offer of training form summer 2019 - naughton fellowships · 2019-12-04 · offer of training form...

OFFER OF TRAINING FORM SUMMER 2019

Proposer details:

Title: Generating, storing and releasing oxygen for biomedical applications

Name: Prof. Dr. Mathias O. Senge

Email: [email protected]

Website: http://chemistry.tcd.ie/staff/people/mos/Home.html

If your grade does not allow you to supervise students, please supply the name of support PI:

Student required:

Specify any previous training / experience the student should have:

Fundamentals in chemistry, physics, biology

Study level (3rd year, 4th year) 3rd year and 4th year

Any other requirements: none

Traineeship offered:

Brief job description: (please include (1) type of work, (2) what student should hope to achieve at end of the process, (3) who will supervise student on daily basis (post-doc etc.))

(1) Synthetic bioorganic chemistry, (2) work in an internationally leading, multicultural and multidisciplinary research group, development of research level laboratory skills, planning and executing target oriented syntheses, preparation of results for publication, publication (3) supervision by PI and Susan Callaghan (postgraduate student)

Link to research group or supervisor webpage:

http://chemistry.tcd.ie/staff/people/mos/Home.html

Location of lab: SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, 7th floor

Working hours: Number of Weeks offered: 12 Hours per week: 40 Earliest Start Date possible: Any time Latest End Date possible: Any time

mailto:[email protected]




Proposer details:

Title: An electroactive, non-viral gene delivery biomaterial platform for external enhancement and control of gene therapy and regeneration

Name: Michael Monaghan


Website: www.monaghanlab.com


n/a

Student required:


Wet lab skills, materials fabrication, biomaterials, some knowledge of biology

Study level (3rd year, 4th year) Preferably 4th

Any other requirements:


Brief job description: (please include (1) type of work, (2) what student should hope to achieve at end of the process, (3) who will supervise student on daily basis (post-doc etc.)) Background: Myocardium infarction is the leading cause of death in the western world, causing 1 of every 7 deaths. Current clinical solutions consist of bridge therapies for the whole organ transplantation. In the context of tissue engineering and regenerative medicine, researchers in the lab of Dr. Michael Monaghan are developing cell-based strategies to obtain adult cardiac tissues differentiated from stem cell sources to repair damaged myocardium or engineer cardiac organoids in vitro. The recapitulation of the cardiac electro-mechanical environment can be a pivotal trigger for the mature cardiac phenotype maturation. Conductive polymers such as poly(3,4-ethylenedioxythiophene) :poly(styrenesulfonate) (PEDOT:PSS) are electrically conductive, easily processable, biocompatible and are being harnessed into both 2D and 3D structures for in vitro cardiac tissue engineering (www.monaghanlab.com). Recently, the Dr. Monaghan’s Team have had performed successful feasibility studies in employing these electroconductive materials as controllable platforms of non-viral delivery. Non-viral delivery can be used as a therapeutic to reprogram cells to make proteins that can be therapeutic and enhance wound healing and stem cell differentiation. This breakthrough is a novel approach in employing electrical stimulation to enhance and control gene-delivery


http://www.monaghanlab.com/


which allows the merging of smart biomaterials with genetic engineering The overall goal of this project is to apply defined electric field patterns (using an established custom-bioreactor system) to 3D electroconductive scaffolds loaded with non-viral gene vectors and study their effect on prolonged and transient protein expression. Objectives: 1) To load, conjugate and characterise a non-viral gene vector encapsulated in 3D scaffolds 2) To investigate the correlation between electrical field stimulation of 3D PEDOT:PSS porous scaffolds already developed in the Monaghan Lab with expression of reporter proteins 3) To design a prototype able to apply electric field stimulation to a porous scaffold PEDOT:PSS scaffold. Methods Employed: non-viral gene therapy, nucleic acids research, polymer chemistry, biomaterial fabrication, in vitro cell culture, cell isolation, electro-conductivity testing, mechanical testing (dynamic compression), statistical analysis, 3D modelling, 3D printing. Deliverable: This project will lay a strong framework towards impacting the field of flexible electroconductive 3D biomaterials as drug delivery and/or gene activating matrices. Mentorship: Student will work on a team with one PhD student as a main contact point and will be supported by the PI and the rest of the team.


www.monaghanlab.com

Location of lab: Trinity Biomedical Sciences Institute

Working hours:

Number of Weeks offered: Minimum of 12

Hours per week: 40

Earliest Start Date possible: 1st May 2019

Latest End Date possible: 14th September 2019

C

B

Figure 1 (A) 3D porous PEDOT:PSS scaffold employed in this research. . (B &C) Fibroblasts that have been subjected to delivery of green fluorescent protein (GFP) gene delivery using non-viral gene therapy with (B) merging of brightfield and GFP channels and (C) GFP channel alone. Both micrographs are co-incident on identical imaging regions. Scale bar equals 500 um.



