY 10027 2 Department of Chemistry, The James Franck Institute, Institute for
Biophysical Dynamics, and Computation Institute, The University of
Chicago, Chicago, Illinois 60637, USA
3 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich and Facoltà di Informatica, Istituto di
Scienze Computazionali, Università della Svizzera italiana, 6900 Lugano,
Switzerland
Description:
Metadynamics is a popular enhanced sampling scheme wherein by periodic application of a
repulsive bias, one can surmount high free energy barriers and explore complex landscapes.
Recently, metadynamics was shown to be mathematically well founded, in the sense that the
biasing procedure is guaranteed to converge to the true free energy surface in the long time limit
irrespective of the precise choice of biasing parameters. A differential equation governing the post-
transient convergence behavior of metadynamics was also derived. In this short communication,
we revisit this differential equation, expressing it in a convenient and elegant Riccati-like form. A
perturbative solution scheme is then developed for solving this differential equation, which is valid
for any generic biasing kernel. The solution clearly demonstrates the robustness of metadynamics
to choice of biasing parameters and gives further confidence in the widely used method.
References: J. Chem. Phys., 143, 2015, 234112
DOI: 10.1063/1.4937945
64
Title: General Protein Data Bank-Based Collective Variables for Protein Folding
Researchers: A. Ardévol1
F. Palazzesi1
G. A. Tribello2
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, and Facoltà di Informatica, Istituto di
Scienze Computazionali, Università della Svizzera italiana, 6900 Lugano,
Switzerland 2 Atomistic Simulation Centre, School of Mathematics and Physics,
Queen’s University Belfast, Belfast, BT7 1NN, United Kingdom
Description:
New, automated forms of data analysis are required to understand the high-dimensional trajectories
that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction
algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-
dimensional representations of the trajectory using only the information encoded in the trajectory.
The downside of this approach is that a different set of coordinates are required for each different
chemical system under study precisely because the coordinates are constructed using information
from the trajectory. In this paper, we show how one can resolve this problem by using the sketch-
map algorithm that we recently proposed to construct a low-dimensional representation of the
structures contained in the protein data bank. We show that the resulting coordinates are as useful
for analyzing trajectory data as coordinates constructed using landmark configurations taken from
the trajectory and that these coordinates can thus be used for understanding protein folding across
a range of systems.
References: J. Chem. Theory Comput., 12 (1) 2016, pages 29-35
DOI: 10.1021/acs.jctc.5b00714
65
Title: Enhanced, targeted sampling of high-dimensional free-energy landscapes
using variationally enhanced sampling, with an application to chignolin
Researchers: P. Shaffer1
O. Valsson1,2
M. Parrinello1,2
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich and Facoltà di Informatica, Istituto di
Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano,
Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900 Lugano,
Switzerland
Description:
The capabilities of molecular simulations have been greatly extended by a number of widely used
enhanced sampling methods that facilitate escaping from metastable states and crossing large
barriers. Despite these developments there are still many problems which remain out of reach for
these methods which has led to a vigorous effort in this area. One of the most important problems
that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are
not easily described by a small number of collective variables. In this work we demonstrate a new
way to compute free-energy landscapes of high dimensionality based on the previously introduced
variationally enhanced sampling, and we apply it to the miniprotein chignolin.
References: PNAS, 113 (5), 2016, 1150-1155
DOI: 10.1073/pnas.1519712113
66
Title: Enhancing Important Fluctuations: Rare Events and Metadynamics from a
Conceptual Viewpoint
Researchers: O. Valsson1,2
P. Tiwary3
M. Parrinello1,2
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich and Facoltà di Informatica, Istituto di
Scienze Computazionali, Università della Svizzera italiana, 6900 Lugano,
Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900 Lugano,
Switzerland 3 Department of Chemistry, Columbia University, New York, NY 10027
Description:
Atomistic simulations play a central role in many fields of science. However, their usefulness is
often limited by the fact that many systems are characterized by several metastable states separated
by high barriers, leading to kinetic bottlenecks. Transitions between metastable states are thus rare
events that occur on significantly longer timescales than one can simulate in practice. Numerous
enhanced sampling methods have been introduced to alleviate this timescale problem, including
methods based on identifying a few crucial order parameters or collective variables and enhancing
the sampling of these variables. Metadynamics is one such method that has proven successful in a
great variety of fields. Here we review the conceptual and theoretical foundations of metadynamics.
As demonstrated, metadynamics is not just a practical tool but can also be considered an important
development in the theory of statistical mechanics.
References: Annurev. Phys. Chem., 67, 2016, 59-184
DOI: 10.1146/annurev-physchem-040215-112229
67
Title: Bespoke bias for Obtaining Free Energy Differences within Variationally
Enhanced Sampling
Researchers: J. McCarty1
O. Valsson1,2
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, ETH Zurich, and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900, Lugano,
Switzerland
Description:
Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence
determining free energy differences is central for understanding many important phenomena. Here
we present a new biasing strategy, which employs the recent variationally enhanced sampling
approach (Valsson and Parrinello Phys. Rev. Lett. 2014, 113, 090601). The bias is constructed from
an intuitive model of the local free energy surface describing fluctuations around metastable
minima and depends on only a few parameters which are determined variationally such that
efficient sampling between states is obtained. The bias constructed in this manner largely reduces
the need of finding a set of collective variables that completely spans the conformational space of
interest, as they only need to be a locally valid descriptor of the system about its local minimum.
We introduce the method and demonstrate its power on two representative examples.
References: J. Chem. Theory Comput., 12 (5), 2016, Pages 2162-2169
DOI: 10.1021/acs.jctc.6b00125
68
Title: Characterization of Vanadium Species in Mixed Chloride-Sulfate
Solutions: An Ab Initio Metadynamics Study
Researchers: M. Bon1,2
T. Laino1
A. Curioni1
M. Parrinello2
Institute/Group: 1 IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland 2 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, and Facoltà di Informatica, Istituto di
Scienze Computazionali, Università della Svizzera italiana, 6900 Lugano,
Switzerland
Description:
All-vanadium redox flow batteries have attracted considerable interest as promising electrical
energy storage devices, because of their ability to store large amounts of energy and to resist
fluctuating power supplies. A crucial parameter for battery efficiency is the solubility of vanadium
in the electrolyte solutions. Recently, it has been shown that sulfate–chloride mixed electrolytes
increase vanadium solubility. In this work, we identify the most stable complexation structures in
this improved electrolyte, by means of ab initio molecular dynamics together with the well-
tempered metadynamics algorithm. We characterize the first solvation shell of vanadium cations
in solution and estimate the free energy difference of all of the configurations. Our results suggest
that chloride ions play an important role in stabilizing V(II), V(III), and V(V) species. In the
specific case of V(V), we find that the most stable configuration exhibits a simultaneous
complexation operated by chloride and sulfate ions, suggesting possible strategies to design novel
agents to prevent the precipitation of the vanadium cation.
References: J. Phys. Chem. C., 120 (20), 2016, Pages 10791-10798
DOI: 10.1021/acs.jpcc.6b02642
69
Title: Chemical potential calculations in dense liquids using metadynamics
Researchers: C. Perego1
F. Giberti2
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, 8093 Zurich, Switzerland and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 The University of Chicago, Institute for Molecular Engineering, 5640
South Ellis Avenue, Chicago, IL 60637
Description:
The calculation of chemical potential has traditionally been a challenge in atomistic simulations.
One of the most used approaches is Widom's insertion method in which the chemical potential is
calculated by periodically attempting to insert an extra particle in the system. In dense systems this
method fails since the insertion probability is very low. In this paper we show that in a
homogeneous fluid the insertion probability can be increased using metadynamics. We test our
method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain
efficiently converged results even when Widom's method fails.
References: Phys. J. Spec. Top., 2016, accepted manuscript
DOI:10.1140/epjst/e2016-60094-x
70
Title: A variational approach to nucleation simulation
Researchers: P. Piaggi1,2
O. Valsson1,2
M. Parrinello1,2
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, 8093 Zurich, Switzerland and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900, Lugano,
Switzerland
Description:
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the
liquid phase. The large free energy barriers to transition make the time scale of this process
impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently
developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601
(2014)] based on the variational determination of a bias potential. We differ from previous
applications of this method in that the bias is constructed on the basis of the physical model
provided by the classical theory of nucleation. We examine the technical problems associated with
this approach. Our results are very satisfactory and will pave the way for calculating the nucleation
rates in many systems.
References: Faraday Discuss., 2016, accepted manuscript
DOI: 10.1039/C6FD00127K
71
Title: Dimer Metadynamics
Researchers: M. Nava1
F. Palazzesi1
C. Perego1
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, 8093 Zurich, Switzerland and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland
Description:
Sampling complex potential energies is one of the most pressing challenges of contemporary
computational science. Inspired by recent efforts that use quantum effects and discretized
Feynman's path integrals to overcome large barriers we propose a replica exchange method. In
each replica two copies of the same system with halved potential strengths interact via inelastic
springs. The strength of the spring is varied in the different replicas so as to bridge the gap between
the infinitely strong spring, that corresponds to the Boltzmann replica and the less tight ones. We
enhance the spring length fluctuations using Metadynamics. We test the method on simple yet
challenging problems.
References: J. Chem. Theory Comput., submitted July 2016
72
Title: Crucial Role of Explicit Water Models in the Helix Folding/Unfolding
Processes
Researchers: F. Palazzesi1
M. Salvalaglio2
A. Barducci3
M. Parrinello1
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, 8093 Zurich, Switzerland and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 Department of Chemical Engineering, University College London
London WC1E 7JE, United Kingdom 3 Centre de Biochimie Structurale, Montpellier, France
Description:
In the last years it becomes evident that computer simulations can assume a relevant role in
modeling proteins dynamical motions for their ability to provide a full atomistic image of the
processes under investigation. The ability of the current protein force-fields in reproducing the
correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve
our understanding of many relevant biological functionalities. In this work employing the last
developments of the Metadynamics framework we compare the ability of state-of-the-art all-atom
empirical functions and water models to consistently reproduce the folding and unfolding of a helix
turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water
models can influence the thermodynamic and the kinetics of the system under investigation, and
for this reason can not be consider trivial.
References: J. Chem. Phys., submitted 2016
73
Title: Hierarchical Protein Free Energy Landscapes from Variationally Enhanced
Sampling
Researchers: P. Shaffer1
O. Valsson1,2
M. Parrinello1,2
Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische
Technische Hochschule Zurich, 8093 Zurich, Switzerland and
Facoltà di Informatica, Istituto di Scienze Computazionali, Università della
Svizzera italiana, 6900 Lugano, Switzerland 2 National Center for Computational Design and Discovery of Novel
Materials MARVEL, Università della Svizzera italiana, 6900, Lugano,
Switzerland
Description:
In recent work we demonstrated that it is possible to obtain approximate representations of high
dimensional free energy surfaces with variationally enhanced sampling (Shaffer, Valsson and
Parrinello, Proc. Natl. Acad. Sci., 2016, 113, 17). The high dimensional spaces considered in that
work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high
dimensional free energy surface was approximated as the sum of many two dimensional terms plus
an additional term which represents an initial estimate. In this paper we build on that work and
demonstrate that we can calculate high dimensional free energy surfaces of very high accuracy by
incorporating additional terms. The additional terms apply to a set of collective variables which are
more coarse than the base set of collective variables. In this way it is possible to build hierarchical
free energy surfaces, which are composed of terms that act on different length scales. We test the
accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing
simple coarse grained models and comparing results from the coarse grained model to results from
atomistic simulations. The approach described in this paper is ideally suited for problems in which
the free energy surface has important features on different length scales or in which there is some
natural hierarchy
References: J. Chem. Theory Comput. submitted August 2016
74
Institute/Group: Laboratory of Physical Chemistry, ETH Zürich
Group of Martin Quack
Researchers: Prof. Martin Quack
Dr. Sieghard Albert
Dr. Ziqiu Chen
Dr. Csaba Fábri
Dr. Ľuboš Horný
Dr. Carine Manca Tanner
Dr. Georg Seyfang
Irina Bolotova, Ph.D student
Description:
Area of Research: Molecular Kinetics and Spectroscopy
The group "Molecular Kinetics and Spectroscopy" of Martin Quack at ETH has as main
research theme the understanding of fundamental, physical-chemical molecular primary
processes. The basic research question concerns the fully quantum mechanical molecular
motion, which is at the origin of all chemical reactions. An essential aspect of the research is
the systematic combination of experimental and theoretical studies. The experimental studies
concentrate on high resolution infrared spectroscopy, infrared multiphoton excitation and time
resolved kinetic spectroscopy. While most of the experiments address fundamental questions,
some practical applications relate to atmospheric and astrophysical spectroscopy and to
isotope separation. The theory covers full-dimensional quantum dynamics by discrete variable
representation techniques, finite basis set representation as well as diffusion quantum Monte
Carlo methods. Approximate theories are developed and tested in relation to exact theories
(an example is the quasiadiabatic channel reaction path hamiltonian theory for tunneling
reactions). Another focus of theory is the time dependent quantum dynamics in intramolecular
energy flow and vibrational redistribution, coherent infrared multiphoton excitation and laser
chemistry as well as time dependent quantum statistical mechanical approaches to these
processes. Finally, the group studies fundamental symmetry principles in molecular processes
and molecular chirality in relation to parity violation. Our theoretical developments have led
to large increases in the predicted parity violating energy differences between enantiomers,
making these now a realistic goal for our current experiments.
Keywords:
Molecular Kinetics, Spectroscopy, Parity Violation, Chiral Molecules, Quantum Dynamics,
Fundamental Symmetries, Quantum Chemical Kinetics, Tunneling, Infrared Spectroscopy,
Terahertz Spectroscopy, Atmospheric Spectroscopy, Methane, Astrophysical Spectroscopy.
75
Institute/Group: Laboratorium für Physikalische Chemie, Group of Prof. Markus Reiher
Researchers: Markus Reiher, Moritz Haag, Stefan Knecht, Sebastian Keller, Arseny Kovyr-
shin, Tamara Husch, Andrea Muolo, Jonny Proppe, Gregor Simm, Christopher J. Stein, Alain
Vaucher, Adrian Mühlbach, Florian Krausbeck, Leon Freitag, Jan-Grimo Sobez, Erik D. Hedegård,
Yingjin Ma, Martin T. Stiebritz.
Description:
Research in the Reiher group is devoted to general theoretical chemistry. The main focus is on
the development of theory and algorithms for the calculation of electronic structures based on
the first principles of quantum mechanics. The aim of our efforts is to derive quantitative means
as well as concepts for understanding chemical processes. All current projects may be grouped
according to four main research directions: Relativistic quantum chemistry, bioinorganic and
coordination chemistry, theoretical spectroscopy, and the description of electron-electron inter-
actions and correlations within wavefunction-based and density-functional methods.
Our research within relativistic quantum chemistry has been focusing on 4-component and
2-component methods including the development of a relativistic implementation of the quan-
tum chemical density matrix renormalization group (DMRG) algorithm. Recent advances are
the development of a relativistic kinetic-balance condition for explicitly correlated basis func-
tions employed in semi-classical relativistic calculation as well new insight in the definition of
electron-correlation energy within 4-component atomic and molecular calculations.
Tackling the so-called electron-correlation problem is therefore at the heart of quantum
chemistry. Although some methods - such as the notorious B3LYP hybrid density functional
theory (DFT) - became standard models in computational chemistry, they may yield unreliable
results for special classes of molecules, for example those with dense-lying frontier orbitals
such as transition metal complexes. We therefore devised a Bayesian framework for DFT that
allows for an error estimation of calculated properties to uncover pathological cases. This in
turn opens up for finding a controlled way to systematically improve these methods. We also
developed a new computational software package which implements the quantum chemical
DMRG algorithm in an efficient matrix-product operator formalism. One of the key challenges
of quantum-chemical multi-configuration methods is the necessity to manually select orbitals
for the active orbital space. In recent works we showed how the iterative nature of DMRG
combined with its capability to include up to about 100 orbitals in the active space can be
exploited for a systematic assessment and selection of active orbitals. These benefits allowed
us to derive a set-up that paves the way for routine black-box multiconfiguration calculations.
For the exploration of chemical reactivity of complex molecular systems, we developed a
new approach which we call Haptic Quantum Chemistry as it exploits our tactile sense to phys-
ically experience quantum mechanical forces that are exerted between reactants on molecular
fragments. This novel concept opens up a new dimension to the chemist’s intuition toward
chemical reactivity and reaction mechanisms. In parallel we are developing reliable models of
reaction networks based on discrete-time kinetic simulations in discrete state space taking free
energy uncertainties into account. An important application of our approach is the detection of
regions in a reaction network which require further investigation, given the uncertainties intro-
duced by both approximate electronic structure methods and kinetic models. Such cases can
then be studied in greater detail with more sophisticated first-principles calculations and kinetic
simulations.
References to research papers are given in Chapter 7.
76
Institute/Group: Laboratory of Physical Chemistry, Computational Chemistry Group Researchers: Dominik Sidler, Sereina Riniker Description: Computational approaches to estimate free-energy differences based on MD simulations belong to the most accurate but also most expensive methods. Enveloping distribution sampling (EDS) presents an attractive alternative that allows for the calculation of multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which “envelopes” the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limited the application of the methodology. To resolve this, we are generalizing the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters is developed. Researchers: Jagna Witek, Sereina Riniker Description: The ability to passively cross cell membranes is crucial for drug absorption in the gastrointestinal tract and thus oral administration. Small peptides have often a low membrane permeability due to their size and high number of hydrogen-bond donors and acceptors. Nevertheless, naturally occurring cyclic peptides such as cyclosporin A (CsA) are able to penetrate cell membranes. Kinetic models of this peptide in chloroform and water based on 10 µs molecular dynamics simulation data revealed the existence of two congruent conformational states which occur in both environments [J. Chem. Inf. Model., 56, 1547 (2016)]. These conformational states can facilitate membrane permeability. A derivate of CsA, cyclosporin E (CsE), contains one backbone N-methylation less and is less permeable by an order of magnitude. Ongoing work on kinetic models of CsE hint at slower interconversion timescales as a source for the lower permeability observed experimentally. Researchers: Annick Renevey, Sereina Riniker Description: Coarse-graining (CG) is a method to increase computational speed by reducing the number of particles in the system and by smoothening the energy landscape. However, this leads per se to a loss of information. We have proposed a hybrid approach [J. Chem. Phys., 137, 044120 (2012)], where the region of interested is modeled at atomistic resolution whereas the surrounding solvent is coarse-grained. Recently, we found that he interactions between atomistic alkanes and CG water are too favorable. Therefore, these interactions are reparametrized based on the solvation free energies of side-chain analogues and water, as well as the properties of atomistic water/CG water mixtures with different ratios. In addition, we validate the revised model by studying the properties of four proteins with diverse secondary-structure motives in CG water.
