chem iisc

2013 In-house ChemE IISc SYMPOSIUM

Saturday, 5th October 2013

Department of Chemical Engineering

Indian Institute of Science, Bangalore - 12

ABSTRACT BOOK

http://chemeng.iisc.ernet.in/

2013 In-house ChemE IISc Symposium

October 5, 2013

Department of Chemical Engineering

Indian Institute of Science, Bangalore

Welcome

On behalf of the members of the Chemical Engineering Association (CEA) at Indian Institute of Science,Bangalore, I extend a warm welcome to all the participants of the 2013 edition of the in-house ChemE IIScSymposium, CIS 2013. We thank all the participants for taking their time this weekend for attending thesymposium.

This symposium is one in a long series of annual symposiums that is organized by the CEA with thehelp of the Department of Chemical Engineering to bring together the researchers working on a diverse setof problems within the department. This edition of the CIS will feature talks and presentations, which arediverse in their approaches as well as span from biological membranes to clathrate hydrates. We also havethe honor of having two distinguished plenary speakers, Mr. S.N. Eisenhower (Saint Gobain, India) andDr. V. Koelman (Shell, India) from the industry for this CIS. We appreciate their generosity and eagernessto attend and present their views at CIS 2013.

CIS 2013 also follows in the footsteps of such previous symposiums in the department to help us pro-mote increased interaction with the industry. We are also grateful to the invited industry guests who havetaken their time to come visit us on this occasion.

We hope that the participants will enjoy the symposium and find time to interact with ChemE depart-ment members.

Rahul Roy

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Technical programme

October 5, 2013

08:45 - 09:00 Coffee09:00 - 09:10 Chairman’s address

Morning session

09:10 - 09:50 S.N. Eisenhower Chemical Engineering research & practices in indus-try: value addition in upstream and downstream pro-cesses

09:50 - 10:10 R. Desikan A novel mechanism for the poration of lipid mem-branes by Cytolysin A

10:10 - 10:30 H.S. Ganesh Understanding selectivity during adsorption of longchain n-alkane binary mixtures in silicalite under con-ditions of high loading

10:30 - 10:50 P. Joshi Low cost, flexible, large scale fabrication of hydrogensensors

10:50 - 11:10 S.S. Sandeep The effects of chemical signaling on motility andbiofilm formation in bacteria

11:10 - 11:20 Coffee break

Pre lunch session

11:20 - 11:40 K.K. Rao In memorium: a tribute to Prof. David Bourgin11:40 - 12:00 T. Dasgupta Effect of functional groups on separating carbon

dioxide-nitrogen mixtures using edge functionalizedgrapheme nanoribbons

12:00 - 12:20 G. Madabatulla Modeling of supercapacitors12:20 - 12:40 V. Shinde Ce0.85M0.1Ru0.05O2−δ (M = Si, Fe): new oxygen stor-

age materials for environmental and energy applica-tions

12:40 - 13:00 M.N. Nandanwar A mathematical model for the soluble lead-acid flowbattery with non-uniform current density distribution:parallel plate vs cylindrical configuration

13:00 - 13:10 Department’s brochure release

13:10 - 14:10 Lunch

Post lunch session

14:10 - 14:50 V. Koelman The power of high performance computing in chemicalengineering

vi

14:50 - 15:10 S. Perala An alternative mechanism of synthesis of goldnanoparticles

15:10 - 15:30 P. Pranesh Emergent properties of the interferon signaling net-work may underlie the success of current treatmentsfor hepatitis C virus

15:30 - 15:50 S. Ravipati Calculation of three-phase methane-ethane binaryclathrate hydrate phase equilibrium from Monte Carlomolecular simulations

15:50 - 16:10 S.J. Jaju Study of lamellar mesophases

16:10 - 17:10 Coffee break and poster session

Evening session

17:10 - 17:30 S.N. Punnathanam Towards a consistent theory for clathrate hydrates17:30 - 17:35 Prize distribution17:35 - 17:40 Vote of thanks by CEA President

Poster presentations

N. Pradeep Mathematical modelling of viral decay dynamics after initiation of com-bination antiretroviral treatment in HIV-1 subtype C infection

V. Vadhana Investigation of liquid stucture and dynamics under nanoscale confine-ment

S. Pradeep E. coli Cytolysin A: understanding the mechanism of pore formationK. Sahoo Development of a novel continuous mixer and exploration of it’s appli-

cation as a flow reactor for nanoparticle synthesisJ. Panwar Super spectral resolution microscopy with single laser sourceM. Simna Expression of therapeutic proteins in humanized Pichia