Proposer details:

Title: Postdoctoral Researcher

Name: Dr. Mathieu Riffault


Website: https://www.tcd.ie/bioengineering/biomaterials/hoeylab/


Prof. David Hoey

Student required:


Ideally theoretical knowledge of mammalian cell culture and immunohistochemistry techniques.

Study level (3rd year, 4th year) 3rd or 4th year undergraduate preferable




This project aims to characterise the role of bone marrow stem cells in bone formation and during osteoporosis in mice and evaluate the effect of a novel therapy.

1. This internship will consist of performing immunohistochemistry labelling and histological staining and then acquisition and analysis of images of mouse tissue, the intern will also be involved in micro-CT analysis of bone formation.

2. The student should hope to leave the process with a proficient knowledge of histology, basic fluorescent microscopy, and analysis of bone formation as well as some experience in basic statistical analysis.

The project will run alongside the work of a PhD student and the intern will be trained and supervised on a day to day basis by a post-doc. Prof. Hoey will provide additional supervision and guidance at structured lab meetings.


https://www.tcd.ie/bioengineering/biomaterials/hoeylab/

Location of lab: Trinity Biomedical Sciences Institute, 152-160 Pearse St.




Working hours:

Number of Weeks offered: 8 to 12 weeks

Hours per week: 35 hours per week

Earliest Start Date possible: 1st April 2019

Latest End Date possible: 30th August 2019


Proposer details:

Title: Prof

Name: Jane Stout


Website: https://www.tcd.ie/research/profiles/?profile=stoutj


Student required:


Knowledge and interest in environmental issues, entomology, pollination biology, agroecology.

Study level (3rd year, 4th year) Either

Any other requirements: Willingness to work in both field and lab, and to work with insects, including bees



(1) Type of Work: The student will work alongside PhD students collecting field data (from farmland sites outside Dublin, as well as possibly sites within Dublin), and processing it in the lab. This may include: field surveys of plants and insects, collection of bee nests and floral components (nectar and pollen), dissection of nests and identification of disease, pollen analysis, landscape mapping, data entry and basic analysis. The student will attend weekly research group meetings and gain an understanding of ongoing research and practical conservation of plants and pollinators. (2) The student will achieve an understanding of issues with regards to bee health and pollination ecology; some practical lab and field skills in entomology, botany and ecology; and transferable skills like teamwork, presentation skills, data handling. (3) The student will be supervised by a Post-doctoral researcher and PhD students on a day to day basis, and meet regularly with Prof Stout.


https://www.tcd.ie/Botany/research/groups/plantanimal.php

Location of lab: Watts Building, Trinity College Dublin

Working hours:

Number of Weeks offered: 8-10

Hours per week: Full time

Earliest Start Date possible: March 2019

Latest End Date possible: August 2019


Proposer details:

Title: Assistant Professor

Name: Robert Baker


Website: https://sites.google.com/site/bakeresearchgroup/home http://tcdlocalportal.tcd.ie/pls/public/staff.detail?p_unit=chemistry&p_name=bakerrj


Student required:


Chemistry and some laboratory work

Study level (3rd year, 4th year) 3rd or 4th year




(1) The student will be required to prepare some uranyl complexes that are relevant to environmental speciation of uranium and fully characterise them using spectroscopic techniques including vibrational photoluminescence and NMR spectroscopy. (2) The student should achieve a hands on approach to synthetic actinide chemistry and how to use and interpret spectroscopic data and how to work in a research group (e.g. communicating results to the group). The student will also appreciate the cultural differences between the US and Ireland, both in research environment and in every day life. (3) The student will be supervised by a 2nd year PhD student on a daily basis, but with significant input from the supervisor .


https://sites.google.com/site/bakeresearchgroup/home


http://tcdlocalportal.tcd.ie/pls/public/staff.detail?p_unit=chemistry&p_name=bakerrj


Location of lab: School of Chemistry, Trinity College

Working hours:


Hours per week: 35-40

Earliest Start Date possible: 29th April

Latest End Date possible: 1st September


Proposer details:

Title: Assistant Professor in Chemical Energy Systems

Name: Max García-Melchor


Website: www.ccem-group.com


N.A.