77
Title: Climate Change and the Water Cycle: Processes and Scenarios
Researchers: Nikolina Ban, Tanja Dallafior, Erich Fischer, Doris Folini, Adel
Imamovic, Michael Keller, Nico Kröner, David Leutwyler, Daniel Lüthi,
Guido Müller, Davide Panosetti, Anna Possner, Jan Rajczak, Christoph
Schär, Linda Schlemmer, Matthias Schwarz, Silje Sørland, Yawen Wang,
Martin Wild.
Institute/Group: Institute for Atmospheric and Climate Science
Group of Christoph Schär
Description:
We are using global and regional atmospheric models on a wide range of temporal and spatial
scales. The high-resolution regional modeling uses the COSMO-CLM limited-area
atmospheric model, and is coordinated by Drs. D. Lüthi, N. Ban, S. Sørland and L.
Schlemmer. Comprehensive European-scale climate-change scenario simulations were
conducted in the framework of the COordinated Regional climate Downscaling Experiment
(Euro-CORDEX) at horizontal resolutions of 12 and 50 km covering the period 1950-2100.
Recent work in this context is addressing a standard validation of all models participating in
Euro-CORDEX, the calibration of the COSMO-CLM, the analysis of changes in heat-wave,
heavy precipitation events and snow cover, the height-dependence of the climate change
signals, the representation of aerosol effects, and the quantification of different drivers behind
the European summer climate. In addition, we are downscaling a thousand-year-long
simulation using COSMO-CLM at horizontal resolution of 50 km, with aim of assessing the
role of internal variability for extreme events.
In parallel, we are further developing a high-resolution climate simulation capability with
horizontal resolutions at the km-scale. The main motivation behind this work is the desire to
explicitly simulate convective clouds (as opposed to using convective cloud parameterization
schemes in lower-resolution models). Within the SNF-Sinergia project crCLIM, we are now
using a GPU version of the COSMO model. This has enabled us to produce one of the first
10-year long simulations over the European continent at such a high resolution. In addition,
we are running another 10-year long simulation as a Pseudo-Global Warming experiment.
The aim of this work is to estimate the effect of thermodynamic changes on climate. The long
simulations are complemented by idealized simulations and by detailed analyses of
precipitation processes over mountainous terrain, using a combination of satellite data and
idealized large-eddy simulations.
The global scale simulations are carried out with the climate model ECHAM6-HAM,
developed at the Max Planck Institute in Hamburg, Germany. This work is led by Prof.
Martin Wild and Dr. Doris Folini, and it also exploits collaborations with the group of Prof.
Ulrike Lohmann. The model contains sophisticated aerosol and cloud microphysics schemes.
These are essential for realistic simulations of radiation and precipitation processes in the
atmosphere. This model is used to study the link between anthropogenic and natural
perturbations of the radiation balance and the intensity of the hydrological cycle. The time
period under consideration covers 1870-2100. The global model simulations provide also
boundary conditions to drive the regional model. Currently, ECHAM6-HAM is expanded into
a coupled atmosphere-ocean climate modeling system, which allows to exploit the full
response of the climate system in general and the water cycle in particular to the imposed
radiative forcings in transient mode.
References:
A series of papers has been published (see references for further details).
78
Title: Space-Time Approximation of Parabolic Equations
Researchers: Denis DevaudChristoph Schwab
Institute: Seminar for Applied MathematicsETH Zurich
Description:
Parabolic equations play an important role in many areas such as fluid dynamics ormore generally in time dependent systems. Well-known systems such as heat and Stokesequations fit in that setting. The classical well-posedness theory involves dual spacesin the so-called space variable which can not be treated in numerical simulation. It istherefore of great interest to develop a theory not involving dual spaces.
Considering fractional order Sobolev spaces H1/200 (a, b) in time, we present a natural
framework for parabolic equations involving only spaces of positive differentiation order.In that setting, well-posedness can be obtained over the time horizon R+ for equations in-cluding general coercive operators A ∈ L(V, V ∗). We also derive several useful regularityresults based on semigroup theory.
It is then necessary to investigate approximation properties of functions in such spaces.Based on Jacobi-weighted Sobolev spaces, we introduce an interpolation operator andpresent error bounds which are explicit in the weight, the polynomial order, as well as inthe smoothness order of the function. This allows us to derive error estimates for generalhp-finite element (FEM) approximation in such fractional norms. Together with theregularity results, we can then show exponential convergence of the time discretizationin the natural norm.
Since this analysis is valid for any space operator fulfilling the above assumptions, it ispossible to build a space-time approximation of the full system considering a discretizationof the space variable. Exploiting the tensor structure of the trial space, we then deriveconvergence rates for the full system.
This research is supported by the Swiss National Science Foundation (SNSF) underproject No. 149819.
79
Title: Multilevel Higher-Order Quasi-Monte Carlo for Bayesian Inverse Prob-lems
Researchers: Robert N. Gantner, Christoph Schwab
Institute: Seminar for Applied Mathematics, ETH Zurich
Description: We consider Bayesian inversion of partial differential equationswith distributed uncertain inputs, which reduces to the computation of high-dimensional integrals. Under certain sparsity conditions on the parametric in-put, the resulting integrands fulfill the same conditions, implying applicabilityof recently developed higher-order QMC methods. We focus on computationalaspects of this problem, including fast CBC construction of interlaced polyno-mial lattice rules achieving higher order convergence rates, as well as single andmultilevel formulations of the discretized Bayesian inverse problem. Numericalresults showing improvements of the time-to-solution compared to traditional,Monte Carlo-based approaches confirm the theoretical results. Additionally, weprovide software that can be applied to these problems in a high-performancesetting.
This work was supported by CPU time from the Swiss National Supercom-puting Centre (CSCS) under project ID d41, by the Swiss National ScienceFoundation (SNF) under Grant No. SNF149819.
References
[1] J. Dick, R. N. Gantner, Q. Le Gia, and Ch. Schwab. Higher Order Quasi-Monte Carlo integration for Bayesian Estimation. Technical Report 2016-13,Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016.
[2] J. Dick, R. N. Gantner, Q. T. Le Gia, and Ch. Schwab. Multilevel Higherorder Quasi-Monte Carlo integration for Bayesian Estimation. Technical Re-port 2016-34, Seminar for Applied Mathematics, ETH Zurich, Switzerland,2016.
[3] R. N. Gantner. A Generic C++ Library for Multilevel Quasi-Monte Carlo,Proc. PASC16, Lausanne, Switzerland, 2016.
[4] R. N. Gantner and Ch. Schwab. Computational Higher Order Quasi-MonteCarlo Integration. In Ronald Cools and Dirk Nuyens, editors, Monte Carlo
and Quasi-Monte Carlo Methods: MCQMC, Leuven, Belgium, April 2014,pages 271–288. Springer International Publishing, Cham, 2016.
[5] R. N. Gantner, L. Herrmann, and Ch. Schwab, Quasi-Monte Carlo inte-gration for affine-parametric, elliptic PDEs: local supports imply productweights, Technical Report 2016-32, Seminar for Applied Mathematics, ETHZurich, Switzerland, 2016.
1
80
Title: Boundary integral formulation for modeling cells underelectrical stimulation
Researchers: Fernando Henrıquez (1)
Carlos Jerez–Hanckes (2)
Institute: (1) Seminar for Applied MathematicsETH Zurich(2) School of EngineeringPontificia Universidad Catolica de Chile.
Description:
Many medical procedures rely on external stimulation of biological cells using electricfields: localization of peripheral nerves for anesthesia, cardiac defibrillation or electro-chemotherapy of tumors constitute a few examples. In view of the risks and financialcosts partaken, much effort and interest is given to the development of suitable high-performance computational tools to model, better understand and improve such proce-dures [1].
On one hand, the electrophysiological behavior of cells is described by a non–linearsystem of ordinary differential equations dependent on the electric potential jump acrossthe cell membrane [2], being the model proposed by Hodgkin and Huxley [3] the mostwidely known. On the other hand, electrical potentials in both intra– and extracellulardomains follow an electrostatic approximation described by a partial differential equation.
This project aims at modeling the electrical activity of biological cells via a boundaryintegral formulation coupled to a suitable numerical discretization scheme. In particular,we explore the use of the so–called Multiple Traces Formulation to reduce the problem tothe cell membrane [4] and second-order time-stepping semi-implicit numerical schemes [5]to treat the system of non–linear ordinary differential equations. Moreover, we theoreti-cally and numerically study convergence and stability properties of the overall numericalscheme, for both single and multiple cell configurations [6, 7].
This project is partially funded by projects Fondecyt 11121166, Conicyt ACT1118and PUC Chile VRI Interdisciplina 11/2012.
References
[1] A. Agudelo–Toro and A. Neef. Computationally efficient simulation of electricalactivity at cell membranes interacting with self-generated and externally imposedelectric fields. J. Neural Eng., 10(2): 19 pp., 2013.
81
[2] J. Keener and J. Sneyd. Mathematical Physiology I: Cellular Physiology. Springer–Verlag, New York (1998).
[3] A. Hodgkin and H. Huxley. A quantitative description of membrane current andits application to conduction and excitation in nerve. The Journal of Physiology,117(4): 500–544, 1952.
[4] R. Hiptmair and C. Jerez–Hanckes. Multiple traces boundary integral formulation forhelmholtz transmission problems. Advances in Computational Mathematics, 37(1):39–91, 2012.
[5] M. Ethier and Y. Bourgault. Semi–implicit time–discretization schemes for thebidomain model. SIAM Journal on Numerical Analysis, 46(5): 2443–2468, 2008.
[6] F. Henrıquez, C. Jerez–Hanckes, and F. Altermatt, Boundary integral formulationand semi-implicit scheme coupling for modeling cells under electrical stimulation,Numer. Math. (2016). doi:10.1007/s00211-016-0835-9.
[7] F. Henrıquez, Numerical Modeling in Peripheral Nerve Stimulation, Master’s thesis,Pontificia Universidad Catolica de Chile, 2014.
82
Title: Numerical analysis of stochastic partial differentialequations
Researchers: Lukas HerrmannChristoph Schwab
Institute: Seminar for Applied MathematicsETH Zurich
Description:
Random fields are used to model random quantities that arise in science and engineeringin a mathematical way. Isotropic covariance kernels of these fields result in variousproperties of the random fields.
Isotropic spherical random fields are defined and analyzed, especially isotropic Gaus-sian spherical random fields. The connection between the angular power spectrum, thepath regularity and the integrability of these fields is in particular investigated. As aresult the possible convergence rates with Finite Elements to approximate solutions toelliptic partial differential equations on the sphere with lognormal isotropic coefficientscan be essentially determined.
Approximations of statistics of solutions to physical systems such as PDEs with para-metric or stochastic input entail the problem of the approximation of high-dimensionalintegrals. Quasi-Monte Carlo (QMC) methods are capable to achieve higher convergencerates than well established Monte Carlo methods for these problems. The known the-ory was extended with an QMC analysis, which exploits locality of supports of functionsystems that represent the parametric or stochastic input. As a result QMC rules areapplicable with product weights instead of computationally more expensive product and
order dependent weights. This has been shown in the case of affine- and lognormal -parametric input.
This research is in part supported by the Swiss National Science Foundation (SNSF)under grant SNF 200021 159940/1.
References:
[1] R.N. Gantner, L. Herrmann, and Ch. Schwab, Quasi-Monte Carlo integration for
affine-parametric, elliptic PDEs: local supports imply product weights, TechnicalReport 2016-32, Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016
[2] L. Herrmann, Isotropic random fields on the sphere – stochastic heat equation and
regularity of random elliptic PDEs, Master’s thesis, ETH Zurich, 2013
83
[3] L. Herrmann, A. Lang, and Ch. Schwab, Numerical analysis of lognormal diffusions
on the sphere, Technical Report 2016-02, Seminar for Applied Mathematics, ETHZurich, Switzerland, 2016
[4] L. Herrmann and Ch. Schwab, QMC integration for lognormal-parametric, elliptic
PDEs: local supports imply product weights, Technical Report 2016-39, Seminar forApplied Mathematics, ETH Zurich, Switzerland, 2016
[5] A. Lang and Ch. Schwab, Isotropic Gaussian random fields on the sphere: regular-
ity, fast simulation, and stochastic partial differential equations, Ann. Appl. Prob.,25(6):3047–3094, 12 2015
84
Title: Shape Holomorphy for Parametric PDEs
Researchers: Christoph SchwabJakob Zech
Institute: Seminar for Applied MathematicsETH Zurich
Description: Parametric PDEs allow the modelling of systems subject to varying inputdata. The parameter may either represent a known but flexible quantity, or reflectuncertainty in the data, in which case it can be treated as a random variable. In eithercase, efficient computational approximation requires sparsity in the dependence on thepossibly high dimensional parameter. By showing that the systems’ response dependssmoothly on it, such results can be established.
We investigate this dependence for (linear and nonlinear) PDEs, notably the Maxwellequations and the stationary Navier-Stokes equations. Our emphasis lies on parametricdomains, i.e. the variable data consists of a transformation deforming a nominal domain
to a physical domain on which the PDE is posed. We prove shape holomorphy, bywhich we mean holomorphic dependence of the pullback solutions in the nominal domainon the transformation. In the terminology of shape optimization, this amounts to theexistence of the material derivative in a neighbourhood of the real transformations in thecomplexified spaces.
As a consequence, best N -term convergence rates for polynomial approximation of thesolution manifold can be shown. These rates are achieved by polynomial interpolationin the case of uniform approximation. In order to compute the solution at the interpo-lation points, methods such as FEM or BEM need to be employed. This introduces anadditional discretization error. Its influence on the overall error is investigated. Mul-tilevel algorithms allow to reduce the total computational complexity to the equivalentof one single PDE solve. Similarly, expectations of the solution or quantities of interestdepending on it, may be approximated by quadrature on sparse grids or higher orderquasi Monte Carlo methods, whose multilevel equivalents show similar features.
This research is supported by the Swiss National Science Foundation under grantSNF 159940.
References:
[1] A. Cohen, Ch. Schwab and J. Zech, Shape Holomorphy of the stationary Navier-
Stokes Equations, Technical Report 2016-45, Seminar for Applied Mathematics,ETH Zurich, Switzerland, 2016.
[2] C. Jerez-Hanckes, Ch. Schwab and J. Zech, Shape Holomorphy for Maxwell equa-
tions, 2016 (in preparation).
85
Institute/Group: Institute of Geophysics / Geophysical Fluid Dynamics Group
Researchers: Profs. Paul Tackley, Taras Gerya; Drs. Antoine Rozel, Maxim Ballmer, Dan
Bower, Jie Liao, Kosuke Ueda, Frank Wagner, Patrick Sanan; PhD students S. Brändli, I.
Fomin, R. Herrendörfer, C. Jain, T. Lichtenberg, D. Lourenco, C. Petrini, C. Pranger, S.
Preuss, J. Schierjott
Description: Our research is based on simulations of solid Earth processes using
computational fluid dynamics techniques, in particular mixed Eulerian-Lagrangian codes
solving the variable-viscosity Stokes equations on fixed grids (finite volume or finite element)
while using moving particles to track different materials and properties.
Prof. Paul Tackley and his students, postdocs and international collaborators perform
global simulations of Earth and other planets such as Mars, Venus, and extrasolar super-Earth
planets. They collaborate on two ERC projects: iGEO, the goal of which is to use neural
networks to compare simulations of Earth to actual data, and AUGURY, the goal of which is
to use data assimilation to constrain Earth evolution in the last few 100 million years. We are
involved with the Swiss-wide PlanetS NCCR, with projects to model coupled interior-
atmosphere evolution and to constrain the composition of exoplanets. Key technical
developments are being made in the GeoPC PASC Co-design project, which brings recent
advances in communication-hiding and hybrid computing to geodynamics simulation.
Working with the StagYY and pTatin3D application codes on the Piz Daint supercomputer,
this project is able to support ongoing modelling research while contributing new methods
and open-source software components to the community.
Prof. Taras Gerya and his students, postdocs and international collaborators work on
high-resolution thermomechanical modelling (2D and 3D) of plate tectonics processes:
subduction, continental collision, oceanic spreading, continental breakup, numerical modeling
of Alpine evolution and seismicity, seismo-thermomechanical modeling of seismic cycles at
tectonic plate boundaries, tectono-magmatic modeling of Archean geodynamics, modeling of
plume-lithosphere interactions and related surface evolution, thermomechanical modeling of
planetesimals evolution, modeling of effects of grainsize evolution on subduction, slab
breakoff and transform development. They use the 3D thermo-mechanical coupled numerical
code I3ELVIS (Gerya, 2013) based on finite differences and marker-in-cell techniques to
solve mass, momentum and energy conservation equations in a fully staggered grid, running
on the Euler cluster at ETH. Postdoc Dr. Kosuke Ueda engages in geodynamic modelling of
lithosphere-crust-surface interaction. To this end, he also maintains code development to
improve coupled surface process-tectonic methods that can produce data comparable to
natural observables.
Oberassistant Dr. Antoine Rozel is involved in several research projects involving
heavy computational resources. His current work requires hundreds of simulations of mantle
convection involving complex rheologies including grain size, as well as Archean (early
Earth) geodynamics, which involves partial melting and crust production.
ETH Fellow Dr. Dan Bower has devised a new interior evolution code that
encapsulates the behaviour of both melt and solid in a single formulation to determine the
energy transport in a planetary mantle. The code considers heat transfer by convection and
conduction, and mass transfer by mixing and gravitational separation of melt and solid
phases. A novel feature is its ability to resolve the ultra-thin thermal boundary layers at the
surface and base of a magma ocean (a few cms thickness) that are critical to determine the
energy radiated to space and transferred from the core, respectively.
86
Institute/Group: Theoretical Physics / Computational Physics
Researchers:
Brown, Ethan William
Carleo, Giuseppe
Darulová, Jana
Dolfi, Michele
Gresch, Dominik
Guo, Tao
Guy, Julia
Havlicek, Vojtech
Häner, Thomas
Kosenkov, Alexandr
Könz, Mario
Liu, Yehua, Dr.