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Contents

Welcome message iii

Technical programme v

Chemical engineering research & practices in industry: value addition in upstream anddownstream processes 1

S.N. Eisenhower

A novel mechanism for the poration of lipid membranes by Cytolysin A 2Rajat Desikan and K. Ganapathy Ayappa

Understanding selectivity during adsorption of long chain n-alkane binary mixtures insilicalite under conditions of high loading 3

Hari S. Ganesh and Sudeep N. Punnathanam

Low cost, flexible, large scale fabrication of hydrogen sensors 4Pushkaraj Joshi and Venugopal Santhanam

The effects of chemical signaling on motility and biofilm formation in bacteria 5S.S. Sandeep, Deepak K. Saini and Prabhu R. Nott

In memorium: a tribute to Prof. David Bourgin 6K. Kesava Rao

Effect of functional groups on separating carbon dioxide-nitrogen mixtures using edgefunctionalized graphene nanoribbons 7

Tonnishtha Dasgupta, Sudeep N. Punnathanam and K. Ganapathy Ayappa

Modeling of supercapacitors 8Ganesh Madabattula and Sanjeev Kumar

Ce0.85M0.1Ru0.05O2−δ (M = Si, Fe): new oxygen storage materials for environmental andenergy applications 9

Vijay M. Shinde and Giridhar Madras

A mathematical model for the soluble lead-acid flow battery with non-uniform currentdensity distribution: parallel plate vs cylindrical configuration 10

Mahendra N. Nandanwar and Sanjeev Kumar

The power of high performance computing in chemical engineering 11Vianney Koelman

An alternative mechanism of synthesis of gold nanoparticles 12Siva Rama Krishna Perala and Sanjeev Kumar

Emergent properties of the interferon signaling network may underlie the success of cur-rent treatments for hepatitis C virus 13

Pranesh Padmanabhan and Narendra M Dixit

viii

Calculation of three-phase methane-ethane binary clathrate hydrate phase equilibriumfrom Monte Carlo molecular simulations 14

Srikanth Ravipati and Sudeep N Punnathanam

Study of lamellar mesophases 15S.J. Jaju and V. Kumaran

Towards a consistent theory for clathrate hydrates 16Sudeep N. Punnathanam

Mathematical modelling of viral decay dynamics after initiation of combination antiretro-viral treatment in HIV-1 subtype C infection 17

Ujjwal Neogi, Pradeep Nagaraja, Riya Palchaudhuri, Narendra M. Dixit, Karthika Arumugam,Ayesha De Costa, Anita Shet

Investigation of liquid stucture and dynamics under nanoscale confinement 18V. Vadhana and K. Ganapathy Ayappa

E. coli Cytolysin A: understanding the mechanism of pore formation 19Pradeep Sathyanarayana, K. Ganapathy Ayappa and Sandhya S. Visweswariah

Development of a novel continuous mixer and exploration of it’s application as a flowreactor for nanoparticle synthesis 20

Kshetramohan Sahoo and Sanjeev Kumar

Super spectral resolution microscopy with single laser source 21Jatin Panwar and Rahul Roy

Expression of therapeutic proteins in humanized Pichia 22Simna Manoharan, Dighe R.R. and Modak J.M.

ChemE IISc Symposium (CIS 2013) 1

Chemical engineering research & practices in industry: value addition in upstream and

downstream processes

S.N. Eisenhower

Director - Operations, Saint Gobain Glass India

Chemical Engineers scope of research in industry hitherto had been confined largely to processes with

chemical reactions and that too particularly in chemical and petro-chemical industry. Industrial Research

in Chemical Engineering over the past 3 decades to admit has lost its sheen. Its time to have a re-look at

the current perspectives of Industry and its needs and how Chemical Engineering research can meet these

requirements in contemporary industry.

This presentation focuses on the mining and solar industry in addition to the innovation that Chemical

Engineers could offer to Industrial research in downstream processes.