Student required:


Good knowledge of quantum chemistry, physical chemistry, and reaction mechanisms. Experience with Unix operating systems and programming languages is not mandatory but it is a plus.


Any other requirements: The candidate should also show ability to (1) adapt to the new environment and interact with the other members of the host research group, (2) express constructive criticism, (3) contribute to the discussions in the group meetings, and (4) collect pertinent scientific literature.



With a global production of 150 million tons in 2017, ammonia (NH3) is regarded as a key chemical building block for the synthesis of most nitrogen-containing compounds with a vast range of applications including pharmaceuticals, propellants, and particularly fertilizers. Indeed, 80% of the world production of NH3 is devoted to sustaining the food supply of almost half of the global population, and it is forecast to continue growing due to the demographic increase in developing countries. Despite this enormous demand, the industrial production of NH3 still relies on the high-energy intensive and environmentally unfriendly Haber-Bosch process invented over 100 years ago, which requires high temperatures (ca. 500 C) and pressures (ca. 200 atm), as well as considerable infrastructure. Furthermore, it consumes approximately 1-2% of the world’s energy and is responsible for the emission of over 500 million tons of CO2 into the atmosphere, accounting for 1.4% of total annual emissions of this greenhouse gas. This, together with the depleting natural gas reserves and geopolitical issues associated with their trade, urges the need for developing an alternative technology which minimizes resource and energy consumption. One promising solution is the electrochemical reduction of N2


http://www.ccem-group.com/

to NH3 (N2RR) under ambient conditions, whereby an aqueous electrolyte acts as the hydrogen source, reducing the cost of NH3 production and its carbon footprint. The project offered in this internship aims to use state-of-the-art density functional theory (DFT) methods to shed light into the reaction mechanism of the N2RR catalyzed by transition metal catalysts. This project is expected to provide a detailed understanding of the N2RR catalyzed by molecular catalysts, and it is envisioned to lead to the publication of a research article in a high-impact journal. At the end of the internship, the candidate will be capable of modelling reaction mechanisms of electrocatalytic processes involving transition metal complexes using Gaussian09; this includes geometry optimization of reaction intermediates and transition states, as well as some basic knowledge of computational electrocatalysis. In addition, the candidate will be trained to use the supercomputers based at the Trinity Centre for High Performance Computing (TCHPC) and the Irish Centre of High-End Computing (ICHEC). The project will be directly supervised by Prof. García-Melchor.


www.ccem-group.com

Location of lab: Lloyd Institute, Trinity College Dublin

Working hours:

Number of Weeks offered: Minimum 12

Hours per week: 35-40 (schedule is flexible)

Earliest Start Date possible: N.A.

Latest End Date possible: N.A.

http://www.ccem-group.com/


Proposer details:

Title: Generating, storing and releasing oxygen for biomedical applications

Name: Prof. Dr. Mathias O. Senge


Website: http://chemistry.tcd.ie/staff/people/mos/Home.html


Student required:


Fundamentals in chemistry, physics, biology

Study level (3rd year, 4th year) 3rd year and 4th year

Any other requirements: none



(1) Synthetic bioorganic chemistry, (2) work in an internationally leading, multicultural and multidisciplinary research group, development of research level laboratory skills, planning and executing target oriented syntheses, preparation of results for publication, publication (3) supervision by PI and Susan Callaghan (postgraduate student)



Location of lab: SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, 7th floor

Working hours: Number of Weeks offered: 12 Hours per week: 40 Earliest Start Date possible: Any time Latest End Date possible: Any time





Proposer details:

Title: Mr

Name: Conor O’Shea


Website:


Prof Dr Joeran Beel

Student required:


Programming (Python/Java/SQL preferred). Knowledge of recommender systems would be desirable.