Mazzola, Guglielmo
Osorio Iregui, Juan
Pakrouski, Kiryl
Pearson, Natalie
Rodic, Donjan
Savenko, Svyatoslav
Soluyanov, Alexey
Steiger, Damian
Troyer, Matthias
Winkler, Georg Wolfgang
Wu, Quansheng
Description:
Using computer simulations the group explores the intriguing properties of complex
many-body systems from quantum gases, exotic materials, and quantum devices to
interdisciplinary simulations of ecosystems. For more details see the group web page
at http://www.comp.phys.ethz.ch/the-group.html
87
Group of W.F. van Gunsteren
Title: A molecular dynamics simulation investigation of the relative stability of the
cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted
analogs in different solvents
Researchers: L. J. Smith*
G. Rought Whitta*
J. Dolenc
D. Wang
W. F. van Gunsteren
Institute/ Group: Laboratory of Physical Chemistry, ETH Zürich, Switzerland
*Inorganic Chemistry Laboratory, Department of Chemistry, University of
Oxford, U.K.
Description:
The cyclic octa-peptide octreotide and its derivatives are used as diagnostics and therapeutics
in relation to particular types of cancers. This led to investigations of their conformational
properties using spectroscopic, NMR and CD, methods. A CF3-substituted derivative, that was
designed to stabilize the dominant octreotide conformer responsible for receptor binding, turned
out to have a lower affinity. The obtained spectroscopic data were interpreted as to show an
increased flexibility of the CF3 derivative compared to the unsubstituted octreotide, which could
then explain the lower affinity.
In this project, we use MD simulation without and with time-averaged NOE distance and time-
averaged local-elevation 3J-coupling restraining representing experimental NMR data to
determine the conformational properties of the different peptides in the different solvents for
which experimental data are available, that are compatible with the NOE atom–atom distance
bounds and the 3JHNHα-couplings as derived from the NMR measurements. The conformational
ensembles show that the CF3 substitution in combination with the change of solvent from water
to methanol leads to a decrease in flexibility and a shift in the populations of the dominant
conformers that are compatible with the experimental data.
References: Bioorg. Med. Chem. 24 (2016) 4936-4948, DOI:
10.1016/j.bmc.2016.08.001, incl. suppl. mat.
88
Title: On the Use of Time-Averaging Restraints when Deriving Biomolecular
Structure from 3J-coupling Values Obtained from NMR Experiments
Researchers: L.J. Smith*
W.F. van Gunsteren
N. Hansen#
Institute/ Group: Laboratory of Physical Chemistry, ETH Zürich, Switzerland
*Inorganic Chemistry Laboratory, Department of Chemistry, University of
Oxford, U.K.
#Institute of Thermodynamics and Thermal Process Engineering, University
of Stuttgart, Germany
Description:
Deriving molecular structure from 3J-couplings obtained from NMR experiments is a challenge
due to (1) the uncertainty in the Karplus relation 3J(θ) connecting a 3J-coupling value to a
torsional angle θ, (2) the need to account for the averaging inherent to the measurement of 3J-
couplings, and (3) the sampling road blocks that may emerge due to the multiple-valuedness of
the inverse function θ(3J) of the function 3J(θ). Ways to properly handle these issues in structure
refinement of biomolecules are discussed and illustrated using the protein hen egg white
lysozyme as example.
References: J. Biomol. NMR 66 (2016) 69-83, DOI: 10.1007/s10858-016-0058-5, incl.
suppl. mat.
89
Title: Deriving structural information from experimentally measured data on
biomolecules: a review
Researchers: W. F. van Gunsteren1
J. R. Allison2
X. Daura3
J. Dolenc1
N. Hansen4
A. E. Mark5
C. Oostenbrink6
V. H. Rusu1
L. J. Smith7
Institute/ Group: 1Laboratory of Physical Chemistry, ETH Zürich, Switzerland
2Centre for Theoretical Chemistry and Physics & Institute of Natural and
Mathematical Sciences, Massey University, Auckland, New Zealand
3Institute of Biotechnology and Biomedicine, Universitat Autonoma de
Barcelona (UAB), Barcelona, Spain
4Institute of Thermodynamics and Thermal Process Engineering, University
of Stuttgart, Stuttgart, Germany
5School of Chemistry and Molecular Biosciences, University of Queensland,
St. Lucia, Australia
6Institute of Molecular Modeling and Simulation, University of Natural
Resources and Life Sciences, Vienna, Austria
7Department of Chemistry, University of Oxford, Inorganic Chemistry
Laboratory, Oxford, United Kingdom
Description:
During the past half century, the number and accuracy of experimental techniques that can
deliver values of observables for biomolecular systems have been steadily increasing. The
conversion of a measured value Qexp of an observable quantity Q into structural information is,
however, a task beset with theoretical and practical problems: (i) insufficient or inaccurate
values of Qexp, (ii) inaccuracies in the function Q(r) used to relate the quantity Q to structure r,
(iii) how to account for the averaging inherent in the measurement of Qexp, (iv) how to handle
the possible multiple-valuedness of the inverse r(Q) of the function Q(r), to mention
a few. These apply to a variety of observable quantities Q and measurement techniques such as
X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser
imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic
resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy
transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving
structural information from measured data is reviewed with an eye to non-experts and
newcomers in the field using examples from the literature of the effect of the various choices
and approximations involved in the process. A list of choices to be avoided is provided.
References: Angew. Chem. Int. Ed. (2016) in press
90
6
High-performance Hardware
91
5.2 Information Technology Services
The IT Services of ETH are currently managing two large Linux clusters called BRUTUS
(“Better Reliability and Usability Thanks to Unified System”) and EULER (Erweiterbarer,
Umweltfreundlicher, Leistungsfähiger ETH Rechner”).
Both clusters have been financed and are operated according to a “shareholder” model.
Professors, institutes and even whole departments can become shareholders by financing a
number of compute nodes in the cluster. In return, they are guaranteed a share of CPU time
proportional to their investment. The share financed by the IT Services is made available to
the whole scientific community of ETH at no cost.
To make it easier for users to switch back and forth between Brutus and Euler, both clusters
use the same operating system (CentOS), batch system (Platform LSF), development tools
(GNU, Intel and PGI compilers) and applications.
Brutus
The Brutus cluster has been in operation at ETH since 2008 and will be retired at the end of
2016. Its oldest components have been decommissioned since the last CSE report. Currently
720 compute nodes remain in operation, with a total of 17,632 cores and a peak performance
of approximately 166 TF.
Two Lustre parallel file systems, with a capacity of 400 TB each, are configured respectively
as permanent and scratch storage. A Panasas parallel file system with a capacity of 75 TB is
configured as medium-term storage, while an NFS system with a capacity of 50 TB is used
for home directories and centrally installed applications. This NFS file system is backed up
every night to the ETH’s central tape archive (TSM).
All compute nodes are connected to the cluster’s internal Ethernet network via 1 Gb/s links.
The login nodes are connected to this network and to the ETH’s network via 10 Gb/s links.
All nodes are connected to a low-latency 40 Gb/s InfiniBand QDR network.
The two Lustre file systems are attached directly to the cluster’s InfiniBand QDR network.
The Panasas and NFS file systems, as well as the ETH’s central NAS, are connected to the
cluster’s Ethernet network via 10 Gb/s links.
Euler
Due to lack of space, power and cooling in the computer rooms at ETH in Zurich, the Euler
cluster is housed in CSCS’s data center in Lugano and managed remotely from Zurich by the
IT Services.
The first phase (Euler I) was installed in 2014. It consists of 448 compute nodes (HP BL460c
Gen8), each equipped with 24 cores (two 12-core Intel Xeon E5-2697v2 CPUs) and between
64 and 256 GB of memory. All compute nodes are connected to two high-speed networks:
56 Gb/s InfiniBand FDR for inter-node communication (typically MPI);
10 Gb/s Ethernet for file access and for global communication (system management,
monitoring, batch system, etc.).
92
A second phase (Euler II) was installed in 2015. It consists of 768 compute nodes of a newer
generation (HP BL460c Gen9), each equipped with 24 cores (two 12-core Intel Xeon E5-
2680v3 CPUs) and between 64 and 512 GB of memory. Euler II also contains four very-large-
memory nodes with 64 cores (Four 16-core Intel Xeon E7-8867v3 CPUs) and 3072 GB of
memory. Euler II uses similar high-speed networks as Euler I.
Euler I and II are operated as a single cluster containing 1,220 compute nodes, with a total of
29,440 processor cores and a peak performance of about 1 PF.
A third phase (Euler III), consisting of 1,215 compute nodes of a new generation, will be
installed in December 2016 and will enter production in January 2017.
Due to the distance (latency) between Zurich and Lugano, it was decided early on that Euler
would need its own local storage systems. A Panasas parallel file system with a capacity of
400 TB provides high-performance storage for both permanent and temporary (scratch) data.
An NFS system with a capacity of 1,200 TB, based on four redundant NetApp servers,
provides high-reliability storage for home directories and centrally installed applications, as
well as long-term storage for user projects. Like Brutus, home directories and applications are
backed up every night to the ETH’s central tape archive (TSM) in Zurich.
A special feature of Euler is the use of virtualization. The cluster’s head nodes (login and
management nodes) are not physical servers but virtual machines. Virtual servers and
compute nodes allow Euler to offer “software as a service” (SaaS) to the scientific community
of ETH, for programs like CLC Genomics Server and MATLAB.
93
.
94
7
Publications*
*only CSE-related articles
in refereed journals
95
Group of P. Arbenz
D. Hupp, P. Arbenz, and D. Obrist. A parallel Navier–Stokes solver using spectral dis-
cretization in time. Int. J. Comput. Fluid Dyn., 2016. doi:10.1080/10618562.2016.
1242725.
N. Ohs, F. Keller, O. Blank, W.-Y. W. Lee, C.-Y. J. Cheng, P. Arbenz, R. Muller, andP. Christen. Towards in silico prognosis using big data. Current Directions in BiomedicalEngineering. 2 (1): 57–60 (2016), doi:10.1515/cdbme-2016-0016,
P. Benedusi, D. Hupp, P. Arbenz, R. Krause: A parallel multigrid solver for time-periodic
incompressible Navier–Stokes equations in 3D. In: Numerical Mathematics and AdvancedApplications - ENUMATH 2015. B. Karasozen, M. Manguoglu, M. Tezer–Sezgin, S.Goktepe, O. Ugur (eds.). To appear 2016.
D. Hupp, D. Obrist, P. Arbenz: Multigrid preconditioning for time-periodic Navier-Stokes
problems. Proc. Appl. Math. Mech. (PAMM) 15, 595–596 (2015), doi:10.1002/pamm.201510287.
P. Arbenz, L. Grigori, R. Krause, O. Schenk: ”Guest editorial: Special issue on ParallelMatrix Algorithms and Applications (PMAA’14)”. Parallel Comput. 49: 99–100 (2015),doi:10.1016/j.parco.2015.10.004.
S. Pauli, P. Arbenz: Determining optimal multilevel Monte Carlo parameters with ap-
plication to fault tolerance. Comput. Math. Appl. 70 (11): 2638–2651 (2015), doi:
10.1016/j.camwa.2015.07.011.
S. Pauli, P. Arbenz, Ch. Schwab: Intrinsic fault tolerance of multilevel Monte Carlo
methods. J. Parallel Distrib. Comput. 84: 24–36 (2015), doi:10.1016/j.jpdc.2015.07.005.
S. Pauli, R. Gantner, P. Arbenz, A. Adelmann: Multilevel Monte Carlo for the Feynman–
Kac formula for the Laplace equation. BIT Numer. Math. 55 (4): 1125–1143 (2015),doi:10.1007/s10543-014-0543-8.
96
Group of K. Boulouchos publications
1. B.O. Arani, C.E. Frouzakis, J. Mantzaras, K. Boulouchos Three-dimensional direct nu-
merical simulations of turbulent fuel-lean H2/air hetero-/homogeneous combustion over
Pt with detailed chemistry, Proc. Combust. Inst., 36 (in press)
2. M. Schmitt, C.E. Frouzakis, Y.M. Wright, A.G. Tomboulides, K. Boulouchos, Direct
numerical simulation of the compression stroke under engine relevant conditions: Local
wall heat flux distribution, Int. J. Heat Mass Transfer, 92, 718-731, 2016.
3. D.M. Manias, E.A. Tingas, C.E. Frouzakis, K. Boulouchos, D.A. Goussis, The mecha-
nism by which CH2O and H2O2 additives affect the autoignition of CH4/air mixtures,
Combust. Flame, 164, 111-125, 2016.
4. M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. Karlin, Spectral Quasi-Equilibrium
Manifold for Chemical Kinetics, J. Phys. Chem. A, 34063413, 120(20), 2016.
5. D. Farrace, K. Chung, S.S. Pandurangi, Y. M Wright, K. Boulouchos, N. Swaminathan,
Unstructured LES-CMC modelling of turbulent premixed bluff body flames close to
blow-off, Proc. Combust. Inst., 36 (in press).
6. S. Schlatter, B. Schneider, Y.M. Wright, K. Boulouchos, N-heptane micro pilot assisted
methane combustion in a Rapid Compression Expansion Machine, Fuel, 179, 339-352,
2016.
7. S.S. Pandurangi, M. Bolla, Y.M. Wright, K. Boulouchos, S.A. Skeen, J. Manin, L.M.
Pickett, Onset and progression of soot in high-pressure n-dodecane sprays under diesel
engine conditions, Int. J. Engine Res., 1468087416661041, 2016.
97
Publication List
Group Name: Comas-Vives and Copéret
List of publications:
1. Improved promoter effect in NiWS cataltsts through a molecular approach and an
optimized Ni edge decoration, Alphazan, T. et. al. J. Catal. 2016, 340, 60-65.
2. Surface Sites in Cu-Nanoparticles: Chemical Reactivitt or Microscopt? Larmier,
K. et. al. J. Phys. Chem. Lett. 2016, 7, 3259-3263.
3. Structural Characterization of the EtOH–TiCl4–MgCl2 Ziegler–Natta Precataltst,
D’Anna, V. et. al. J. Phts. Chem. C, 2016, 120, 18075.
4. CO2 Activation on Ni/γ–Al2O3 Cataltsts bt First-Principles Calculations: From
Ideal Surfaces to Supported Nanoparticles, Silaghi, M. et. al. ACS Catal. 2016, 6,
4501-4505.
5. The Role of Tri-Coordinate Al–Sites in CH3ReO3/Al2O3 Olefin Metathesis
Cataltsts, Valla, M. et. al. J. Am. Chem. Soc. 2016, 138, 6774-6785.
6. Correlating Stnthetic Methods, Morphologt, Atomic-Level Structure, and Catalttic
Activitt of Sn-β Cataltsts, Wolf, P. et. al. ACS Catal. 2016, 6, 4047-4063.
7. Atomistic Description of Reaction Intermediates for Supported Metathesis
Catalysts Enabled by DNP SENS, Ong, T.-C. et. al. Angew. Chem. Int. Ed. 2016, 55,
4743-4747.
8. The Nature of Secondart Interactions at Electrophilic Metal Sites of Molecular and
Silica-Supported Organolutetium Complexes from Solid-State NMR Spectroscopt,
Conlet, M. P. et. al. J. Am. Chem. Soc. 2016, 138, 3831-3843.
9. Intrinsic reactivitt of Ni, Pd and Pt surfaces in drt reforming and competitive
reactions: Insights from first principles calculations and microkinetic modeling
simulations, Foppa, L. et. al. J. Catal. 2016, in press.
10. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in
d0 Olefin Metathesis Cataltsts, Halbert, S. J. Am. Chem. Soc. 2016, 138, 2261-2272.
98
11. Amorphous SiO2 Surface Models: Energetics of the Dehtdroxtlation Process,
Strain, Ab Initio Atomistic Thermodtnamics and IR Spectroscopic Signatures,
Comas-Vives, A. Phys. Chem. Chem. Phys. 2016, 18, 7475-7482.
12. Predictive Morphologt, Stoichiometrt and Structure of Surface Species in
Supported Ru Nanoparticles under H2 and CO atmospheres from Combined
Experimental and DFT Studies. Comas-Vives, A. et. al., Phys. Chem. Chem. Phys.
2016, 18, 1969-1979.
13. Atomic Description of the Interface Between Silica and Alumina in
Aluminosilicates Through Dtnamic Nuclear Polarization Surface-Enhanced NMR
Spectroscopt and First-Principles Calculations. Valla, M. et. al. J. Am. Chem. Soc.,
2015, 137, 10710–10719.
14. Cooperativitt between Al-sites Promotes H-Transfer and Carbon-Carbon Bond
Formation upon Dimethtlether Activation on Alumina. Comas-Vives, A. et. al., ACS
Cent. Sci., 2015, 1, 313-319.
15. Quantitativelt Analtzing Metathesis Cataltst Activitt and Structural Features in
Silica-Supported Tungsten Imido–Alktlidene Complexes. Mougel, V. et. al. J. Am.
Chem. Soc., 2015, 137, 6699-6704.
16. The Effect of the Electronic Nature of Spectator Ligands in the C–H Bond
Activation of Ethtlene bt Cr(III) Silicates: An Ab Initio Studt. Núñez-Zarur, F.;
Comas-Vives, A. Chimia, 2015, 69, 225-229.
17. Metallactclobutanes from Schrock-ttpe d0-Metal Alktlidene Cataltsts: Structural
Preferences and Consequences in Alkene Metathesis. Solans-Monfort, X. et. al.,
Organometallics, 2015, 34, 1668-1680.
18. Heterolttic activation of C-H bonds on Cr(III)–O surface sites is a ket step in
catalttic poltmerization of ethtlene and dehtdrogenation of propane. Conlet, M. et.
al., Inorg. Chem., 2015, 54, 5065-5078.
19. Carbon-Carbon Bond Formation bt Activation of CH3F on Alumina. Comas-
Vives, A. et. al. J. Phys. Chem. C, 2015, 119, 7156-7163.
20. Atomistic description of thiostannate-capped CdSe nanocrtstals: retention of four-
coordinate SnS4 motif and preservation of Cd-rich stoichiometrt. Protesescu, L. et.
al., J. Am. Chem. Soc., 2015, 137, 1862-1874.
21. Simultaneous generation of mild acidic functionalities and small supported Ir NPs
from alumina-supported well-defined iridium siloxide. Héroguel, F. et. al., J. Catal.,
2015, 321, 81-89. 99
Group of J. Leuthold and Ch. Hafner
Reviewed Journals
1. Coupled FEM-MMP for Computational Electromagnetics, Jasmin Smajic, Christian Hafner, and
Juerg Leuthold, IEEE Transactions on Magnetics, Vol. 52, Issue 3 (2016).