A Saint Gobain example of value addition of

a mined material is given as an example for the

synopsis. In addition to converting a widely avail-

able mineral into a high value added product, the

method of mining, wastage and environmental /

health concerns associated with it call for urgent ac-

tions particularly in India. This presentation high-

lights the actions of Saint Gobain in this regard

and also outlines the scope of Industrial research

for Chemical Engineers

The Presentation also outlines the scope of In-

dustrial research on Thin film coatings. Rather

than establishing a production unit after a successful research & development of a product, the cur-

rent needs of faster new products demand that the production units are amenable to research in existing

facilities. Saint Gobain Glass Indias example in this regard over the past 12 years is presented in brief

The presentation also outlines the need for radical change in the way Logistics is done, particularly

in India. Chemical Engineers scope of work in packing materials and storage practices could redefine the

logistics of several products that would enable a lean logistics.


A novel mechanism for the poration of lipid membranes by Cytolysin A

Rajat Desikan and K. Ganapathy Ayappa

Pore Forming Toxins (PFTs) are ubiquitous weapons in the armoury of many organisms ranging from

pathogenic bacteria to the human immune system. It is often observed that small numbers of these potent

proteins form stable unregulated pores, permeabilize the cell membrane and cause cell lysis. The complex

role of the membrane in the formation of these pores, the influence of the pore on the structure and

dynamics of the surrounding membrane and the expulsion of the central lipids upon pre-pore formation

are important phenomena that are poorly understood due to the paucity of structural data. Using a recent

high resolution structure of the membrane inserted dodecameric form of the PFT Cytolysin-A (ClyA),

multi-scale molecular dynamics of intermediate oligomers of ClyA in a variety of membranes was carried

out. The results show a rapid evacuation of the central lipids from the octamer and nonamer interior

to the bulk membrane. This implies that concerted lipid evacuation occurs prior to the formation of the

dodecameric pore complex. This alternative hypothesis challenges the notion that destabilization and the

ejection of a membrane patch corresponding to the pore-lumen occurs after the pre-pore assembly on the

membrane surface is complete. This mechanism could occur across PFT families and has implications on

membrane re-sealing and cell recovery.


Understanding selectivity during adsorption of long chain n-alkane binary mixtures in

silicalite under conditions of high loading

Hari S. Ganesh and Sudeep N. Punnathanam

Adsorption experiments of mixtures of long chain alkanes into silicalite under liquid phase conditions

show selectivity inversion and azeotrope formation. These effects are due to the subtle interplay between

the size of the adsorbed molecules and pore topology of the adsorbent. In this study, the selective uptake of

lighter component during liquid phase adsorption of C14 /C15 and C15 /C16 n-alkane binary mixtures in

the zeolite silicalite is understood through configurational bias grand canonical Monte Carlo (CB-GCMC)

molecular simulation technique and a course-grained siting analysis. The simulations are conducted under

conditions of low and high loading. The siting pattern of the adsorbates inside the zeolite pores is used to

explain the selectivity as seen in experiments.


Low cost, flexible, large scale fabrication of hydrogen sensors

Pushkaraj Joshi and Venugopal Santhanam

Use of hydrogen based energy requires hydrogen storage which has sparked increased interest in devel-

oping fast, reliable hydrogen sensors. Hydrogen sensors are useful to detect leakage in hydrogen storages

for rockets for space shuttles, fuel-cell storages, process control in the chemical industry etc. The lower

explosive limit of hydrogen in the air is extremely low ∼4 %. Lot of effort has been made to achieve these

metrics. Pd thin films respond to hydrogen environment by an increase in resistance due to the formation

of Pd-Hx which swells due to higher lattice constant. Pd-Hx has a lower resistance than Pd, the value is

proportional to x [1].

Nanomaterials made of CNT [2], Pd meso/nano wires, Pd and Pd alloy nanoparticles [3, 4] have

also been used as hydrogen sensors. Penner et al. [4] developed Pd mesowires for hydrogen sensing by

electrodeposition. Herein, the sensor responds much faster because resistance responds exponentially to

nanogap decrease due to swelling. However, the fabrication process itself is highly unreliable subject to

deterioration due to fractures. We have developed a simple inkjet printer based fabrication process of

silver-palladium alloy nanowires on paper which respond to hydrogen.

References

[1] Lewis, F.A., The Palladium Hydrogen System (Academic Press: London, 1967).

[2] Sippel-Oakley, J., et al., Nanotechnology, 16, 2218 (2005).

[3] Ibanez, F.J. and F.P. Zamborini, Langmuir, 22, 9789 (2006).

[4] Favier, F., et al., Science, 293, 2227 (2001).


The effects of chemical signaling on motility and biofilm formation in bacteria

S.S. Sandeep, Deepak K. Saini† and Prabhu R. Nott

†Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India.