Study level (3rd year, 4th year) No preference

Any other requirements: None



The student will work as part of a team developing the live recommender system http://mr-dlib.org/ within the ADAPT Centre. The student will be exposed to both front end and back end systems, and their work could include 1) implementation of recommendation algorithms 2) development of analytics dashboards 3) UX design. The final project will be discussed and adjusted based on the student’s preferences and skills. Through their work, the student will develop their programming skills, and gain experience working within an Agile environment. They will learn to develop and release within a live system and work with continuous integration tools. They will learn to maintain high code quality based on our team’s standards.


http://scss.tcd.ie/joeran.beel/ https://github.com/BeelGroup

Location of lab: Lloyd Institute/ADAPT Centre

Working hours:


http://mr-dlib.org/

http://mr-dlib.org/

http://scss.tcd.ie/joeran.beel/

https://github.com/BeelGroup


Hours per week: 35

Earliest Start Date possible: May 2019

Latest End Date possible: Oct 2019


Proposer details:

Title: Professor

Name: Stefan Weber


Website: htpp://www.scss.tcd.ie/~sweber


Student required:


The student should have experience in basic software development and communication protocols; knowledge of development frameworks such as Unity or Unreal would be of advantage but not required.

Study level (3rd year, 4th year) 3rd- and 4th-year student would be suitable




The project will focus on the development of a virtual-reality application for the teaching of the development of communication protocols. The intern will develop an application that will allow students a construct protocols in an immersive environment by assembling protocol headers out of building blocks on a workbench. The application will then allow the students to observe their protocols in a simulated environment and inspect the processing of their protocols in network elements. The outcome of the project should be a prototype implementation that allows users to understand the concept of the application. It should allow a user to assemble simplistic protocols on a workbench and evaluate these protocols through a limited number of network elements. Depending on the progress, the interaction with the protocols and the complexity and scale of the network elements can be increased to offer a more complete experience of the development of communication protocols. The learning outcome for the intern should include the experience of developing applications for virtual reality environments, a deeper understanding of communication protocols and their interaction with network elements, and the simulation of communication networks. The project is based on a constructivist learning approach for

teaching telecommunication protocols to undergraduate students. As part of the project, the intern will be exposed to learning approaches and their application in new technologies. The project will be supervised by the principal investigator on a daily basis.


htpp://www.scss.tcd.ie/~sweber

Location of lab: Lloyd Institute

Working hours:

Number of Weeks offered: 12

Hours per week: 35

Earliest Start Date possible: 15 Mar 2019

Latest End Date possible: 31 Aug 2019


Proposer details:

Title: Prof

Name: Werner Blau


Website: www.tcd.ie/Physics/Molecular_Electronics


Student required:


Basic electronics and solid state technology

Study level (3rd year, 4th year) Both okay




This is a laser laboratory based project where the student will acquire practical expertise in both nanomaterials preparation and nonlinear optical measurement techniques. The student will work closely with the group’s laser postdoc, Dr Gaozhong Wang.

Recently two-dimensional (2D) materials have attracted tremendous research interest and developed rapidly thanks to their novel electronic and optoelectronic properties. In comparison to the bulk limit of many layered structure semiconductors with indirect band gap, their monolayers exhibit excellent photonic performances such as strong photoluminescence due to the direct band gap. Some 2D semiconductors show unique broadband nonlinear optical response from visible to mid-infrared region. These outstanding preponderances open up a door for investigation on basic scientific problems and indicates the huge market potential application of photonics devices based on 2D semiconductors. This proposal is to systematically study the nonlinear performance of photonics devices based on two-dimensional semiconductors doped polymer composites.

Liquid-phase exfoliation technique will be utilized to prepared defect-free 2D semiconductors like ReS2 (Rhenium sulfide), ReSe2 (Rhenium selenide), SnSe2(Tin selenide), CdSe (Cadmium selenide) and PtSe2 (platinum selenide), and their monolayers are enrich by using size-selectable techniques. Transparent polymers are selected as a host

http://www.tcd.ie/Physics/Molecular_Electronics

material to wrap these 2D semiconductors using solution-casting, dip-coating and spin-coating methods.

I-scan and Z-scan techniques based on femtosecond lasers from visible to near-infrared wavelengths are utilized to study the nonlinear parameters such as absorption and refraction coefficients of the above 2D semiconductors. This aims to exploit the possibility of the new 2D semiconductors using as mode-lockers for ultrafast lasers.


www.tcd.ie/Physics/Molecular_Electronics

Location of lab: SNIAM and CRANN

Working hours:


Hours per week: 38

Earliest Start Date possible: negotiable

Latest End Date possible: negotiable

http://www.tcd.ie/Physics/Molecular_Electronics


Proposer details:

Title: Assistant Professor of Vibrations, Acoustics and Dynamics

Name: John Kennedy


Website: https://www.tcd.ie/research/profiles/?profile=jkenned5


Student required:


Knowledge of acoustics, vibrations, signal processing or additive manufacturing would be of great benefit to the research work.