2. Digital Plasmonic Absorption Modulator Exploiting Epsilon-Near-Zero in Transparent
Conducting Oxides, Ueli Koch, Claudia Hössbacher, Jens Niegemann, Christian Hafner, and
Juerg Leuthold, IEEE Photonics Journal, (2016).
3. Plasmonic Organic Hybrid Modulators - Scaling Highest Speed Photonics to the Microscale,
Christian Haffner, Wolfgang Heni, Yuriy Fedoryshyn, Arne Josten, Benedikt Baeuerle, Claudia
Hoessbacher, Yannick Salamin, Ueli Koch, Nikola Dordevic, Pol Mousel, Romain Bonjour,
Alexandros Emboras, David Hillerkuss, Pascal Leuchtmann, Delwin L. Elder, Larry R. Dalton,
Christian Hafner, and Juerg Leuthold, Proceedings of the IEEE, (2016).
4. Atomic Scale Plasmonic Switch, Alexandros Emboras, Jens Niegemann, Ping Ma, Christian
Haffner, Andreas Pedersen, Mathieu Luisier, Christian Hafner, Thomas Schimmel, and Juerg
Leuthold, Nano Letters, (2016).
5. Ultra-fast Millimeter Wave Beam Steering, Romain Bonjour, Matthew Singleton, Simon A.
Gebrewold, Yannick Salamin, Felix C. Abrecht, Baeuerle Baeuerle, Arne Josten, Pascal
Leuchtmann, Christian Hafner, and Juerg Leuthold, IEEE Journal of Quantum Electronics, (2016)
6. Modelling and Simulation Aspects of Transient Electromagnetic-Mechanical Analysis for
Industrial Applications, Zeljko Tanasic, Thomas Werder-Schläpfer, and Jasmin Smajic, IEEE
Transactions on Magnetics, (2016).
7. Data-sparse numerical models for SNOM tips, Christian Hafner, Ralf Hiptmair, Pegah Souzangar,
Int. J. of Numerical Modelling: Electronic Networks, Devices and Fields, June (2016)
8. High speed plasmonic modulator array enabling dense optical interconnect solutions, W. Heni, C.
Hoessbacher, C. Haffner, Y. Fedoryshyn, B. Baeuerle, A. Josten, D. Hillerkuss, Y. Salamin, R.
Bonjour, A. Melikyan, M. Kohl, D. L. Elder, L. R. Dalton, C. Hafner, and J. Leuthold, Optics
Express, Vol. 23, Issue 23 (2015).
9. Shape optimization of microlenses, Paganini, A.; Sargheini, S.; Hiptmair, R.; Hafner, Ch.,
Optics Express Vol. 23, No. 10 (2015).
100
Group name: Computational Physics for Engineering Materials
List of Publications:
Published:
F. Mohseni, M. Mendoza, S. Succi, H.J. Herrmann, Lattice Boltzmann model for resistiverelativistic magnetohydrodynamics, Phys. Rev. E 92, 023309 (2015)
A. Leondardi, M. Cabrera, F.K. Wittel, R. Kaitna, M. Mendoza, W. Wu, H.J. Herrmann,Granular front formation in free-surface flow of concentrated suspensions, Phys. Rev. E92, 052204 (2015)
M. M. Hassani, F.K. Wittel, S. Ammann, P. Niemz, H.J. Herrmann: Moisture InducedDamage Evolution in Laminated Beech, Wood Science and Technology 50 (5/2016), 917-940 (2016)
J.J. Kranz, N.A.M. Araujo, J.S. Andrade JR., H.J. Herrmann, Complex networks ofspace-filling bearings, Phys. Rev. E 92, 012802 (2015)
F. Lombardi, H.J. Herrmann, D. Plenz, L. de Arcangelis, Temporal correlations in neu-ronal avalanche occurence, accepted for Sci. Rep.
K. Melnikov, R. Mani, F.K. Wittel, M. Thielmann and H.J. Herrmann, Grain ScaleModeling of Arbitrary Fluid Saturation in Random Packings, Phys. Rev. E 92, 022206(2015)
R. Vetter, F.K. Wittel, H.J. Herrmann, Packing of elastic wires in flexible shells, EPL121, 44003 (2015)
Y.S. Cho, J.S. Lee, H.J. Herrmann and B. Kahng, Hybrid percolation transition in clustermerging processes: continuously varying exponents, Phys. Rev. Lett. 116, 025701 (2016)
D.V. Stager, N.A.M. Araujo, H.J. Herrmann, Prediction and control of slip-free rotationstates in sphere assemblies, Phys. Rev. Lett. 116, 254301 (2016)
T.A. Amor, S.D.S. Reis, D. Campos, H.J. Herrmann, J.S. Andrade Jr., Persistence in eyemovement during visual search, Sci. Rep. 6, 20815 (2016)
F.G.R. Magalhaes, A.P.F. Atman, J.G. Moreira, H.J. Herrmann, Analysis of the velocityfield of granular hopper flow, Granular Matter 18, 33 (2016)
H.F. Credidio, A.A. Moreira, H.J. Herrmann, J.S. Andrade Jr., Stochastic Loewner Evo-lution Relates Anomalous Diffusion and Anisotropic Percolation, Phys. Rev. E 93,042124 (2016)
I. Giordanelli, M. Mendoza, J.S. Andrade Jr., M.A.F. Gomez, H.J. Herrmann, Crumplingdamaged graphene, Sci. Rep. 6, 25891 (2016)
101
C.L.N. Oliveira, A.P. Vieira, D. Helbing, J.S. Andrade Jr., H.J. Herrmann, Keep-leftbehavior induced by asymmetrically profiled walls, Phys. Rev. X 6, 011003 (2016)
L. Bottcher, N.A.M. Araujo, J. Nagler, J.F.F. Mendes, D. Helbing, H.J. Herrmann,Gender gap in the ERASMUS mobility program, PLOS ONE 11, e0149514 (2016)
I. Giordanelli, N. Pose, M. Mendoza, H.J. Herrmann, Conformal invariance of graphenesheets, Sci. Rep. 6, 22949 (2016)
C. Hu, G. Munglani, H. Vogler, F.K. Wittel, C. Eichenberger, U. Grossniklaus, B.K.Nelson, H.J. Herrmann: Characterization of size-dependent mechanical properties of tip-growing cells using a lab-on-chip device, under review by Lab on a Chip (7/2016)
Z. Danku, F. Kun, H.J. Herrmann, Fractal frontiers of bursts and cracks in a fiber bundlemodel of creep rupture, Phys. Rev. E 92, 062402 (2015)
M. Fauconneau, F.K. Wittel, H.J. Herrmann, Continuous Fiber Reinforcement for JammedGranular Architecture, Granular Matter 18, 27 (2016)
K.J. Schrenk, M.R. Hilario, V. Sidoravicius, N.A.M. Araujo, H.J. Herrmann, M. Thiel-mann, A. Texeira, Critical fragmentation properties of random drilling: How many ran-dom holes need to be drilled to collapse a wooden cube?, Phys. Rev. Lett. 116, 055701(2016)
H.J.Herrmann, Discontinuous percolation, J. Phys. Conf. Series 681, 012003 (2016)
K. Melnikov, F.K. Wittel, H.J. Herrmann, Micro-mechanical failure analysis of wet gran-ular matter, Acta Geotecnica, 11, 539-548 (2016)
T. Verma, F. Russmann, N.A.M. Araujo, J. Nagler, H.J. Herrmann, Emergence of core-peripheries by pruning, Nature Comm. 7, 10441 (2016)
A. Leonardi, F.K. Wittel, M. Mendoza, R. Vetter, H.J. Herrmann: Particle-fluid-structureinteraction for debris-flow impact on flexible barriers, Computer-Aided Civil and In-trastructure Engineering 31(5) (2016)
T. Verma, N.A.M. Araujo, J. Nagler, J.S. Andrade JR., H.J. Herrmann, Model for thegrowth of the World Airline Network, IJMPC 27, 165141 (2016)
L. Bottcher, O. Woolley-Meza, E. Goles, D. Helbing, H.J. Herrmann, Connectivity dis-ruption sparks explosive epidemic spreading, Phys. Rev. E 93, 042315 (2016)
L.M. van Kessenich, L. de Arcangelis, H.J. Herrmann, Synaptic plasticity and neuronalrefractory time cause scaling behaviour of neuronal avalanches, Sci. Rep. 6, 32071 (2016)
In press:
J.-D. Debus, M. Mendoza, S. Succi, H.J. Herrmann, Poiseuille flow in curved spaces,accepted for Phys. Rev. E
102
R. Yoshimatsu, N.A.M. Araujo, T. Shinbrot, H.J. Herrmann, Field driven charging of a
fluidized granular bed, accepted for Soft Matter
S. Solorzano, M. Mendoza, H.J. Herrmann, Second order kinetic Kohn-Sham lattice
model, accepted for Phys. Rev. A, arXiv:1605.05032
Preprints:
N. Pose, K.J. Schrenk, N.A.M. Araujo, H.J. Herrmann, Schramm-Loewner Evolution and
isoheight lines of correlated landscapes, preprint, arXiv:1508.07942
A.M.C. Souza, R.F.S. Andrade, N.A.M. Araujo, H.J. Herrmann, How the site degree influ-
ences quantum probability on inhomogeneous substrate, submitted to PRE, arXiv:1606.00224
A. Baule, F. Morone, H.J. Herrmann, H.A. Makse, Edwards Statistical Mechanics for
Jammed Granular Matter, preprint, arXiv:1602.04369
L. Bottcher, M. Lukovic, J. Nagler, S. Havlin, H.J. Herrmann, Embedding networks in
the presence of failure and recovery makes them highly predictable, arXiv:1610.00997
D.V. Stager, H.J. Herrmann, Self-similar space-filling sphere packings in three and four
dimensions, submnitted to Fractals, arXiv:1607.08391
M.S. Araujo, A.P. Vieira, J.S. Andrade JR., H.J. Herrmann, A mesoscopic approach to
subcritical fatigue crack growth, submnitted to PRE, arXiv:1608.02613
R. Yoshimatsu, N.A.M. Araujo, G. Wurm, H.J. Herrmann, T. Shinbrot, Something from
nothing: self-charging of identical grains, preprint, arXiv:1608.03210
C.I.N. Sampaio Filho, A.A. Moreira, N.A.M. Araujo, J.S. Andrade JR., H.J. Herrmann,
Itinerant conductance in fuse-antifuse networks, preprint, arXiv:1608.08147
R. Jager, M. Mendoza, H.J. Herrmann, Channelization in Porous Media driven by Erosion
and Deposition, preprint, arXiv:1609.03746
D.V. Stager, H.J. Herrmann, Cutting self-similar space-filling sphere packings, preprint,
arXiv:1609.03811
C.P. de Castro, M. Lukovic, R.F.S. Andrade, H.J. Herrmann, The influence of statistical
properties Fourier coeffcients on random surfaces, preprint
103
References:
[1] Manopulo, N., Peters, P., Hora, P., Assessment of anisotropic hardening models for
conventional deep drawing processes, International Journal of Material
Forming,2016,1-9, ISSN 1960-6214, http://dx.doi.org/10.1007/s12289-016-1306-7
[2] Raemy C., Manopulo N., Hora P., On the modelling of plastic anisotropy, asymmetry
and distortional hardening of commercially pure titanium: A Fourier series approach,
International Journal of Plasticity, (submitted)
[3] Gorji, M., Berisha B., Manopulo N., Hora P., Effect of through thickness strain
distribution on shear fracture hazard and its mitigation by using multilayer aluminum
sheets, Journal of Materials Processing Technology, Volume 232, June 2016, Pages 19-
33, ISSN 0924-0136, http://dx.doi.org/10.1016/j.jmatprotec.2016.01.014.
[4] Hippke H., Manopulo N., Yoon J-W., Hora P., On the efficiency and accuracy of stress
integration algorithms for constitutive models based on non-associated flow rule,
submitted to International Journal of Material Forming, (in review).
104
Group name: Prof P.H. Hunenberger - Computer Simulation of Molecular Systems (CSMS)List of publications:
M. Laner, B.A.C. Horta and P.H. Hunenberger.Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using moleculardynamics simulation.J. Mol. Graph. Model. 55 (2015) 48-64.
M. Laner and P.H. Hunenberger.Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayersinvestigated using molecular dynamics simulations: In quest of the biphasic effect.J. Mol. Graph. Model. 55 (2015) 85-104.
M. Laner & P.H. Hunenberger.Phase-transition properties of glycerol-dipalmitate lipid bilayers investigated using moleculardynamics simulation.J. Mol. Graph. Model. 59 (2015) 136-147.
N.S. Bieler & P.H. Hunenberger.On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical con-formations of decaalanine in water.J. Chem. Phys. 142 (2015) 165102/1-165102/17.
N.S. Bieler, J.P. Tschopp & P.H. Hunenberger.Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): Method and application to thecomplexation of cations by crown ethers.J. Chem. Theory. Comput. 11 (2015) 2575-2588.
N.S. Bieler & P.H. Hunenberger.Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI vs.
λ-LEUS.J. Comput. Chem. 36 (2015) 1686-1697.
O.M. Szklarczyk, N.S. Bieler, P.H. Hunenberger & W.F. van Gunsteren.Flexible boundaries for multi-resolution solvation: An algorithm for spatial multi-scaling inmolecular dynamics simulation.J. Chem. Theory Comput 11 (2015) 5447-5463.
W. Plazinski, A. Lonardi & P.H. Hunenberger.Revision of the GROMOS 56A6CARBO force field for hexopyranose-based carbohydrates: Im-proving the description of ring-conformational equilibria in oligo- and polysaccharide chains.J. Comput. Chem. 37 (2016) 354-365.
Horta, B.A.C., Merz, P.T., Fuchs, P.F.J., Dolenc, J., Riniker, S. & Hunenberger, P.H.A GROMOS-compatible force field for small organic molecules in the condensed phase: The2016H66 parameter set.J. Chem. Theory Comput. 12 (2016) 3825-3850.
Reif, M.M. & Hunenberger, P.H.Origin of asymmetric solvation effects for ions in water and organic solvents investigated usingmolecular dynamics simulations: The Swain acity-basity scale revisited.J. Phys. Chem. B 120 (2016) 8485-8517
Lonardi, A., Oborsky, P. & Hunenberger, P.H.Solvent-modulated influence of intramolecular hydrogen-bonding on the conformational prop-erties of the hydroxymethyl group in glucose and galactose: A molecular dynamics simulationstudy.Helvetica Chimica Acta, Submitted (2016).
105
Institute of Fluid Dynamics / Prof. Patrick Jenny, Computational Fluid Dynamics and
Multi-Scale Modeling
List of submitted manuscripts and publications in-press or having appeared in peer-
reviewed journals between July 2015 and July 2016
1. Delgoshaie, A.H., D.W. Meyer, P. Jenny, and H.A. Tchelepi, Non-local formulation for
multiscale flow in porous media. Journal of Hydrology, 2015. 531, Part 3: p. 649-654.
2. Gorji, M.H., N. Andric, and P. Jenny, Variance reduction for Fokker-Planck based particle
Monte Carlo schemes. Journal of Computational Physics, 2015. 295: p. 644-664.
3. Ibrahima, F., D.W. Meyer, and H.A. Tchelepi, Distribution Functions of Saturation for
Stochastic Nonlinear Two-Phase Flow. Transport in Porous Media, 2015. 109(1): p.
81-107.
4. Swiderski, K., D. Caviezel, M. Labois, D. Lakehal, and C. Narayanan, Computational
Modelling Of Gas–liquid Multiphase Flows With DQMOM And The N-phase Algebraic
Slip Model, in Multiphase Flow 2015, P. Vorobieff, Editor. 2015, WIT Press: Valencia,
Spain.
5. Andric, N., M.H. Gorji, and P. Jenny, Influence of the gas-surface interaction model on
time-dependent rarefied gas simulations. Vacuum, 2016. 128: p. 244-251.
6. Karvounis, D.C. and P. Jenny, Adaptive Hierarchical Fracture Model for Enhanced
Geothermal Systems. Multiscale Modeling and Simulation, 2016. 14(1): p. 207-231.
7. Dünser, S. and D.W. Meyer, Predicting field-scale dispersion under realistic conditions
with the polar Markovian velocity process model. Advances in Water Resources, 2016.
92: p. 271-283.
8. Khayrat, K. and P. Jenny, Subphase Approach to Model Hysteretic Two-Phase Flow in
Porous Media. Transport in Porous Media, 2016. 111(1): p. 1-25.
9. Meyer, D.W. and B. Bijeljic, Pore-scale dispersion: Bridging the gap between
microscopic pore structure and the emerging macroscopic transport behavior. Physical
Review E, 2016. 94(1): p. 013107.
10. Meyer, D.W. and F. Saggini, Testing the Markov hypothesis in fluid flows. Physical
Review E, 2016. 93(5): p. 053103.
11. Sui, R., N.I. Prasianakis, J. Mantzaras, N. Mallya, J. Theile, D. Lagrange, and M. Friess,
An experimental and numerical investigation of the combustion and heat transfer
characteristics of hydrogen-fueled catalytic microreactors. Chemical Engineering
Science, 2016. 141: p. 214-230.
12. Swiderski, K., C. Narayanan, and D. Lakehal, Application of N-phase algebraic slip
model and direct quadrature method of moments to the simulation of air-water flow in
vertical risers and bubble column reactor. Computers & Chemical Engineering, 2016. 90:
p. 151-160.
13. Müller, F., P. Jenny, and D.W. Meyer, Parallel Multilevel Monte Carlo for Two-Phase
Flow and Transport in Random Heterogeneous Porous Media With Sampling-Error and
Discretization-Error Balancing. SPE Journal, 2016. in press.
106
14. Sui, R., J. Mantzaras, and R. Bombach, A comparative experimental and numerical
investigation of the heterogeneous and homogeneous combustion characteristics of fuel-
rich methane mixtures over rhodium and platinum. Proceedings of the Combustion
Institute, 2016. in press.
15. Sui, R., J. Mantzaras, R. Bombach, and A. Denisov, Hetero-/homogeneous combustion of
fuel-lean methane/oxygen/nitrogen mixtures over rhodium at pressures up to 12 bar.
Proceedings of the Combustion Institute, 2016. in press.
16. Ibrahima, F., H. Tchelepi, and D. Meyer, An efficient distribution method for nonlinear
two-phase flow in highly heterogeneous multidimensional stochastic porous media.
Computational Geosciences, 2016. submitted.