Vibrio fischeri , a marine bacterium, has two signaling mechanisms, ainS and luxI, which involve secre-

tion of C6-HSL (C6) and C8-HSL (C8) autoinducers. LuxR is the cognate receptor for both C6 and C8.

Motility drops sharply above a critical concentration of C8. The critical concentration of C8 is roughly

insensitive to bacterial density, whereas, C6 is found to have no effect on motility. Various mutant strains

of V. fischeri also exhibit a drop in motility. The drop in motility for luxI mutant, which produces C8,

but not C6, has been found to occur at a lower C8 concentration than that for ainS and wild-type strain.

C8 has been found to have no effect on the motility of luxR mutant, which indicates that luxR is the key

link between C8 and motility.

Biofilm formation is an important consequence of signaling in bacteria. V. fischeri responds positively

to exogenous addition of C8 by forming biofilms much earlier than the culture to which no C8 is added.

The dynamics of film formation is understood by using the technique of RT PCR. The real time changes

in the expression levels of biofilm genes are found out by quantitative PCR.


In memorium: a tribute to Prof. David Bourgin

K. Kesava Rao

The eccentric teaching style of my mathematics teacher Prof. David G. Bourgin will be discussed.

On the face of it, one may wonder how his method of teaching could possibly be of interest to chemical

engineers. The answer will hopefully be evident in my talk, which I will also use as a platform to reflect

on our present methods on instruction, and share some jokes/thoughts of Profs. Bourgin and Neal R.

Amundson.


Effect of functional groups on separating carbon dioxide-nitrogen mixtures using edge

functionalized graphene nanoribbons

Tonnishtha Dasgupta, Sudeep N. Punnathanam and K. Ganapathy Ayappa

Separation of carbon dioxide and nitrogen is significant because they are the two main components in

flue-gas emissions from thermal plants. To reduce global carbon dioxide emissions, it is important to capture

and store the carbon dioxide selectively from the effluent gas. In this regard microporous materials are

widely studied to assess their selective adsorption capacity. Using a combination of ab initio and classical

grand canonical Monte Carlo (GCMC) simulations we study the influence of commonly occurring functional

groups on the adsorption selectivity to CO2 in a CO2/N2 mixture. Benzene molecules functionalized with

OH, NH2, NO2, CH3 and COOH are used in the MP2 (Mller-Plesset with second order perturbation)

calculations where CO2 binding energies are studied. An edge functionalized graphene nanoribbon(GNR)

bilayer is used in the classical GCMC simulations. The OPLS all-atom force-field is used for the classical

simulations and the three-site TraPPE model is used for both carbon dioxide and nitrogen. Adsorption

isotherms and isosteric heats of adsorption are obtained from Grand Canonical Monte Carlo simulations

at 298 K and pressures up to 20 bars. Carbon dioxide selectivity is used to measure the effectiveness of the

separation. The CO2:N2 molar ratios studied are 1:1 and 1:4 for two different concentrations of functional

groups (4.2 mol% and 6.25 mol%) on the GNRs.

COOH functionalized GNRs show the highest uptake for both carbon dioxide and nitrogen and has the

highest selectivity toward carbon dioxide when compared with the other functional groups investigated.

The trend observed in the surface excess obtained above is seen to be consistent with the trend in the

binding energies obtained from MP2 calculations. In almost all the cases, there is a local enhancement in

adsorbate density near the functional groups and for COOH the density of carbon dioxide in the vicinity

of the functional group exceeds the density on the bare graphene part of the GNR. The trends in the pure

CO2 heats of adsorption and adsorption isotherms observed in the GCMC simulations are similar to the

trends in the binding energies obtained from the MP2 calculations on functionalized benzenes.

NO2 follows COOH in proving to be the best for both carbon dioxide and nitrogen uptake, as sub-

stantiated by the heat of adsorption data, but unlike COOH does not show good selectivity. NH2 and

OH are seen to be comparable in both uptake and separation. This study conclusively shows that certain

functional groups have a higher preference for uptake and separation of CO2 These results can be used

while functionalizing materials such as metal organic frameworks, which can be constructed in a modular

fashion, for storage and separation applications.