Study level (3rd year, 4th year) 3rd/4th year

Any other requirements: NA



In recent years a new class of materials with highly unusual properties has been proposed known as a metamaterial. In simple terms these materials have behaviours that are unlike any traditional or natural material. This research placement will focus on the design and testing of metamaterial intended to have unusual dynamic properties. Considerable research has been conducted on materials intended to display unusual properties under static loads, such as a negative Poisson’s ratio, however little work has been done on the dynamic behaviour of such materials. These materials are often based on a lattice of unit cells which must be precision manufactured. The student will make use of the department’s world leading additive manufacturing facilities to 3D print a structural or dynamic metamaterial. They will then test this material under static and dynamic loads to determine the material properties. The design phase will include numerical modelling and optimisation of the metamaterial lattice. The experimental testing phase will include a parametric study of samples and investigation of the material properties, with a focus on the effects of anisotropy in the material lattice. The area of metamaterial research is rapidly moving and evolving. The student will have the opportunity to acquire valuable skills in structural and dynamic testing, signal processing,


https://www.tcd.ie/research/profiles/?profile=jkenned5

additive manufacturing and material inspection. Due to the cutting edge nature of the research a dedicated project student could reasonably be expected to produce a conference or journal level publication over the course of the summer. The student will be supervised by Dr. John Kennedy, Assistant Professor of Vibrations, Acoustic and Dynamics in the School of Engineering and the Principal Investigator and lead of the European funded AERIALIST project on acoustic metamaterials at TCD.


https://www.aerialist-project.eu/ http://www.tcd.ie/mecheng/research/fluids-acoustics-vibration/

Location of lab: Department of Mechanical and Manufacturing Engineering, Parsons Building Trinity College

Working hours:

Number of Weeks offered: 8-16 weeks

Hours per week: 35 hours


Latest End Date possible: 30th of September 2018

https://www.aerialist-project.eu/

http://www.tcd.ie/mecheng/research/fluids-acoustics-vibration/

http://www.tcd.ie/mecheng/research/fluids-acoustics-vibration/


Proposer details:


Name: Tim Persoons


Website: www.tcd.ie/mecheng/research/fluids-heat-transfer


n/a

Student required:


Strong background in fluid mechanics

Study level (3rd year, 4th year) Preferably 4th year, but 3rd year with experience is acceptable

Any other requirements: Aptitude for either experimental work (e.g., particle image velocimetry) and/or computational fluid dynamics work with commercial packages such as ANSYS Fluent)



(1) Description of the traineeship project Title: Active Flow Control for Drag Reduction of a Bluff Body in Cross-Flow Although tidal stream power generation is still in its infancy, the International Energy Agency (IEA) projects a significant investment in this technology in the coming decades [1]. However, some researchers are concerned about the current development of horizontal-axis turbines that sit on the sea floor, where the flow field is weakened and disturbed by the boundary layer [2]. For wind turbine farms, each machine creates a turbulent wake, which affects downstream turbine generators. Adverse wake interactions and flow-induced vibrations are concerns for the further expansion of wind turbine technology. For both cases (tidal and wind turbines), it could therefore be advantageous to have blade-by-blade control over the flow conditions. Devices such as synthetic jet actuators can be embedded within streamlined bodies to actively control the hydrodynamic boundary layers and prevent or delay separation.