17. Jenny, P. and D.W. Meyer, Non-Local Generalization of Darcy's Law Based on
Empirically Extracted Conductivity Kernels. Computational Geosciences, 2016.
submitted.
18. Khayrat, K. and P. Jenny, A multi-scale network model for two-phase flow in porous
media. Journal of Computational Physics, 2016. submitted.
19. Küchlin, S. and P. Jenny, Parallel Fokker-Planck-DSMC Algorithm for Rarefied Gas
Flow Simulation in Complex Domains at all Knudsen Numbers. Journal of
Computational Physics, 2016. submitted.
20. Lücker, A., T.W. Secomb, W. B., and J. P., The relative influence of hematocrit and red
blood cell velocity on oxygen transport from capillaries to tissue. Microcirculation, 2016.
submitted.
21. Meyer, D.W., Density Estimation with Distribution Element Trees. Journal of
Computational and Graphical Statistics, 2016. submitted.
22. Sui, R., E. Es-Sebbar, J. Mantzaras, and R. Bombach, Homogeneous ignition during fuel-
rich H2/O2/N2 combustion in platinum-coated channels at elevated pressures.
Combustion and Flame, 2016. submitted.
107
Publications and preprints of the research group
of Prof. Arnulf Jentzen in 2016
[1] Andersson, A., Hefter, M., Jentzen, A. & Kurniawan, R.,
Regularity properties for solutions of infinite dimensional Kolmogorov equa-tions
in Hilbert spaces.
arXiv:1611.00858 (2016), 36 pages, https://arxiv.org/abs/1611.00858.
[2] Jentzen, A. & Pusnik, P.,
Exponential moments for numerical approximations of stochastic partialdifferential equations.
arXiv:1609.07031 (2016), 44 pages, https://arxiv.org/abs/1609.07031.
[3] Hutzenthaler, M., Jentzen, A., & Salimova, D.,
Strong convergence of full-discrete nonlinearity-truncated accelerated
exponential Euler-type approximations for stochastic Kuramoto-Sivashinsky equations.
arXiv:1604.02053 (2016), 43 pages,
http://arxiv.org/abs/1604.02053.
[4] Becker, S. & Jentzen, A.,
Strong convergence rates for nonlinearity-truncated Euler-type
approximations of stochastic Ginzburg-Landau equations.
arXiv:1601.05756 (2016), 58 pages, http://arxiv.org/abs/1601.05756.
[5] Cox, S., Hutzenthaler, M., Jentzen, A., van Neerven, J., & Welti, T.,
Convergence in Holder norms with applications to Monte Carlo
methods in infinite dimensions.
arXiv:1605.00856 (2016), 38 pages,
http://arxiv.org/abs/1605.00856.
Minor revision requested from the IMA J. Numer. Anal.
[6] Andersson, A., Jentzen, A., & Kurniawan, R.,
Existence, uniqueness, and regularity for stochastic evolution equationswith irregular initial values.
arXiv:1512.06899 (2015), 31 pages, http://arxiv.org/abs/1512.06899.
Revision requested from the J. Math. Anal. Appl.
[7] Da Prato, G., Jentzen, A., & Rockner, M.,
A mild Ito formula for SPDEs.
arXiv:1009.3526 (2012),
39 pages, http://arxiv.org/abs/1009.3526.
To appear in the Trans. Amer. Math. Soc.
108
[8] Hutzenthaler, M., Jentzen, A., & Wang, X.,
Exponential integrability properties of numerical approximation processesfor nonlinear stochastic differential equations.
arXiv:1309.7657 (2013), 32 pages,
http://arxiv.org/abs/1309.7657.
To appear in Math. Comp.
[9] Jentzen, A., Muller-Gronbach, T., & Yaroslavtseva, L.,
On stochastic differential equations with arbitrary slow convergence ratesfor strong approximation.
Commun. Math. Sci. 14 (2016), no. 6, 1477–1500.
[10] E, W., Jentzen, A., & Shen, H.,
Renormalized powers of Ornstein-Uhlenbeck processes and well-posednessof
stochastic Ginzburg-Landau equations.
Nonlinear Anal. 142 (2016), 152–193.
[11] Becker, S., Jentzen, A., & Kloeden, P. E.,
An exponential Wagner-Platen type scheme for SPDEs.
SIAM J. Numer. Anal. 54 (2016), no. 4, 2389–2426.
109
Computational Polymer Physics, D-MATL, ETH Zurich
Martin Kroger www.complexfluids.ethz.ch
List of peer-reviewed publications
Z. Shen, D.T. Loe, J.K. Awino, M. Kroger, J.L. Rouge, Y. Li,
Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their
potential as drug delivery vehicles,
Nanoscale 8 (2016) 14821-14835.
Y.R. Sliozberg, M. Kroger, T.L. Chantawansri,
Fast equilibration protocol for million atom systems of highly entangled linear
polyethylene chains,
J. Chem. Phys. 144 (2016) 154901.
Y. Li, S. Tang, M. Kroger, W.K. Liu,
Molecular simulation guided constitutive modeling on finite strain viscoelasticity of
elastomers,
J. Mech. Phys. Solids 88 (2016) 204-226.
S.H. Jeong, J.M. Kim, J. Yoon, C. Tzoumanekas, M. Kroger, C. Baig,
Influence of molecular architecture on the entanglement network: topological analy-
sis of entangled linear, long- and short-chain branched polyethylene melts via Monte
Carlo simulation,
Soft Matter 12 (2016) 3770-3786.
S. Costanzo, L.F. Scherz, T. Schweizer, M. Kroger, G. Floudas, A.D. Schluter, D. Vlas-
sopoulos,
Rheology and packing of dendronized polymers,
Macromolecules 49 (2016) 7054-7068.
P.S. Stephanou, M. Kroger,
Solution of the complete Curtiss-Bird model for polymeric liquids subjected to sim-
ple shear flow,
J. Chem. Phys. 144 (2016) 124905.
M.K. Singh, P. Ilg, R.M. Espinosa-Marzal, N.D. Spencer, M. Kroger,
Influence of chain stiffness, grafting density and normal load on the tribological
and structural behavior of polymer brushes: a nonequilibrium-molecular-dynamics
study,
Polymers 8 (2016) 254.
M.K. Singh, P. Ilg, R.M. Espinosa-Marzal, M. Kroger, N.D. Spencer,
Effect of crosslinking on the microtribological behavior of model polymer brushes,
Tribol. Lett. 63 (2016) 17.
110
M. Schuppler, F.C. Keber, M. Kroger, A.R. Bausch,
Boundaries steer the contraction of active gels,
Nat. Commun. 7 (2016) 13120.
A. Karatrantos, N. Clarke, M. Kroger,
Modeling of polymer structure and conformations in polymer nanocomposites from
atomistic to mesoscale: A Review,
Polym. Rev. 56 (2016) 385-428.
Y. Li, M. Kroger, W.K. Liu,
Shape effect in cellular uptake of PEGylated nanoparticles: Comparison between
sphere, rod, cube and disk,
Nanoscale 7 (2015) 16631-16646.
A. Halperin, M. Kroger, F.M. Winnik,
Poly(N-isopropylacrylamid)-Phasendiagramme: 50 Jahre Forschung,
Angew. Chem. 127 (2015) 15558-15586.
O. Bertran, B. Zhang, A.D. Schluter, M. Kroger, C. Aleman,
Modeling nanosized single molecule objects: Dendronized polymers adsorbed onto
mica,
J. Phys. Chem. C 119 (2015) 3746-3752.
M. Kroger,
Simple, admissible, and accurate approximants of the inverse Langevin and Bril-
louin functions, relevant for strong polymer deformations and flows,
J. Non-Newtonian Fluid Mech. 223 (2015) 77-87.
M.K. Singh, P. Ilg, R. M. Espinosa-Marzal, M. Kroger, N.D. Spencer,
Polymer brushes under shear: Molecular dynamics simulations compared to exper-
iments,
Langmuir 31 (2015) 4798-4805.
E. Cordova-Mateo, O. Bertran, A.D. Schluter, M. Kroger, C. Aleman,
Internal organization of macromonomers and dendronized polymers based on thio-
phene dendrons,
Soft Matter 11 (2015) 1116-1126.
A. Halperin, M. Kroger, F.M. Winnik,
Poly(N-isopropylacrylamide) phase diagrams: Fifty years of research,
Angew. Chem. Int. Ed. 54 (2015) 15342-15367.
111
Group of M. Luisier
1. H. Carrillo-Nuñez, M. Luisier, and A. Schenk, “Design of High-Performance InAs–Si
Heterojunction 2D–2D Tunnel FETs With Lateral and Vertical Tunneling Paths”, IEEE
Trans. Elec. Dev. 63, 5041 (2016).
2. Y. Lee, M. Lanoo, N. Cavassilas, M. Luisier, and M. Bescond, “Efficient quantum
modeling of inelastic interactions in nanodevices”, Phys. Rev. B 93, 205411 (2016).
3. A. Ziegler, M. Frey, L. Smith, and M. Luisier, “A Nonparabolic Bandstructure Model for
Computationally Efficient Quantum Transport Simulations”, IEEE Trans. Elec. Dev. 63,
2050 (2016).
4. D. Bozyigit, N. Yazdani, M. Yarema, O. Yarema, W. M. M. Lin, S. Volk, K.
Vuttivorakulchai, M. Luisier, F. Juranyi, and V. Wood, “Soft surfaces of nanomaterials
enable strong phonon interactions”, Nature 531, 618-622 (2016).
5. R. Rhyner and M. Luisier, “Minimizing Self-Heating and Heat Dissipation in Ultrascaled
Nanowire Transistors”, Nano Letters 16, 1022-1026 (2016).
6. M. H. Bani-Hashemian, S. Brück, M. Luisier, and J. VandeVondele, “A generalized
Poisson solver for first-principles device simulations”, J. Chem. Phys. 144, 044113
(2016).
7. G. Zerveas, E. Caruso, G. Baccarani, L. Czornomaz, N. Daix, D. Esseni, E. Gnani, A.
Gnudi, R. Grassi, M. Luisier, T. Markussen, P. Osgnach, P. Palestri, A. Schenk, L. Selmi,
M. Sousa, K. Stokbro, and M. Visciarelli, “Comparison of modeling approaches for band-
structure calculation in III-V semiconductor quantum wells”, Solid-State Electronics 115,
92-102 (2016).
8. A. Emboras, J. Niegemann, P. Ma, C. Haffner, A. Pedersen, M. Luisier, C. Hafner, T.
Schimmel, and J. Leuthold, “Atomic Scale Plasmonic Switch”, Nano Letters 16, 709-714
(2016).
9. A. Ueda, M. Luisier, and N. Sano, “Enhanced impurity-limited mobility in ultra-scaled Si
nanowire junctionless field-effect transistors”, Appl. Phys. Lett. 107, 253501 (2015).
10. M. Luisier, R. Rhyner, A. Szabo, and A. Pedersen, “Atomistic simulation of nanodevices”,
2016 International Conference on Simulation of Semiconductor Processes and Devices
(SISPAD), pp. 281-286 Nürnberg, Germany, September 2016.
11. M. Rau, T. Markussen, E. Caruso, D. Esseni, E. Gnani, A. Gnudi, P. A. Khomyakov, M.
Luisier, P. Osgnach, P. Palestri, S. Reggiani, A. Schenk, L. Selmi, and K. Stokbro,
“Performance study of strained III–V materials for ultra-thin body transistor applications”,
2016 46th European Solid-State Device Research Conference (ESSDERC), pp. 184-187,
Lausanne, Switzerland, September 2016.
112
12. H. Carrillo-Nuñez, R. Rhyner, M. Luisier, and A. Schenk, “Effect of surface roughness
and phonon scattering on extremely narrow InAs-Si Nanowire TFETs”, 2016 46th
European Solid-State Device Research Conference (ESSDERC), pp. 188-191, Lausanne,
Switzerland, September 2016.
13. S. Sant, H. Carrillo-Nuñez, M. Luisier, and A. Schenk, “Transfer matrix based
semiclassical model for field-induced and geometrical quantum confinement in tunnel
FETs”, 2016 International Conference on Simulation of Semiconductor Processes and
Devices (SISPAD), pp. 77-80, Nürnberg, Germany, September 2016.
14. K. Vuttivorakulchai, M. Luisier, and A. Schenk, “Modeling the thermal conductivity of Si
nanowires with surface roughness”, 2016 International Conference on Simulation of
Semiconductor Processes and Devices (SISPAD), pp. 19-22, Nürnberg, Germany,
September 2016.
15. P. Lenarczyk and M. Luisier, “Physical modeling of ferroelectric field-effect transistors in
the negative capacitance regime”, 2016 International Conference on Simulation of
Semiconductor Processes and Devices (SISPAD), pp. 311-314, Nürnberg, Germany,
September 2016.
16. P. Aguirre, H. Carrillo-Nuñez, A. Ziegler, M. Luisier, and A. Schenk, “Drift-diffusion
quantum corrections for In0.53Ga0.47As double gate ultra-thin-body FETs”, 2016
International Conference on Simulation of Semiconductor Processes and Devices
(SISPAD), pp. 53-56, Nürnberg, Germany, September 2016.
17. A. Szabo, R. Rhyner, and M. Luisier, “Phonon-limited performance of single-layer,
single-gate black phosphorus n- and p-type field-effect transistors”, Proceedings of the
IEDM 2015, pp. 12.1.1-12.1.4, Washington DC, USA, December 2015.
18. H. Carrillo-Nuñez, M. Luisier, and A. Schenk, “InAs-GaSb/Si Heterojunction Tunnel
MOSFETs: An Alternative to TFETs as Energy-Efficient Switches?”, Proceedings of the
IEDM 2015, pp. 34.6.1-34.6.4, Washington DC, USA, December 2015.
19. M. Calderara, S. Brück, A. Pedersen, M. H. Bani-Hashemian, J. VandeVondele, and M.
Luisier, “Pushing Back the Limit of Ab-initio Quantum Transport Simulations on Hybrid
Supercomputers”, Proceedings of the International Conference for High Performance
Computing, Networking, Storage and Analysis (SC15), Article 3, Austin, TX, USA,
November 2015.
113
Group of S. Mishra
Published papers
1. A. Hiltebrand and S. Mishra, A well-balanced space-time Discontinuous Galerkinmethod for the shallow water equations, Netw. Het. Med., 11 (1), 2016, 145-162.
2. K. Pressel, C. Kaul, Z. Tan, T. Schneider and S. Mishra, Large-eddy simulation in anan elastic framework with closed water and entropy balances, Journal of Advancesin Modeling Earth Systems (JAMES), 7 (3), 1425-1456.
3. S. Mishra, Ch. Schwab and J. Sukys, Multi-Level Monte Carlo Finite Volumemethods for uncertainty quantification of acoustic wave propagation in random het-erogeneous layered medium, J. Comput. Phys., 312, 2016, 192-217.
4. G. M. Coclite, M. M. Coclite, and S. Mishra. On a model for the evolution ofmorphogens in a growing tissue, SIAM J. Math. Anal., 48 (3), 2016 1575-1615.
5. S. Mishra, N.H. Risebro, Ch. Schwab and S. Tokareva Numerical solution of scalarconservation laws with random flux functions, SIAM/ASA Jl. Uncertainty Quan-tification., 4 (1), 2016, 552-591.
6. D. Ray, P. Chandrasekhar, U. S. Fjordholm and S. Mishra, Entropy stable scheme ontwo-dimensional unstructured grids for Euler equations, Commun. Comput. Phys.,19 (5), 2016, 1111-1140.
7. U. S. Fjordholm, R. Kappeli, S. Mishra and E. Tadmor, Construction of approxi-mate entropy measure valued solutions for hyperbolic systems of conservation laws.Found. Comput. Math., 2016 doi:10.1007/s10208-015-9299-z.
8. U. S. Fjordholm, S. Mishra and E. Tadmor, On the computation of measure-valuedsolutions, Acta Numerica, 25, 2016, 567-679.
9. R. Kappeli and S. Mishra, A well-balanced finite volume scheme for the Euler equa-tions with gravitation-The exact preservation of hydrostatic equilibrium with arbi-trary entropy stratification, Astronomy and Astrophysics, 587, 2016, A94.
10. T. Zimmermann, S. Mishra, B. R. Doran, D. F. Gordon, A. Landsman, Tunnelingtime and weak measurement in strong field ionization., Phys. Rev. Lett., 116 (23),2016, 233603.
11. C. Sanchez-Linares, M. de la asuncion, M. Castro, J. M. Gonzalez-Vida, J. Maciasand S. Mishra, Uncertainty quantification in tsunami modeling using Multi-levelMonte Carlo finite volume method, Jl. Math. Ind., 6, 2016, Art 5, 26 pages.
In Press
12. A. BelJadid, P. G. LeFloch, S. Mishra and C. Pares, Schemes with well-controlleddissipation-Hyperbolic systems in non-conservative form, Commun, Comput. Phys.,2016, to appear.
114
13. F. Leonardi, S. Mishra and Ch. Schwab, Numerical approximation of statistical
solutions of incompressible flow. Math. Mod. Meth. Appl. Sci. (M3AS), 2016, toappear.
Preprints
14. U. S. Fjordholm, S. Lanthaler and S. Mishra, Statistical solutions of hyperbolic
conservation laws I: Foundations, Preprint, 2016, Available from ArXiv:1605.05960.
15. K. G. Pressel, S. Mishra, T. Schneider, C. M. Kaul and Z. Tan, Numerics and
Subgrid-Scale Modeling in Large Eddy Simulations of Stratocumulus Clouds, Preprint
2016.
115
Group name: Laboratory for Bone Biomechanics, Prof. Ralph Müller
List of publications:
K. S. Mader, L. R. Donahue, R. Müller and M. Stampanoni. High-throughput phenotyping and
genetic linkage of cortical bone microstructure in the mouse. BMC Genomics, 16:493, 2015.
Z. Li, G. Kuhn, M. von Salis-Soglio, S. J. Cooke, M. Schirmer, R. Müller and D. Ruffoni. In
vivo monitoring of bone architecture and remodeling after implant insertion: the different
responses of cortical and trabecular bone. Bone, 81:468-477, 2015.
P. Christen, F. A. Schulte, A. Zwahlen, B. van Rietbergen, S. Boutroy, L. J. Melton III, S. Amin,
S. Khosla, J. Goldhahn and R. Müller. Voxel resolution dependency, reproducibility, and
sensitivity of an in vivo bone loading estimation algorithm. Journal of the Royal Society
Interface, 13:20150991, 2016.