Modeling of supercapacitors

Ganesh Madabattula and Sanjeev Kumar

Electrolytic double layer capacitors (EDLC’s) achieve high capacitance by using electrodes made of

high interfacial area porous materials, such as activated porous carbon, and limiting the charge separation

distance to double layer (Debye length) using mobile ions in electrolyte. The present work uses a funda-

mental transport process based approach to model a EDLC unlike the RC circuit models, already available

in the literature. In this work, a 1D transport model is developed for porous activated carbon coated elec-

trodes inserted in an electrolyte solution. The model considers diffusive and convective movement of ions

in a straight narrow channel and double layer formation at the electrode-electrolyte interface in response to

concentration gradient and electric field. The governing equations are solved using COMSOL multiphysics.

The model explains variation of anodic and cathodic potentials during (dis)charging, recovery of potential

during relaxation phase after high rate of discharge, limiting current densities, and relative contributions

from migration and diffusion of ions to the dynamics of (dis)charging process.

The model further shows that the constant capacitance assumption for double layer needs to be relaxed

to incorporate voltage dependent capacitance to better reflect the non-linear response of double layers to

potential drop across them.


Ce0.85M0.1Ru0.05O2−δ (M = Si, Fe): new oxygen storage materials for environmental and

energy applications

Vijay M. Shinde and Giridhar Madras

Materials with high oxygen storage capacity (OSC) have attracted considerable attention due to their

wide applications in auto exhaust catalysis, fuel cells and solar cells. Ceria and ceria containing materials

are promising candidates because of their excellent electrical, catalytic, and mechanical properties. Ceria is

also a major component of a three way catalyst in automotive exhaust emissions. The facile Ce4+ ↔ Ce3+

redox couple allows these materials to store and release oxygen under oxidizing and reducing conditions,

respectively. The performance of these materials as catalyst depends on the OSC and the enhancement

in the catalytic activity is directly correlated with increase in the OSC. Therefore, it is highly desirable

to increase the active oxygen content of ceria based materials for the low temperature CO oxidation,

hydrocarbon oxidation, and water gas shift (WGS) reaction.

With these motivations, we have synthesized new catalysts that are essentially a solid solution of

Ce0.85M0.1Ru0.05O2−δ (M = Si, Fe) and explored their potential application for CO oxidation. The substi-

tution of Fe and Si was rationalized based on their small ionic radii compared to host Ce ions which distort

the ceria lattice and give high OSC. Ru substitution is justified based on the fact that the higher rates of

CO oxidation cannot be obtained by the utilization of lattice oxygen alone and CO adsorption sites over

the catalyst are essential. Therefore, in this study, we report the synthesis, structure and CO oxidation

activity of Ce0.85M0.1Ru0.05O2−δ (M = Si, Fe) solid solution synthesized by low temperature sonication

method. The reducibility of the catalyst was studied by temperature programmed reduction (H2-TPR)

method and the increase in the OSC was correlated to the enhancement in CO oxidation activity. The

spectroscopic and experimental observation was used to describe bifunctional redox mechanism over these

catalysts. Finally, we have extended the application of these materials toward the production of hydrogen

by performing the WGS reaction. Both the solid solutions showed excellent activity for both the reactions.


A mathematical model for the soluble lead-acid flow battery with non-uniform current

density distribution: parallel plate vs cylindrical configuration

Mahendra N. Nandanwar and Sanjeev Kumar

A soluble lead acid flow battery (SLFB) with a single active material in a solvent offers a number

of advantages. Issues related to low efficiencies and electrode degradation need resolution. In this work,

a mathematical model that incorporates ion transport, faraidic reactions on electrode, fluid flow, and

realistic initial and boundary conditions, is used to simulate a parallel plate SLFB, studied experimentally

in the literature. The model captures charge-discharge cycles well. As the model allows for non-uniform

current density on electrode surface, simulations show non-uniform deposition during charging, and residual

solid build up after every charge-discharge cycle. The rapid decrease in cell voltage towards the end of a

discharge cycle, observed experimentally, is initiated with baring of the electrodes from the trailing end side.

Although the flow field is responsible for non-uniform current density, an increase in flow rate is predicted to

change battery characteristics only marginally, in agreement with the experimental observations. Finally,

the validated model is used to compare parallel plate geometry with cylindrical electrode geometry with

the anode on the outer side. The simulations show significantly improved performance for the later in

terms of charge efficiency, energy efficiency, capacity, and cycle life.


The power of high performance computing in chemical engineering

Vianney Koelman

Shell Chief Scientist & Vice President Computational R&D

Shell Technology Center Bangalore, Shell India Markets Private Limited, Bengaluru 560 048.

The energy scenario in the future and the responses of Royal Dutch Shell Plc will be presented. An

overview of research activities in the Computational Centre of Expertise (CCoE) at Shell Technology Centre

Bangalore will be presented with specific emphasis on few case studies in predicting physical properties

of complex hydrocarbons. The shear viscosity of linear alkanes is predicted to the required accuracy by

molecular dynamics (MD) simulations at high temperature and high pressure conditions. The effect of

different simulation methodologies and force fields on the accuracy of the prediction will be brought out

in this talk. The talk will also describe few leading computational innovations in the energy industry.


An alternative mechanism of synthesis of gold nanoparticles

Siva Rama Krishna Perala and Sanjeev Kumar

Brust-Schiffrin synthesis (BSS) of metal nanoparticles has emerged as a major breakthrough in the

field for its ability to produce highly stable thiol functionalized nanoparticles. In this work, we use a

detailed population balance model to conclude that particle formation in BSS is controlled by a new

synthesis route—continuous nucleation, growth, and capping of particles throughout the synthesis process.

The new mechanism, quite different from the others known in the literature—classical LaMer mechanism,

sequential nucleation-growth-capping, and thermodynamic mechanism—successfully explains key features

of BSS, including size tuning by varying the amount of capping agent instead of the widely used approach

of varying the amount of reducing agent. The new mechanism captures a large body of experimental

observations quantitatively, including size tuning and only a marginal effect of the parameters otherwise

known to affect particle synthesis sensitively. The new mechanism predicts that in a constant synthesis

environment, continuous nucleation-growth-capping mechanism leads to complete capping of particles (no

more growth) at the same size, while the new ones are born continuously, in principle leading to synthesis

of more monodisperse particles. This prediction is validated through new experimental measurements.


Emergent properties of the interferon signaling network may underlie the success of current

treatments for hepatitis C virus

Pranesh Padmanabhan and Narendra M. Dixit

Interferon alpha-based treatment, the current standard-of-care for hepatitis C virus (HCV) infection,

fails to cure a sizeable fraction of HCV patients treated. The cause of this treatment failure has remained

poorly understood. Interferon triggers a signaling cascade leading to the expression of several hundred

interferon-stimulated genes that together induce an antiviral state in cells. HCV interferes at several

points in the interferon signaling network and thwarts its antiviral activity. It is of clinical importance

to understand when HCV overcomes interferon and results in treatment failure. Here, we predict that

treatment response is a consequence of emergent properties of the interferon signaling network in the

presence of HCV. Using a reaction kinetics based model of the key components of the network, we found

that the network exhibited bistability, with one stable steady state where HCV established persistent

infection and the other where it was cleared by interferon. Cells could admit one or both steady states,

given intrinsic variations in gene expression, resulting in diverse phenotypic responses to interferon. Cells

that admitted the former steady state alone were refractory to interferon. We next integrated the single

cell level description of interferon responsiveness to a population dynamics model of HCV infection and

predicted treatment response. We found that when the fraction of cells refractory to interferon in a

patient exceeded a critical value, treatment failed. Response rates to treatment increased significantly

when interferon was used in conjunction with new direct acting antiviral agents (DAAs). DAAs that

suppressed HCV replication weakened the influence of HCV on the interferon network. Incorporating

DAA activity into our model, we found that beyond a critical DAA efficacy, the network exhibited a single

steady state where HCV was cleared. DAAs thus altered the emergent properties of the network, reducing

the fraction of cells refractory to interferon and improving treatment response. Our study presents a new

conceptual basis for understanding the response of HCV patients to interferon-based therapies and provides

a framework for rational treatment optimization.


Calculation of three-phase methane-ethane binary clathrate hydrate phase equilibrium

from Monte Carlo molecular simulations

Srikanth Ravipati and Sudeep N. Punnathanam

Methane and ethane are the simplest hydrocarbon molecules that can form clathrate hydrates. Previous

studies have reported methods for calculating the three-phase equilibrium using Monte Carlo simulation

methods in systems with a single component in the gas phase. Here we extend those methods to a binary gas

mixture of methane and ethane. Methane-ethane system is an interesting one in that the pure components

form sI clathrate hydrate where as a binary mixture of the two can form the sII clathrate. The phase

equilibria computed from Monte Carlo simulations show a good agreement with experimental data and

are also able to predict the sI-sII structural transition in the clathrate hydrate. This is attributed to the

quality of the TIP4P/Ice and TRaPPE models used in the simulations.