M. R. Rubin, A. Zwahlen, D. W. Dempster, H. Zhou, N. E. Cusano, C. Zhang, R. Müller and
J. P. Bilezikian. Effects of parathyroid hormone administration on bone strength in
hypoparathyroidism. Journal of Bone and Mineral Research, 31:1082-1088, 2016.
N. Ohs, F. Keller, O. Blank, W.-Y. W. Lee, C.-Y. J. Cheng, P. Arbenz, R. Müller and P.
Christen. Towards in silico prognosis using big data. Current Directions in Biomedical
Engineering, 2(1):57-60, 2016.
S. D. Badilatti, P. Christen, I. Parkinson and R. Müller. Load-adaptive bone remodeling
simulations reveal osteoporotic microstructural and mechanical changes in whole human
vertebrae. Journal of Biomechanics, accepted, 2016.
J. R. Vetsch, R. Müller and S. Hofmann. The influence of curvature on three-dimensional
mineralized matrix formation under static and perfused conditions: An in-vitro bioreactor
model. Journal of the Royal Society Interface, in press, 2016.
J. R. Vetsch, D. C. Betts, R. Müller and S. Hofmann. Flow velocity-driven differentiation of
human mesenchymal stem cells in silk fibroin scaffolds: A combined experimental and
computational approach. Journal of Tissue Engineering and Regenerative Medicine, revised
and resubmitted, 2016.
S. D. Badilatti, P. Christen, S. J. Ferguson and R. Müller. Computational modeling of long-
term effects of prophylactic vertebroplasty on bone adaptation. Proceedings of the Institution
of Mechanical Engineers, Part H: Journal of Engineering in Medicine, under revision, 2016.
Z. Li, G. Kuhn, M. Schirmer, R. Müller and D. Ruffoni. Ovariectomized mice show a reduced
response to implant insertion. Osteoporosis International, submitted, 2016.
J. J. A. de Jong, P. Christen, S. Boutroy, P. P. Geusens, J. P. W. van den Bergh, R. Müller and
B. van Rietbergen. 3D image registration applied to high resolution computed tomography
images of healing distal radius fractures. PLoS ONE, submitted, 2016.
116
Group of Michele Parrinello
List of publications:
Variationally Optimized Free-Energy Flooding for Rate Calculation
J. McCarty, O. Valsson, P. Tiwary and M. Parrinello
Phys. Rev. Lett., 115 (7), 070601 (2015), DOI: 10.1103/PhysRevLett.115.070601
de Broglie Swapping Metadynamics for Quantum and Classical Sampling
M. Nava, R. Quhe, F. Palazzesi, P. Tiwary and M. Parrinello
J. Chem. Theory Comput., 11 (11), pp 5114–5119 (2015), DOI: 10.1021/acs.jctc.5b00818
A perturbative solution to metadynamics ordinary differential equation
P. Tiwary, J. Dama and M. Parrinello
J. Chem. Phys. 143, 234112 (2015), DOI: 10.1063/1.4937945
General Protein Data Bank-Based Collective Variables for Protein Folding
A. Ardévol, F. Palazzesi, G. A. Tribello and M. Parrinello
J. Chem. Theory Comput., 12 (1), pp 29–35 (2016), DOI: 10.1021/acs.jctc.5b00714
Enhanced, targeted sampling of high-dimensional free-energy landscapes using
variationally enhanced sampling, with an application to chignolin
P. Shaffer, O. Valsson and M. Parrinello
PNAS, 113 (5), 1150-1155 (2016), DOI: 10.1073/pnas.1519712113
Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual
Viewpoint
O. Valsson, P. Tiwary and M. Parrinello
Annurev. Phys. Chem., 67, 59-184 (2016), DOI: 10.1146/annurev-physchem-040215-
112229
Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced
Sampling
J. McCarty, O. Valsson and M. Parrinello
J. Chem. Theory Comput., 12 (5), pp 2162–2169 (2016), DOI: 10.1021/acs.jctc.6b00125
Characterization of Vanadium Species in Mixed Chloride-Sulfate Solutions: An Ab Initio
Metadynamics Study
M. Bon, T. Laino, A. Curioni and M. Parrinello
J. Phys. Chem. C, 120 (20), pp 10791–10798 (2016), DOI: 10.1021/acs.jpcc.6b02642
A variational approach to nucleation simulation
P. Piaggi, O. Valsson and M. Parrinello
Faraday Discuss., (2016), accepted manuscript, DOI: 10.1039/C6FD00127K
Chemical potential calculations in dense liquids using metadynamics
C. Perego, F. Giberti and M. Parrinello
Phys. J. Spec. Top. (2016), accepted manuscript, DOI:10.1140/epjst/e2016-60094-x,
117
Dimer Metadynamics
M. Nava, F. Palazzesi, C. Perego and M. Parrinello
J. Chem. Theory Comput., submitted, July 2016
Crucial Role of Explicit Water Models in the Helix Folding/Unfolding Processes
F. Palazzesi, M. Salvalaglio, A. Barducci and M. Parrinello
J. Chem. Phys., submitted 2016
Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling
P. Shaffer, O. Valsson and M. Parrinello
J. Chem. Theory Comput., submitted, August 2016
118
Group name: Molecular Kinetics and Spectroscopy,
Group of Prof. M. Quack
List of publications:
Computation of Molecular Parity Violation Using the Coupled Cluster Linear Response
Approach
L. Horný, M. Quack
Mol. Phys., 113, 1768-1779 (2015)
High-resolution rovibrational spectroscopy of fluorobenzene, C6H5F: analysis of the B1
fundamentals ν4, ν10b, ν17b, the B2 fundamental ν15 and assignment of the A1 levels ν12, 2ν16a
and 2ν18b
S. Albert, K. Keppler, M. Quack
Mol. Phys., 113, 2267–2289 (2015)
Line shape of amplitude or frequency-modulated spectral profiles including resonator
distortions
M. Suter, M. Quack
Applied Optics, 54, 4417 – 4421 (2015)
Synchrotron based highest resolution FTIR spectroscopy of chlorobenzene
S. Albert, K. Keppler, P. Lerch, M. Quack, A. Wokaun,
J. Mol. Spectr. 315, 92–101 (2015)
Investigation of the ν₂ + 2ν₃ subband in the overtone icosad of ¹³CH₄ by pulsed supersonic jet
and diode laser cavity ring-down spectroscopy: partial rovibrational analysis and nuclear spin
symmetry conservation,
Z. Bjelobrk, C. Manca Tanner, M. Quack
Z. Phys. Chem., 229, 1575–1607 (2015)
Tunneling and Parity Violation in Trisulfane (HSSSH): An Almost Ideal Molecule for
Detecting Parity Violation in Chiral Molecules,
C. Fábri, Ľ. Horný, M. Quack
ChemPhysChem 16, 3584–3589 (2015)
Wavepacket Dynamics of the Axially Chiral Molecule Cl-O-O-Cl under Coherent Radiative
Excitation and Including Electroweak Parity Violation
R. Prentner, M. Quack, J. Stohner, M. Willeke
J. Phys. Chem. A., 119, 12805–12822 (2015), doi: 10.1021/acs.jpca.5b08958
Infrared laser induced population transfer and parity selection in 14
NH3: A proof of principle
experiment towards detecting parity violation in chiral molecules,
P. Dietiker, E. Miloglyadov, M. Quack, A. Schneider, G. Seyfang,
J. Chem. Phys., 143, 244305-1 – 244305-23 (2015)
119
Molecules and Clusters in Motion: Looking Back and Looking Forward, SASP and Beyond
M. Quack
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 22 – 26,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
Intramolecular Vibrational Energy Redistribution in Cyano-Acetylene (HCCCN)
A. Kushnarenko, E. Miloglyadov, M. Quack, G. Seyfang
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 109 – 113,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
High resolution GHz and THz (FTIR) spectroscopy and theory of parity violation and
tunneling for 1,2-dithiine (C4H4S2) as a candidate for measuring the parity violating energy
differences between enantiomers of chiral molecules
S. Albert, I. Bolotova, Z. Chen, C. Fábri, Ľ. Horný, M. Quack, G. Seyfang, D. Zindel in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 127 – 130,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
Synchrotron-based THz Spectroscopy at the Swiss Light Source
S. Albert, S. Bauerecker, I. Bolotova, Ph. Lerch, M. Quack and A. Wokaun
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 157 – 160,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
GHz and synchrotron-based THz spectroscopy of mono deuterated oxirane (c-CH2OCHD)
S. Albert, Z. Chen, Ph. Lerch, K. Keppler, M. Quack, V. Schurig and O. Trapp
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 161 – 164,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
THz Spectroscopy of cyano-oxirane (c-C2H3OCN) and methyl oxirane (c-C2H3OCH3) with
synchrotron light
S. Albert, Ph. Lerch, K. Keppler, M. Quack
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 165 – 168,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
Tunneling dynamics of aniline studied by synchrotron-based high resolution THz
spectroscopy
S. Albert, Ph. Lerch, and M. Quack
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 169 – 172,
(J. Stohner and Ch. Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
120
Synchrotron-based THz and FTIR spectroscopy of collisionally cooled NF3
I. Bolotova, O. Ulenikov, S. Albert, S. Bauerecker, Ph. Lerch, M. Quack, T. Peter and
A. Wokaun
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 173 – 176, (J. Stohner and Ch.
Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
High resolution analysis of the FTIR spectra and quantum dynamics of CHF3
I. Bolotova, O. Ulenikov, E. Bekhtereva, S. Albert, S. Bauerecker, H. Hollenstein, and
M. Quack
in “Proceedings of the 20th Symposium on Atomic, Cluster and Surface Physics 2016 (SASP
2016), Davos, Switzerland, 7 to 12 February 2016”, pages 177 – 181, (J. Stohner and Ch.
Yeretzian eds., Innsbruck University Press (IUP), Innsbruck, 2016)
Die Spiegelsymmetrie des Raumes und die Chiralität in Chemie, Physik, und in der
biologischen Evolution
Martin Quack
Nova Acta Leopoldina NF 127, 33 (2015) (full paper in press 2016)
Chlorine peroxide (Cl2O2) and its isomers: structures, spectroscopy, formation and
thermochemistry,
Ľ. Horný, M. Quack, H. F. Schaefer, M. Willeke, Mol. Phys. 114, 1135 – 1147 (2016).
High resolution GHz and THz (FTIR) spectroscopy and theory of parity violation and
tunneling for 1,2-dithiine (C4H4S2) as a candidate for measuring the parity violating energy
difference between enantiomers of chiral molecules
S. Albert, I. Bolotova, Z. Chen, C. Fábri, L. Horný, M. Quack, G. Seyfang and D. Zindel,
Phys. Chem. Chem. Phys, 18, 21976 – 21993 (2016)
Synchrotron-Based Highest Resolution Terahertz Spectroscopy of the ν24 Band System of
1,2-Dithiine (C4H4S2): A Candidate for Measuring the Parity Violating Energy Difference
between Enantiomers of Chiral Molecules,
S. Albert, F. Arn, I. Bolotova, Z. Chen, C. Fábri, G. Grassi, P. Lerch, M. Quack, G. Seyfang,
A. Wokaun, D. Zindel,
J. Phys. Chem. Lett. 7, 3847-3853 (2016)
A Combined Gigahertz and Terahertz (FTIR) Spectroscopic Investigation of Meta-D-phenol:
Observation of Tunneling Switching
S. Albert, Z. Chen, C. Fábri, Ph. Lerch, R. Prentner, and M. Quack
Mol. Phys. 00, 000 000 (2016), doi: 10.1080/00268976.2016.1226444
121
Group name: Group of Prof. Markus Reiher
List of publications:
1. Sebastian Keller, Michele Dolfi, Matthias Troyer, and Markus Reiher, An efficient matrix
product operator representation of the quantum chemical Hamiltonian, J. Chem. Phys.,
2015, 143, 244118.
2. Sebastian Keller and Markus Reiher, Spin-adapted matrix product states and operators,
J. Chem. Phys. 2016, 144, 134101.
3. Stefan Knecht, Erik D. Hedegård, Sebastian Keller, Arseny Kovyrshin, Yingjin Ma, An-
drea Muolo, Christopher J. Stein, and Markus Reiher, New approaches for ab initio cal-
culations of molecules with strong electron correlation, Chimia, 2016, 70, 244.
4. Christopher J. Stein, and Markus Reiher, Automated selection of active orbital spaces, J.
Chem. Theory Comput., 2016, 12, 1760.
5. Christopher J. Stein, Vera von Burg, Markus Reiher, The delicate balance of static and
dynamic electron correlation, J. Chem. Theory Comput., 2016, 12, 3764.
6. Mickaël Hubert, Hans Jørgen Aa. Jensen, and Erik D. Hedegård, Excitation spectra of
nucleobases with multiconfigurational density functional theory, J. Phys. Chem. A, 2016,
120, 36.
7. Mickaël Hubert, Erik D. Hedegård, and Hans Jørgen Aa. Jensen, Investigation of multi-
configurational short-range density functional theory for electronic excitations in organic
molecules., J. Chem. Theory Comput., 2016, 12, 2203.
8. Bruno Senjean, Erik D. Hedegård, Mehboob M. Alam, Stefan Knecht, and Emmanuel
Fromager, Combining linear interpolation with extrapolation methods in range-separated
ensemble density-functional theory, Mol. Phys., 2016, 114, 968.
9. Mehboob M. Alam, Stefan Knecht, and Emmanuel Fromager, Ghost interaction cor-
rection in ensemble density-functional theory for excited states with and without range
separation, Phys. Rev. A, 2016, 94, 012511.
10. Maike Bergeler, Gregor N. Simm, Jonny Proppe, and Markus Reiher, Heuristics-guided
exploration of reaction mechanisms, J. Chem. Theory Comput., 2015, 11, 5712.
11. Gregor N. Simm and Markus Reiher, Systematic error estimation for chemical reaction
energies, J. Chem. Theory Comput., 2016, 12, 2762.
12. Alain C. Vaucher, Moritz P. Haag, and Markus Reiher, Real-time feedback from iterative
electronic structure calculations, J. Comput. Chem., 2016, 37, 805.
13. Alain C. Vaucher and Markus Reiher, Molecular propensity as a driver for explorative
reactivity studies, J. Chem. Inf. Model., 2016, 56, 1470.
122
14. Adrian H. Mühlbach, Alain C. Vaucher, and Markus Reiher, Accelerating wave function
convergence in interactive quantum chemical reactivity studies, J. Chem. Theory Com-
put., 2016, 12, 1228.
15. An Vandemeulebroucke, Caroline Aldag, Martin T. Stiebritz, Markus Reiher, and Don-
ald Hilvert, Kinetic consequences of introducing a proximal selenocysteine ligand into
cytochrome P450cam, Biochemistry, 2015, 54, 6692.
16. Marta K. Bruska, Martin T. Stiebritz, and Markus Reiher, Binding of reactive oxygen
species at Fe-S cubane clusters, Chem. Eur. J., 2015, 21, 19081.
17. Michael Leibold, Sandra Kisslinger, Frank W. Heinemann, Frank Hampel, Yuko Ichiyanagi,
Michael Klein, Patrick Homenya, Franz Renz, Hans Toftlund, Georg Brehm, Siegfried
Schneider, Markus Reiher, and Siegfried Schindler, Effect of chelate ring size in iron(II)
isothiocyanato complexes with tetradentate tripyridyl-alkylamine ligands on spin crossover
properties, Z. Anorg. Allg. Chem., 2016, 642, 85.
18. Thomas L. Gianetti, Samuel P. Annen, Gustavo Santiso-Quinones, Markus Reiher, Matthias
Driess, and Hansjörg Grützmacher, Nitrous oxide as a hydrogen acceptor for the dehy-
drogenative coupling of alcohols, Angew. Chem. Int. Ed., 2016, 55, 1854.
19. Benjamin Simmen, Edit Mátyus, and Markus Reiher, Relativistic kinetic-balance condi-
tion for explicitly correlated basis functions, J. Phys. B: At. Mol. Opt. Phys., 2015, 48,
245004.
20. Adel Almoukhalalati, Stefan Knecht, Hans Jørgen Aagaard Jensen, Kenneth G. Dyall,
and Trond Saue, Electron correlation within the relativistic no-pair approximation, J.
Chem. Phys., 2016, 145, 074104.
21. Arseny Kovyrshin and Johannes Neugebauer, Analytical gradients for excitation energies
from frozen-density embedding, Phys. Chem. Chem. Phys., 2016, 18, 20955.
22. Jonny Proppe, Tamara Husch, Gregor N. Simm, and Markus Reiher, Uncertainty quan-
tification for quantum chemical models of complex reaction networks, Faraday Discuss.,
2016, DOI: 10.1039/C6FD00144K.
23. Arseny Kovyrshin and Markus Reiher, Tensor network states with three-site correlators,
New J. Phys., 2016, in press, arXiv:1605.06773.
123
PUBLICATION LIST
Group name: Computational Chemistry Group (Prof. Sereina Riniker) List of publications:
S. Riniker, "Method development for classical molecular dynamics simulations: Coarse-graining and free energy calculations", Bunsen-Magazin, 17, 228 (2015). S. Riniker, G. A. Landrum, "Better informed distance geometry: using what we know to improve conformation generation", J. Chem. Inf. Model., 55, 2562 (2015). B. A. C. Horta, P. T. Merz, P. F. J. Fuchs, J. Dolenc, S. Riniker, P. H. Hünenberger, "GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set ", J. Chem. Theory Comput., 12, 3825 (2016). J. Witek, B. G. Keller, M. Blatter, A. Meissner, T. Wagner, S. Riniker, "Kinetic models of cyclosporin A in polar and apolar environment reveal multiple congruent states ", J. Chem. Inf. Model., 56, 1547 (2016).
124
Group: Group of Christoph Schär
List of publications:
Bellprat, O., Kotlarski S., Lüthi D., De Elìa R., Frigon A., Laprise R., Schär C., 2016: Objective Calibration of Regional Climate Models: Application over Europe and North America. Journal of Climate, 39, 819-838, doi: http://dx.doi.org/10.1175/JCLI-D-15-0302.1
Chiacchio,, M., Solmon,, F., Giorgi,, F., Stackhouse, P., and Wild, M., 2015: Evaluation of the radiation budget with a regional climate model over Europe and inspection of dimming and brightening, J. Geophys. Res. Atmos., 120, 1951-1971, DOI: 10.1002/2014JD022497.
Dallafior, T. N., Folini, D., Knutti, R., and Wild, M., 2016: Mixed-layer ocean responses to anthropogenic aerosol dimming from 1870 to 2000, J. Geophys. Res. Atmos., 121, 49–66, doi:10.1002/2015JD024070.
Giorgi F., C. Torma, E. Coppola, N. Ban, C. Schär and S. Somot, 2016: Enhanced summer convective rainfall at Alpine high elevations in response to climate warming, Nature Geoscience, doi:10.1038/ngeo2761
Hakuba, M.Z., D. Folini, and M. Wild, 2016: On the Zonal Near-Constancy of Fractional Solar Absorption in the Atmosphere. J. Climate 29, 3423–3440, doi: 10.1175/JCLI-D-15-0277.1.
Hassanzadeh, H., Schmidli, J., Langhans, W., Schlemmer, L., and Schär, C., 2016: Impact of topography on the diurnal cycle of summertime moist convection in idealized simulations. Meteorologische Zeitschrift, Vol. 25 No. 2, p. 181-194, doi: 10.1127/metz/2015/0653
Imamovic, A., Tanaka, K., Folini, D., and Wild, M., 2016: Global dimming and urbanization: Did stronger negative SSR trends collocate with regions of population growth? Atmos. Chem. Phys., 16, 2719-2725, doi:10.5194/acp-16-2719-2016.
Jerez, S. R., Tobin, I., Vautard, R., Montavez, J. P., Lopez-Romero, J. M., Thais, F., Bartok, B., Christensen, O.B., Collette, A., Deque, M., Nikulin, G., Kotlarski, S., van Meijgaard, E., Teichmann, C., and Wild, M., 2015: The impact of climate change on photovoltaic power generation in Europe. Nature Communications, 6:10014 doi: 10.1038/ncomms10014.
Jerez, S., Thais, F., Tobin I., Wild, M., Colette, A., Yiou, P., and Vautard, R. 2015: The CLIMIX model: A tool to create and evaluate spatially-resolved scenarios of photovoltaic and wind power development. Renewable and Sustainable Energy Reviews, 42, 1-15. doi: 10.1016/j.rser.2014.09.041.
Keller, M., Fuhrer, O., Schmidli, J., Stengel, M., Stöckli, R. and Schär, C., 2016: Evaluation of convection-resolving models using satellite data: The diurnal cycle of summer convection over the Alps. Meteorologische Zeitschrift, Vol. 25 No. 2, p. 165 – 179, doi: 10.1127/metz/2015/0715
Kendon, E.J., Ban, N., Roberts, N. M., Fowler, H. J., Roberts, M. J., Chan, S. C., Evans, J. P., Fosser, G., and Wilkinson, J. M., 2016: Do convection-permitting regional climate models improve projections of future precipitation change? Bulletin of the American Meteorology Society, doi: http://dx.doi.org/10.1175/BAMS-D-15-0004.1
Keuler, K., Radtke, K., Kotlarski, S., and Lüthi, D., 2016: Regional climate change over Europe in COSMO-CLM: Influence of emission scenario and driving global model., Meteorologische Zeitschrift, Vol. 25 No. 2, p. 121-136, doi: 10.1127/metz/2016/0662
125
Kröner, N., Kotlarski, S., Fischer, E., Lüthi, D., Zubler, E., and Schär, C., 2016: Separating climate change signals into thermodynamic, lapse-rate and circulation effects: Theory and application to the European summer climate. Climate Dynamics, doi: 10.1007/s00382-016-3276-3
Lembo, V., Folini, D., Wild, M, Lionello, P., 2016: Energy budgets and transports: global evolution and spatial patterns during the twentieth century as estimated in two AMIP-like experiments, Climate Dynamics, doi:10.1007/s00382-016-3173-9
Leutwyler, D., Fuhrer, O., Lapillonne, X., Lüthi, D., and Schär, C., 2016: Towards European-Scale Convection-Resolving Climate Simulations, Geosci. Model Dev. Discuss. doi:10.5194/gmd-2016-119.
Ma, Q., Wang, K. C., and Wild, M., 2015: Impact of geolocations of validation data on the evaluation of surface incident shortwave radiation from Earth System Models., J. Geophys. Res. Atmos., 120, 6825-44, doi: 10.1002/2014JD022572.
Nabat, P., Somot, S., Mallet, M., Sevault, F., Chiacchio, M., and Wild, M., 2015: Direct and semi-direct aerosol radiative effect on the Mediterranean climate variability using a coupled Regional Climate System Model. Clim. Dyn., 44, 1127-1155, doi: 10.1007/s00382-014-2205-6.
Possner A., E. M. Zubler, U. Lohmann, and C. Schär, 2016: The resolution dependence of cloud effects and ship-induced aerosol-cloud interactions in marine stratocumulus, J. Geophys. Res. Atmos., 121, 4810–4829, doi:10.1002/2015JD024685.
Rajczak, J., Kotlarski, S., and Schär, C., 2016: Does Quantile Mapping of Simulated Precipitation Correct for Biases in Transition Probabilities and Spell Lengths? Journal of Climate, 29:5, 1605-1615
Raschke, E., Kinne, S., Rossow, W.B.,Stackhouse, P.W., and Wild, M., 2016: Comparison of Radiative Energy Flows in Observational Datasets and Climate Modeling, J. Applied Meteorol. Climatol., 55, 93-117, doi: 10.1175/JAMC-D-14-0281.1
Schär, C., 2015: Climate extremes: The worst heat waves to come. Nature Climate Change 6, 128-129, doi:10.1038/nclimate2864
Schär, C., N. Ban, E.M. Fischer, J. Rajczak, J. Schmidli, C. Frei, F. Giorgi, T.R. Karl, E.J. Kendon, A.M.G. Klein Tank, P.A. O'Gorman, J. Sillmann, X. Zhang, F.W. Zwiers, 2016: Percentile indices for assessing changes in heavy precipitation events. Climatic Change 137: 201, doi:10.1007/s10584-016-1669-2
Schlemmer, L. and Hohenegger, C., 2016: Modifications of the atmospheric moisture field as a result of cold-pool dynamics. Q.J.R. Meteorol. Soc., 142: 30–42. doi: 10.1002/qj.2625
Sørland, S. L., A. Sorteberg, C. Liu, and R. Rasmussen, 2016: Precipitation response of monsoon low-pressure systems to an idealized uniform temperature increase, J. Geophys. Res. Atmos., 121, 6258–6272, doi:10.1002/2015JD024658.
Stegehuis, A.I., Vautard, R., Ciais, P., Teuling, A.J., Miralles, D.G., and Wild, M., 2015: An observation-constrained multi-physics WRF ensemble for simulating European mega heat waves, Geoscientific Model Development, 8, 2285-2298, DOI: 10.5194/gmd-8-2285-2015.
Storelvmo, T., T. Leirvik, U. Lohmann, P.C.B. Phillips and M. Wild, 2016: Disentangling greenhouse warming and aerosol cooling to reveal Earth’s climate sensitivity. Nature Geoscience 9, 286–289, doi:10.1038/ngeo2670
Wild, M., Folini, D., Hakuba, M., Schär, C., Seneviratne, S.I., Kato, S., Rutan, D., Ammann, C., Wood, E.F., and König-Langlo, G., 2015: The energy balance over land and oceans: An assessment based on direct observations and CMIP5 climate models. Clim. Dyn., 44, 3393–3429, doi: 10.1007/s00382-014-2430-z.
126
Wild, M., Folini, D., Henschel, F., Fischer, N., and Mueller, B., 2015: Projections of long-term changes in solar radiation based on CMIP5 climate models and their influence on energy yields of photovoltaic systems, Solar Energy, 116, 12-24, DOI: 10.1016/j.solener.2015.03.039.
Winter, K.J.-.M., Kotlarski, S., Scherrer, S.C., and Schär, C, 2016: The Alpine snow-albedo feedback in regional climate models. Clim. Dyn., doi:10.1007/s00382-016-3130-7
127
Group of Ch. Schwab
A. Barth, Ch. Schwab, and J. SukysMultilevel Monte Carlo Simulation of Statistical Solutions to the NavierStokes Equations,Springer Proceedings in Mathematics & Statistics, 163 (2016), pp. 209-227, SAM Report2013-33
P. Chen and Ch. SchwabAdaptive Sparse Grid Model Order Reduction for Fast Bayesian Estimation and Inver-sion, Lecture Notes in Computational Science and Engineering, 109 (2016), pp. 1-27,SAM Report 2015-08
P. Chen and Ch. SchwabModel Order Reduction Methods in Computational Uncertainty Quantification, pp. 1-53, Springer International Publishing (2016), SAM Report 2015-28
P. Chen and Ch. SchwabSparse-grid, reduced-basis Bayesian inversion: Nonaffine-parametric nonlinear equations,Journal of Computational Physics, 316 (2016), pp. 470-503, SAM Report 2015-21
A. Cohen, Ch. Schwab, and J. ZechShape Holomorphy of the stationary Navier-Stokes Equations, Technical Report 2016-45,Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016
J. Dick, R.N. Gantner, Q.T. Le Gia, and Ch. SchwabMultilevel higher order Quasi-Monte Carlo Bayesian Estimation, Technical Report 2016-34, Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016
J. Dick, R.N. Gantner, Q.T. Le Gia, and Ch. SchwabHigher order Quasi-Monte Carlo integration for Bayesian Estimation, Technical Report2016-13, Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016
J. Dick, F.Y. Kuo, Q.T. LeGia, and Ch. SchwabMulti-level higher order QMC Galerkin discretization for affine parametric operator equa-tions, SIAM Journ. Numer. Analysis (2016), pp. 2541-2568, SAM Report 2014-14
J. Dick, Q.T. Le Gia, and Ch. SchwabHigher order Quasi Monte Carlo integration for holomorphic, parametric operator equa-tions, SIAM Journ. Uncertainty Quantification, 4/1 (2016), pp. 48-79, SAM Report2014-23
J. Dolz, H. Harbrecht, and Ch. SchwabCovariance regularity and H-matrix approximation for rough random fields, NumerischeMathematik (2016), pp. 1-27, SAM Report 2014-19
R.N. Gantner, L. Herrmann, and Ch. SchwabQuasi-Monte Carlo integration for affine-parametric, elliptic PDEs: local supports im-ply product weights, Technical Report 2016-32, Seminar for Applied Mathematics, ETHZurich, Switzerland, 2016
128
R.N. Gantner, C. Schillings, and Ch. SchwabBinned Multilevel Monte Carlo for Bayesian Inverse Problems with Large Data, Proc.Domain Decomposition Methods in Science and Engineering XXII, 104, Springer Inter-national Publishing (2016), pp. 511-519
R.N. Gantner and Ch. SchwabComputational Higher Order Quasi-Monte Carlo Integration, Springer Proceedings inMathematics & Statistics, 163 (2016), pp. 271-288, SAM Report 2014-25
F. Henrıquez, C. Jerez-Hanckes, and F. AltermattBoundary integral formulation and semi-implicit scheme coupling for modeling cells un-der electrical stimulation, Numerische Mathematik (2016), pp. 1-45
L. Herrmann, A. Lang, and Ch. SchwabNumerical analysis of lognormal diffusions on the sphere, Technical Report 2016-02, Sem-inar for Applied Mathematics, ETH Zurich, Switzerland, 2016
L. Herrmann and Ch. SchwabQMC integration for lognormal-parametric, elliptic PDEs: local supports imply prod-uct weights, Technical Report 2016-39, Seminar for Applied Mathematics, ETH Zurich,Switzerland, 2016
V.H. Hoang and Ch. SchwabConvergence rate analysis of MCMC-FEM for Bayesian inversion of log-normal diffusionproblems, Technical Report 2016-19, Seminar for Applied Mathematics, ETH Zurich,Switzerland, 2016
C. Jerez-Hanckes and Ch. SchwabElectromagnetic wave scattering by random surfaces: uncertainty quantification viasparse tensor boundary elements, IMA Journal of Numerical Analysis (2016), SAM Re-port 2015-23
V. Kazeev, I. Oseledets, M. Rakhuba, and Ch. SchwabQTT-Finite-Element Approximation For Multiscale Problems, Technical Report 2016-06,Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2016
A. Kunoth and Ch. SchwabSparse adaptive tensor Galerkin approximations of stochastic PDE-constrained controlproblems, SIAM/ASA J. Uncertainty Quantification, 4/1 (2016), pp. 1034-1059, SAMReport 2015-37
F.Y. Kuo, R. Scheichl, Ch. Schwab, I.H. Sloan and E. UllmannMultilevel Quasi-Monte Carlo methods for lognormal diffusion problems, Math. Comp.(accepted 2016), SAM Report 2015-22
S. Mishra, N.H. Risebro, Ch. Schwab, and S. TokarevaNumerical Solution of Scalar Conservation Laws with Random Flux Functions, SIAM/ASAJ. Uncertainty Quantification, 4/1 (2016), pp. 552-591, SAM Report 2012-35
129
S. Mishra, Ch. Schwab, and J. SukysMulti-level Monte Carlo finite volume methods for uncertainty quantification of acousticwave propagation in random heterogeneous layered medium, Journal of ComputationalPhysics, 312 (2016), pp. 192-217, SAM Report 2014-22
H. Rauhut and Ch. SchwabCompressive sensing Petrov-Galerkin approximation of high-dimensional parametric op-erator equations, Mathematics of Computation (2016), SAM Report 2014-29
C. Schillings and Ch. SchwabScaling Limits in Computational Bayesian Inversion, ESAIM: M2AN , 50/6 (2016), pp.1825-1856, SAM Report 2014-26
D. Schotzau and Ch. SchwabExponential Convergence of hp-FEM for Elliptic Problems in Polyhedra: Mixed Bound-ary Conditions and Anisotropic Polynomial Degrees, Technical Report 2016-05, Seminarfor Applied Mathematics, ETH Zurich, Switzerland, 2016
Ch. Schwab and R. StevensonFractional space-time variational formulations of (Navier-) Stokes equations, TechnicalReport 2015-43, Seminar for Applied Mathematics, ETH Zurich, Switzerland, 2015
130
Group name: Geophysical Fluid Dynamics, Institute of Geophysics, D-ERDW
List of publications:
Agrusta, R., Tommasi, A., Arcay, D., Gonzalez, A., Gerya, T. (2015) How partial melting
affects small‐scale convection in a plume‐fed sublithospheric layer beneath fast‐moving plates. Geochemistry, Geophysics, Geosystems, 16, 3924-3945.
Bello, L., N. Coltice, P. J. Tackley, D. Müller and J. Cannon (2015) Assessing the role of slab
rheology in coupled plate-mantle convection models, Earth Planet. Sci. Lett. 430, 191-
201, doi:10.1016/j.epsl.2015.08.010.
Bocher, M., N. Coltice, A. Fournier and P. J. Tackley (2016) A sequential data assimilation
approach for the joint reconstruction of mantle convection and surface tectonics,
Geophys. J. Int. 204 (1), 200-214, doi:10.1093/gji/ggv427.
Chen, L., Gerya, T.V. (2016) The role of lateral lithospheric strength heterogeneities in
orogenic plateau growth: Insights from 3-D thermo-mechanical modeling. Journal of
Geophysical Research, 121, 3118-3138.
Duretz, T., Agard, P., Yamato, P., Ducassou, C., Burov, E.B., Gerya, T.V. (2016) Thermo-
mechanical modeling of the obduction process based on the Oman Ophiolite case.
Gondwana Research, 32, 1-10.
Dymkova, D., Gerya, T., Burg, J.-P. (2016) 2D thermomechanical modelling of continent–
arc–continent collision. Gondwana Research, 32, 138-150.
Gerya, T. (2015) Tectonic overpressure and underpressure in lithospheric tectonics and
metamorphism. Journal of Metamorphic Geology, 33, 785-800.
Gerya, T.V., Stern, R.J., Baes, M., Sobolev, S., Whattam, S.A. (2015) Plate tectonics on the
Earth triggered by plume-induced subduction initiation. Nature, 527, 221-225.
Gillmann, C., G. Golabek and P. J. Tackley (2016) Effect of a single large impact on the
coupled atmosphere-interior evolution of Venus, Icarus.
doi:10.1016/j.icarus.2015.12.024.
Koptev, A., Burov, E., Calais, E., Leroy, S., Gerya, T., Guillou-Frottier, L., Cloetingh, S.
(2016) Contrasted continental rifting via plume-craton interaction: Applications to
Central East African Rift. Geoscience Frontiers, 7, 221-236.
Labrousse, L., Duretz, T., Gerya, T. (2015) H2O-fluid-saturated melting of subducted
continental crust facilitates exhumation of ultrahigh-pressure rocks in continental
subduction zones. Earth and Planetary Science Letters, 428, 151-161.
Li, Z.H., Liu, M.Q., Gerya, T. (2015) Material transportation and fluid-melt activity in the
subduction channel: Numerical modeling. Science China-Earth Sciences, 58, 1251-
1268.
Li, Y., F. Deschamps, and P. J.Tackley (2016), Small post-perovskite patches at the base of
lower mantle primordial reservoirs: insights from 2-D numerical modelling and
implications for ULVZs, Geophys. Res. Lett., 43, doi:10.1002/2016GL067803.
Li, Y., F. Deschamps and P. J. Tackley (2015) Effects of the post-perovskite phase transition
properties on the stability and structure of primordial reservoirs in the lower mantle of
the Earth, Earth Planet. Sci. Lett. 432, 1-12, doi:10.1016/j.epsl.2015.09.040.
Liao, J., Gerya, T. (2015) From continental rifting to seafloor spreading: Insight from 3D
thermo-mechanical modeling. Gondwana Research, 28, 1329-1343.
Lourenco, D., A. Rozel and P. J. Tackley (2016) Melting and crustal production helps plate
tectonics on Earth-like planets, Earth Planet. Sci. Lett. 439, 18-28,
doi:10.1016/j.epsl.2016.01.024.
131
Mannu, U., K. Ueda, S. D. Willett, T. V. Gerya, and M. Strasser (2016), Impact of
sedimentation on evolution of accretionary wedges: Insights from high-resolution
thermomechanical modeling, Tectonics, 35, doi:10.1002/2016TC004239.
May, Dave A., Patrick Sanan, Karl Rupp, Matthew G. Knepley, and Barry F. Smith (2016)
Extreme-Scale Multigrid Components within PETSc. In Proceedings of the Platform for
Advanced Scientific Computing Conference (PASC '16). ACM, New York, NY, USA, ,
Article 5 , 12 pages. DOI: http://dx.doi.org/10.1145/2929908.2929913
Menant, A., Sternai, P., Jolivet, L., Guillou-Frottier, L., Gerya, T. (2016) 3D numerical
modeling of mantle flow, crustal dynamics and magma genesis associated with slab
roll-back and tearing: The eastern Mediterranean case. Earth and Planetary Science
Letters, 442, 93-107.