Study of lamellar mesophases

S.J. Jaju and V. Kumaran

Water-surfactant-oil mixtures form various micro-phases depending upon the concentration of indi-

vidual components, owing to the amphibilic nature of the surfactant molecules. Anisotropic phases such

as lamellar mesophases have different responses to applied shear, depending upon their orientation with

respect to the flow. In present study, we have used mesoscale simulations to understand the shear align-

ment of initially disordered lamellar phase. The simulations, based on lattice Boltzmann method and free

energy functional for concentration modulation, were performed at Schmidt numbers (ratio of momentum

and mass diffusion) for two dimensional 32λ system with wall as well as periodic boundary conditions. λ

is wavelength of concentration modulation and a system of size L will have Lλ layers at equilibrium.

The layers tend to align along the flow direction at high Schmidt numbers and along extensional axis

of the flow at low Schmidt numbers. The effects of difference in viscosities of individual phases, thickness

of interface of bilayer on alignment process would be discussed.


Towards a consistent theory for clathrate hydrates

Sudeep N. Punnathanam

Flexibility of the water lattice in clathrate hydrates and guest-guest interactions have been shown

in previous studies to significantly affect the values of the thermodynamic properties such as chemical

potentials and free energies. Here we describe methods for computing occupancies, chemical potentials

and free energies that account for the flexibility of water lattice and guest-guest interactions in the hydrate

phase. The methods are validated for a wide variety of guest molecules such as methane, ethane, carbon

dioxide and tetrahydrodfuran by comparing the predicted occupancy values of guest molecules with those

obtained from isothermal isobaric semigrand Monte Carlo simulations. The proposed methods extend the

van der Waals and Platteuw theory for clathrate hydrates and the Langmuir constant is calculated based on

the structure of the empty hydrate lattice. These methods in combination with development of advanced

molecular models for water and guest molecules should lead to more thermodynamically consistent theory

for clathrate hydrates.


Mathematical modelling of viral decay dynamics after initiation of combination

antiretroviral treatment in HIV-1 subtype C infection

Ujjwal Neogi†,∗, Pradeep Nagaraja, Riya Palchaudhuri‡, Narendra M. Dixit, Karthika Arumugam‡,

Ayesha De Costa§, Anita Shet‡

†Haematology Research Unit, St. Johns Research Institute, St. Johns National Academy of Health Sciences, Bangalore,India.

∗Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.‡Clinical Virology, Department of Microbiology and Pediatrics, St. Johns Medical College Hospital, Bangalore, Karnataka,

India.§Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden

Mathematical modelling of viral decay dynamics has significantly enhanced our understanding of the

clinical observations of human immunodeficiency virus-1 (HIV-1) infection. HIV-1 subtype C (HIV-1C)

is the most prevalent subtype worldwide and also in India with nearly 2.4 million infected people. How-

ever, HIV-1C viral load changes in patients undergoing therapy in India is sparse, limiting estimation

of parameters that would guide treatment optimization and predict the transmission of infection in the

Indian setting. In this study, viral response was measured in a randomised clinical trial over a period of

6 months after initiation of antiretroviral combination therapy, providing insight into the decay dynamics

of HIV-1C. Viral load, CD4+ T-cell count and adherence data was used to model the biphasic viral decay

dynamics of the HIV-1C patients under combination therapy. From comparisons between patient data and

our model, we estimated the basic reproductive number to be 3.8 ± 2.2, smaller than that for HIV-1B

(∼6-8), predominant in the west, indicating that the strain circulating in India is less virulent than that in

the west. This perhaps explains why response to treatment in clinical trials appears better in India than

in the west.


Investigation of liquid stucture and dynamics under nanoscale confinement

V. Vadhana and K. Ganapathy Ayappa

Fluids confined in spaces of molecular dimensions exhibit properties different from the bulk. Fluid

molecules have a tendency to order themselves in layers parallel to the confining solid surface and hence,

there could be possible phase transition to a disordered glassy state or an ordered solid-like state. The

stratification is quantitatively described by local density variations in the confined geometry, which is a

damped oscillatory function of the separation distance between the confining surfaces. As a consequence

of the local density variations, the normal stress acting on the solid substrate by the fluid also shows a

damped oscillatory behavior with respect to the separation distance. In this study, we investigate the

behavior of liquid Octamethylcyclotetrasiloxane (OMCTS), using microcanonical ensemble simulations.