Nakagawa, T. and P. J. Tackley (2015) Influence of plate tectonic mode on the coupled
thermochemical evolution of Earth's mantle and core, Geochem. Geophys. Geosyst. 16,
doi:10.1002/2015GC005996.
Petersen, R. I., D. R. Stegman and P. J. Tackley, 2016, The subduction dichotomy of strong
plates and weak slabs, Solid Earth Discuss., doi:10.5194/se-2016-56.
Ruh, J.B., Le Pourhiet, L., Agard, P., Burov, E., Gerya, T. (2015) Tectonic slicing of
subducting oceanic crust along plate interfaces: Numerical modeling. Geochemistry,
Geophysics, Geosystems, 16, 3505-3531.
Sanan, P., S.M. Schnepp, and D.A. May (2016) Pipelined, Flexible Krylov Subspace
Methods, , SIAM Journal on Scientific Computing 38:5, C441-C470
Sheng, J., Liao, J., Gerya, T. (2016) Numerical modeling of deep oceanic slab dehydration:
Implications for the possible origin of far field intra-continental volcanoes in
northeastern China. Journal of Asian Earth Sciences, 117, 328-336.
Sizova, E., Gerya, T., Stuewe, K., Brown, M. (2015) Generation of felsic crust in the
Archean: A geodynamic modeling perspective. Precambrian Research, 271, 198-224.
Thielmann M., A. Rozel, B.J.P. Kaus and Y. Ricard (2015) Intermediate-depth earthquake
generation and shear zone formation caused by grain size reduction and shear heating,
Geology 43 (9), 791-794,
Tosi, N., C. Stein, L. Noack, C. Hüttig, P. Maierova, H. Samuel, D. R. Davies, C. R. Wilson,
S. C. Kramer, C. Thieulot, A. Glerum, M. Fraters, W. Spakman, A. Rozel & P. J.
Tackley (2015) A community benchmark for viscoplastic thermal convection in a 2-D
square box, Geochem. Geophys. Geosys, doi:10.1002/2015GC005807.
Ueda, K., Willett, S.D., Gerya, T., Ruh, J. (2015) Geomorphological-thermo-mechanical
modeling: Application to orogenic wedge dynamics. Tectonophysics, 659, 12-30.
132
Group of M. Troyer
HiroshiiShinaoka,iReiiSakuma,iPhilippiWerner,iMatthiasiTroyer
Accuracy of downfolding based on the constrained random phase approximation
Phys.iRev.iBi91,i245156i(2015)
I.iHen,iJ.iJob,iT.iAlbash,iT.F.iRønnow,iM.iTroyer,iandiD.A.iLidar
Probing for quantum speedup in spin-glass problems with planted solutions
Phys.iRev.iAi92,i042325i(2015)
HiroshiiShinaoka,iShintaroiHoshino,iMatthiasiTroyer,iPhilippiWerner
Phase diagram of pyrochlore iridates: all-in/all-out magnetic ordering and non-Fermi liquid
properties
Phys.iRev.iLett.i115,i156401i(2015)
D.iWecker,iM.iB.iHastings,iM.iTroyer
Progress towards Practical Quantum Variational Algorithms
Phys.iRev.iAi92,i042325i(2015)
A.A.iSoluyanov,iD.iGresch,iZ.iWang,iQ.S.,iWu,iM.iTroyer,iXiiDai,iandiB.iA.iBernevig
A new type of Weyl semimetal
Naturei527,i495i(2015)
HiroshiiShinaoka,iYusukeiNomura,iSilkeiBiermann,iMatthiasiTroyer,iPhilippiWerner
Negative sign problem in continuous-time quantum Monte Carlo: optimal choice of single-
particle basis for impurity problems
Phys.iRev.iBi92,i195126i(2015)
MicheleiDolfi,iBelaiBauer,iSebastianiKeller,iMatthiasiTroyer
Pair Correlations in Doped Hubbard Ladders
Phys.iRev.iBi92,i195139i(2015)
LeiiWang,iHiroshiiShinaoka,iMatthiasiTroyer
Fidelity Susceptibility Perspective on the Kondo Effect and Impurity Quantum Phase
Transitions
Phys.iRev.iLett.i115,i236601i(2015)
LeiiWang,iYe-HuaiLiu,iMauroiIazzi,iMatthiasiTroyer,iGergelyiHarcos
Split orthogonal group: A guiding principle for sign-problem-free fermionic simulations
Phys.iRev.iLett.i115,i250601i(2015)
133
Damian S. Steiger, Troels F. Rønnow, Matthias Troyer
Heavy tails in the distribution of time-to-solution for classical and quantum annealing
Phys. Rev. Lett. 115, 230501 (2015)
D. Wecker, M. B. Hastings, N. Wiebe, B. K. Clark, C. Nayak, M. Troyer
Solving strongly correlated electron models on a quantum computer
Phys. Rev. A 92, 062318 (2015)
Sebastian Keller, Michele Dolfi, Matthias Troyer, Markus Reiher
An Efficient Matrix Product Operator Representation of the Quantum-Chemical Hamiltonian
J. Chem. Phys. 143, 244118 (2015)
Medha Soni, Matthias Troyer, Didier Poilblanc
Effective models of doped quantum ladders of non-Abelian anyons
Phys. Rev. B 93, 035124 (2016)
Georg W. Winkler, Alexey A. Soluyanov, Matthias Troyer
Smooth gauge for topological band structures in arbitrary dimensions
Phys. Rev. B 93, 035453 (2016)
S. M. Griffin, P. Staar, T. C. Schulthess, M. Troyer, N. A. Spaldin
A Bespoke Single-Band Hubbard Model Material
Phys. Rev. B 93, 075115 (2016)
Mauro Iazzi, Alexey Soluyanov and Matthias Troyer
Topological origin of the fermionic sign problem
Phys. Rev. B 93, 115102 (2016)
N. Davies, D. Field, D. Gavaghan, S.J. Holbrook, S. Planes, M. Troyer, M. Bonsall, J Claudet,
G. Roderick, R.J. Schmitt, L. Amaral Zettler, V. Berteaux, H.C. Bossi, C. Cabasse, A. Collin,
J. Deck, T. Dell, J. Dunne, R. Gates, M. Harfoot, J.L. Hench, M. Hopuare, P. Kirch, G.
Kotoulas, A. Kosenkov, A. Kusenko, J.J. Leichter, H. Lenihan, A. Magoulas, N. Martinez, C.
Meyer, B. Stoll, B. Swalla, D.M. Tartakovsky, H. Teavai Murphy, S. Turyshev, F. Valdvinos,
R. Williams, S. Wood (IDEA Consortium)
Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA)
consortium
Gigascience 5, 14 (2016)
Shuta Nakajima, Takafumi Tomita, Shintaro Taie, Tomohiro Ichinose, Hideki Ozawa, Lei
Wang, Matthias Troyer, Yoshiro Takahashi
Topological Thouless Pumping of Ultracold Fermions
Nature Physics (in press)
134
A.A. Soluyanov, D. Gresch, M. Troyer, R.M. Lutchyn, B. Bauer, C. Nayak
Optimizing spin-orbit splittings in InSb Majorana nanowires
Phys. Rev. B 93, 115317 (2016)
J. Shabani, M. Kjaergaard, H. J. Suominen, Younghyun Kim, F. Nichele, K. Pakrouski, T.
Stankevic, R. M. Lutchyn, P. Krogstrup, R. Feidenhans'l, S. Kraemer, C. Nayak, M. Troyer, C.
M. Marcus, C. J. Palmstrøm
Two-dimensional epitaxial superconductor-semiconductor heterostructures: A platform for
topological superconducting networks
Phys. Rev. B 93, 155402 (2016)
Lei Wang, Ye-Hua Liu, Matthias Troyer
Stochastic series expansion simulation of the t-V model
Phys. Rev. B 93, 155117 (2016)
Kiryl Pakrouski, Matthias Troyer, Yang-Le Wu, Sankar Das Sarma, and Michael R. Peterson
Enigmatic 12/5 fractional quantum Hall effect
Phys. Rev. B 94, 075108 (2016)
G. Autès, D. Gresch, A. A. Soluyanov, M. Troyer, O. V. Yazyev
Robust Type-II Weyl Semimetal Phase in Transition Metal Diphosphides XP2 (X = Mo, W)
Phys. Rev. Lett. 117, 066402 (2016)
Ilia Zintchenko, Lei Wang, Matthias Troyer
Ferromagnetism of the Repulsive Atomic Fermi Gas: three-body recombination and domain
formation
European Physics Journal B 89, 1 (2016)
Dave Wecker, Matthew B. Hastings, and Matthias Troyer
Training a quantum optimizer
Phys. Rev. A 94, 022309 (2016)
Jakub Imriška, Emanuel Gull, Matthias Troyer
Thermodynamics of the Hubbard model on stacked honeycomb and square lattices
Eur. Phys. J. B 89, 171 (2016)
Georg W. Winkler, Alexey A. Soluyanov, QuanSheng Wu, Matthias Troyer, Peter Krogstrup
Topological Phases in InAs1-xSbx: From Novel Topological Semimetal to Majorana Wire
Phys. Rev. Lett. 117, 076403 (2016)
Jakub Imriška, Lei Wang, Matthias Troyer
First order topological phase transition of the Haldane--Hubbard model
Phys. Rev. B 94, 035109 (2016)
135
JaniGukelberger,iSebastianiLienert,iEvgenyiKozik,iLodeiPollet,iMatthiasiTroyer
Fulde-Ferrell-Larkin-Ovchinnikov pairing as leading instability on the square lattice
Phys.iRev.iBi94,i075157i(2016)
Z.iWang,iD.iGresch,iA.A.iSoluyanov,iA.iXie,iS.iKushwaha,iXiiDai,iM.iTroyer,iR.iJ.iCava,i
B.iA.iBernevig
MoTe2: Weyl and Line Node Topological Metal
Phys.iRev.iLett.i117,i066402i(2016)
TuomasiI.iVanhala,iTopiiSiro,iLongiLiang,iMatthiasiTroyer,iAriiHarju,iPäiviiTörmä
Topological phase transitions in the repulsively interacting Haldane-Hubbard model
Phys.iRev.iLett.i116,i225305i(2016)
Z.iZhu,iG.iW.iWinkler,iQ.iWu,iJ.iLi,iandiA.iA.iSoluyanov
Triple Point Topological Metals
Phys.iRev.iXi6,i031003i(2016)
IliaiZintchenkoiandiNathaniWiebe
Randomised gap and amplitude estimation
Phys.iRev.iAi93,i062306i(2016)
T.iBzdusek,iQuanShengiWu,iA.iRuegg,iM.iSigristiandiA.A.iSoluyanovi
Nodal-chain metals
Naturei(inipress)
BelaiBauer,iDaveiWecker,iAndrewiJ.iMillis,iMatthewiB.iHastings,iM.iTroyer
Hybrid quantum-classical approach to correlated materials
Phys.iRev.iXi(inipress)
T.iHäner,iD.S.iSteiger,iM.iSmelyanskiiandiM.iTroyer
High Performance Emulation of Quantum Circuitsi
Supercomputing’16i(inipress)
K.M.iSvoreiandiM.iTroyer
The Quantum Future of Computing
IEEEiComputeri(inipress)
JamesiD.iWhitfield,iVojtěchiHavlíček,iMatthiasiTroyer
Local spin operators for fermion simulations
Phys.iRev.iAi(inipress)
136
L.iCevolani,iG.iCarleo,iandiL.iSanchez-Palencia
Spreading of correlations in exactly-solvable quantum models with long-range interactions in
arbitrary dimensions
NewiJournaliofiPhysicsi(inipress)
S.V.iIsakov,iG.iMazzola,iV.N.iSmelyanskiy,iZhangiJiang,iS.iBoixo,iH.iNeven,iM.iTroyer
Understanding Quantum Tunneling through Quantum Monte Carlo Simulations
Preprint,isubmitteditoiPhys.iRev.iLett.
Z.iJiang,iV.N.iSmelyanskiy,iS.V.iIsakov,iS.iBoixo,iG.iMazzola,iM.iTroyer,iH.iNeven
Scaling analysis and instantons for thermally-assisted tunneling and Quantum Monte Carlo
simulations
Preprint
T.iHäner,iD.S.iSteiger,iK.iSvoreiandiM.iTroyer
A Software Methodology for Compiling Quantum Programs
Preprint
MarkusiReiher,iNathaniWiebe,iKrystaiMiSvore,iDaveiWecker,iMatthiasiTroyer
Elucidating Reaction Mechanisms on Quantum Computers
Preprint
GiuseppeiCarleo,iMatthiasiTroyer
Solving the Quantum Many-Body Problem with Artificial Neural Networks
Preprint,isubmitteditoiScience
M.iKaralic,iS.iMueller,iC.iMittag,iK.iPakrouski,iQ.S.iWu,iA.A.iSoluyanov,iM.iTroyer,i
T.iTschirky,iW.iWegscheider,iK.iEnsslin,iT.iIhn
Experimental Evidence for the Topological Insulator Phase in InAs/GaSb Coupled Quantum
Wells
Preprint,isubmitteditoiPhys.iRev.iLett.
MedhaiSoni,iMicheleiDolfi,iMatthiasiTroyer
Density redistribution effects in fermionic optical lattices
Preprint,isubmitteditoiPhys.iRev.iA
GuglielmoiMazzola,iMatthiasiTroyer
Accelerated nuclear quantum effects sampling with open path integrals
Preprint,isubmitteditoiJCP
137
Group of W.F. van Gunsteren
A.P. Eichenberger, W.F. van Gunsteren, S. Riniker, L. von Ziegler, N. Hansen
The key to predicting the stability of protein mutants lies in an accurate description and
proper configurational sampling of the folded and denatured states
Biochim. Biophys. Acta, General Subjects 1850 (2015) 983-995, DOI:
10.1016/j.bbagen.2014.09.014, incl. suppl. mat.
W. Huang, W.F. van Gunsteren
Challenge of representing entropy at different levels of resolution in molecular simulation
J. Phys. Chem. B 119 (2015) 753-763, DOI: 10.1021/jp505045m, incl. suppl. mat.
Z. Lin, S.J. Bachmann, W.F. van Gunsteren
GROMOS polarisable charge-on-spring models for liquid urea: COS/U and COS/U2
J. Chem. Phys. 142 (2015) 094117, DOI: 10.1063/1.4913955
L.J. Smith, W.F. van Gunsteren, N. Hansen
Characterisation of the flexible lip regions in bacteriophage lambda lysozyme using MD
simulations
Eur. Biophys. J. 44 (2015) 235-237, incl. suppl. mat.
O. Szklarczyk, E. Arvaniti, W.F. van Gunsteren
Polarisable coarse-grained models for molecular dynamics simulation of liquid cyclohexane
J. Comput. Chem. 36 (2015) 1311-1321
Z. Lin, W.F. van Gunsteren
On the effects of polarisable solvent models upon the relative stability of an α-helical and a β
hairpin structure of an alanine deca–peptide
J. Chem. Theory Comput. 11 (2015) 1983-1986
Z. Lin, W.F. van Gunsteren
On the use of a weak-coupling thermostat in replica-exchange molecular dynamics
simulations
J. Chem. Phys. 143 (2015) 034110, DOI: 10.1063/1.4926937
A.P. Eichenberger, W. Huang, S. Riniker, W.F. van Gunsteren
A supra-atomic coarse-grained GROMOS force field for aliphatic hydrocarbons in the liquid
phase
J. Chem. Theory Comput. 11 (2015) 2925-2937, DOI: 10.1021/acs.jctc.5b00295, incl. suppl.
mat.
S.J. Bachmann, W.F. van Gunsteren
Structural and energetic effects of the use of polarisable water to solvate proteins
Mol. Phys. 113 (2015) 2815-2828, DOI: 10.1080/00268976.2015.1042085, incl. suppl. mat.
W.F. van Gunsteren
On the pitfalls of peer review
F1000Research 4 (2015) 1244, DOI: 10.12688/f1000research.7342.1
138
O.M. Szklarczyk, N.S. Bieler, P.H. Hünenberger, and W.F. van Gunsteren,
Flexible Boundaries for Multi-Resolution Solvation: an Algorithm for Spatial Multi-scaling in
Molecular Dynamics Simulations
J. Chem. Theory Comput. 11 (2015) 5447-5463, DOI: 10.1021/acs.jctc.5b00406, incl. suppl.
mat.
Z. Lin, W.F. van Gunsteren
A comparison of pathway independent and pathway dependent methods in the calculation of
conformational free enthalpy differences
Protein Science 25 (2016) 184-191, DOI: 10.1002/pro.2695
J. Dolenc, B.H. Meier, V.H. Rusu, W.F. van Gunsteren
Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils
of the HET-s prion
Phys.Chem.Chem.Phys. 18 (2016) 5860-5866, DOI: 10.1039/c6cp00057f, incl. suppl. mat.
V.H. Rusu, S.J. Bachmann, W.F. van Gunsteren
GROMOS polarisable model for acetone
Mol. Phys. 114 (2016) 845-854, DOI: 10.1080/00268976.2015.1126366
W.F. van Gunsteren
Going for a PhD: Joys and Pitfalls
Helv. Chim. Acta 99 (2016) 1-5
L. J. Smith, G. Rought Whitta, J. Dolenc, D. Wang, W. F. van Gunsteren
A molecular dynamics simulation investigation of the relative stability of the cyclic peptide
octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents
Bioorg. Med. Chem. 24 (2016) 4936-4948, DOI: 10.1016/j.bmc.2016.08.001, incl. suppl. mat.
L.J. Smith, W.F. van Gunsteren, N. Hansen
On the Use of Time-Averaging Restraints when Deriving Biomolecular Structure from 3J-
coupling Values Obtained from NMR Experiments
J. Biomol. NMR 66 (2016) 69-83, DOI: 10.1007/s10858-016-0058-5, incl. suppl. mat.
In press or submitted
W.F. van Gunsteren, J.R. Allison, X. Daura, J. Dolenc, N. Hansen, A.E. Mark, C.
Oostenbrink, V.H. Rusu, L.J. Smith
Deriving structural information from measured data on biomolecules: a review
Angew. Chem. Int. Ed. (2016) accepted
139
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Computational Science
and Engineering (CSE) Annual Report
2015/2016
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