OMCTS confined between mica surfaces has been widely investigated using surface force experiments.

We have carried out simulations using both monatomic as well as fully atomistic models. Properties are

estimated for the bulk fluid to benchmark with literature data for furthur studies.


E. coli Cytolysin A: understanding the mechanism of pore formation

Pradeep Sathyanarayana, K. Ganapathy Ayappa and Sandhya S. Visweswariah†


Pore forming toxins are proteins that mediate their activity by forming stable pores in membranes.

These proteins switch from a water soluble to membrane bound form when exposed to biological mem-

branes. E coli Cytolysin A (ClyA) belongs to the alpha group of pore forming toxins (PFT). This toxin

oligomerizes as a dodecamer and this switch in state is accompanied by large topological reorganization

of its tertiary structure. The molecular mechanisms underlying pore formation are not completely under-

stood. To explore this in greater detail, ClyA was cloned, expressed and purified to homogeneity. and

activity was estimated. Upon biochemical analysis, It was observed that a critical concentration (175 ng)

was required for lysis. Deletion mutants were generated to study the role of carboxy-terminus in pore for-

mation. A 12 amino acid deletion rendered the protein inactive, highlighting the importance of C-terminal

residues in pore formation. Interestingly, membrane binding of the deletion mutants were similar to the

full length toxin, suggesting that they may be defective in subsequent steps such as oligomerization or pore

fomation. ClyA could form lethal pores in Caco2 colorectal carcinoma cells, which could be resealed upon

removal of toxin. Kinetic models were proposed to predict cell lysis in response to ClyA. It was found

that the irreversible-sequential model closely mimicked the experimental observations. In future, we plan

to study the pore formation process on synthetic membranes to better understand the dynamics of the

assembly process.


Development of a novel continuous mixer and exploration of it’s application as a flow

reactor for nanoparticle synthesis

Kshetramohan Sahoo and Sanjeev Kumar

Mixing is an important unit operation encountered in various process applications. Impaction of fine

droplets of one liquid on dynamic thin film of another liquid can bring about mixing of the two. The mixer

consisting of a disc and a bowl for creating droplets and thin film of liquid respectively, under the action

of centrifugal force, was developed earlier in our group. The Iodide-iodate competing parallel reaction

was used for characterizing mixing at various operating conditions. Complete understanding of the mixing

mechanism specific to this liquid-liquid mixer is yet to be developed. Barium sulfate nanoparticles of mean

diameter 75 nm could be synthesized at room temperature using this mixer.


Super spectral resolution microscopy with single laser source

Jatin Panwar and Rahul Roy

Conventional super-resolution microscopy based on stochastic localization of single molecules and image

reconstruction relies on collecting all emitted photons into a single image. This allows high spatial resolution

upon fitting of the point spread function but loses the spectral information, in other words, it cannot

differentiate between photons from fluorophores spectrally close to each other.

In order to identify the dyes of different emission wavelengths distinctly, we propose a method which

will help to differentiate between multiple dyes whose emission wavelengths are very close. This can be

done by dividing the emission spectrum space (from a collection of dyes) using various multi-pass filters to

image spectral components on to different parts of a CCD chip in such a way that each emission segment

forms a discrete value fraction of the photon count for a given dye. Upon classification and assignment of

such single molecule spectral signatures to the dyes in the sample, a multi-color super-spectral image will

be reconstructed.


Expression of therapeutic proteins in humanized Pichia

Simna Manoharan, Dighe R.R.† and Modak J.M.


Microbial expression systems are excellent platform for synthesis and manipulation of proteins of thera-

peutic and biopharmaceutical importance. Yeast, unicellular fungi, with advantages such as ability to grow

on low cost media to high cell densities, ease of fermentation and scale-up, high yields of properly folded

functional proteins, are ideal hosts for large scale recombinant protein expression. The current work aims

at engineering the post translational glycosylation pathway in yeast, Pichia pastoris. Engineered Pichia

would combine the advantages of post translational modification of mammalian systems with ease of ma-

nipulation of bacteria, expressing proteins with human like glycan structures rather than high mannose

type yeast glycoform. A glycoprotein hormone Human chorionic gonadotropin (hCG), expressed in this

host showed increased in-vivo half-life when compared to protein expressed in the wild type host.

Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, Phone: +91 080 2293 2138

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