http://www.tcd.ie/mecheng/research/fluids-heat-transfer

As a benchmark case, this project will consider a circular cylinder in cross-flow, with a rectangular slot orifice embedded in its surface from which a synthetic jet can be generated. An initial analysis will use transient computational fluid dynamics (CFD) simulations to study the effect of a synthetic jet emanating from the surface of a cylinder in cross-flow on the behaviour of the wake flow in general, and the instantaneous lift and drag coefficient in particular. Specific attention will go to determining the mechanisms of drag reduction, looking for correlations between the drag force and characteristics of the near wake (e.g., separation zone size, pressure coefficient profile and wake turbulence intensity) and far wake (e.g., far wake width, length, deflection and turbulence characteristics). Depending on the preferences and background of the student, the project can be involve experimental or computational work, or a combination of both. CFD simulations can be carried out, building on earlier work [3]. Additionally, validation experiments can be carried out using a water tunnel test facility equipped with a lift and drag force sensor, and capable of performing time-resolved particle image velocimetry (PIV) measurements. A strong background in fluid mechanics and aptitude for CFD and/or experimental work is required. [1] International Energy Agency (IEA), (http://www.iea.org/topics/oceanenergy/) [2] S.H. Salter, Proceedings of the 2012 International Conference on Ocean Energy, Dublin, Oct. 17, 2012 [3] P. McDonald, T. Persoons, Numerical characterisation of active drag and lift control for a circular cylinder in cross-flow, Applied Sciences, 7: 1166, 2017 (http://www.mdpi.com/2076-3417/7/11/1166) (2) Target outcomes The student will take part in this research project, with a goal of preparing a working paper, which could later be submitted to a conference or journal, depending on progress made during the traineeship project. The student will gain valuable research skills on active flow control and advanced fluid mechanics. For experimental work, the student will gain practical hands-on experience in using and modifying a water tunnel test facility and its associated instrumentation (e.g., lift and drag sensor, flow velocity measurements, ultrasonic flow meters, pumps and variable speed drives, DC motor speed controllers and pressure sensors). For computational work, the student will gain experience with modelling transient turbulent flows using a commercial CFD package such as Ansys Fluent. (3) Supervision The student will become a member of an active research team, working alongside several PhD students and postdoctoral researchers, and supported by the PI. An experimental officer and a team of design engineers are available in the Department to assist the student with practical aspects of lab work. Laser safety training will be provided by Trinity College if the student will be conducting lab work with laser-based instrumentation, such as particle image velocimetry. The PI will supervise the student and a senior PhD student will be assigned to the student on a mentorship basis.

Link to research group or www.tcd.ie/mecheng/research/fluids-heat-transfer

http://www.iea.org/topics/oceanenergy/

http://www.mdpi.com/2076-3417/7/11/1166

http://www.mdpi.com/2076-3417/7/11/1166

http://www.tcd.ie/mecheng/research/fluids-heat-transfer

supervisor webpage:

Location of lab: Dept. Mechanical & Manufacturing Engineering Fluids & Heat Transfer research group Parsons Building Trinity College Dublin 2, Ireland http://www.tcd.ie/mecheng/contact/

Working hours:


Hours per week: 40

Earliest Start Date possible: Late May

Latest End Date possible: End of September

http://www.tcd.ie/mecheng/contact/


Proposer details:

Title: Prof.

Name: Lewys Jones


Website: www.tcd.ie/crann/aml


N/A

Student required:


The project will require some basic physical science concepts including some knowledge around heat, melting/solidification, work, energy conversion. A background in one of Physics / Chemistry / Engineering / Material Science would be best. A student who has experience with thermodynamics would be ideal, with some small amount of calculations also being expected around the latent heat of fusion. Any experience with technical drawing, CAD, metal-working, gears or motors, plumbing or pumps would be a bonus but by no means essential for the candidate as all necessary training and mentoring will be provided.

Study level (3rd year, 4th year) 3rd or 4th both acceptable

Any other requirements: None



Project Type: The project offered is for a summer internship fully embedded in an active research group. The student will have a project of their own to take ownership of, and the project has been designed as a piece of preliminary work to assess the potential for a future larger project in the same area. Any results generated by the student will feed into real ongoing research work.


http://www.tcd.ie/crann/aml

Project Title: “Evaluation of Sustainable Phase-change Materials for Precise Thermal Regulation” Abstract: Phase-change materials (PCM) have been proposed as a sustainable means to store waste heat/cooling across the normal thermal cycle of day and night. These materials use the latent heat of fusion to store energy, totally reversibly and sustainably, for later use. Importantly, the temperature of the transformation (in either direction) is precisely defined by the substance’s melting point. At the same time, high-performance electron microscopes require a hyper-stable coolant-water supply. The stability of this water supply is a performance limiting factor now in some systems. This project seeks to evaluate, whether these PCMs can be used to construct a highly precise temperature regulator for other experimental uses in a modern research laboratory. Project Details: In this project we seek to propose, design, build, and test a phase-change material based temperature regulator for hyper-stable water supply. This is expected to comprise a pair of inter-penetrating heat-exchanger pipes placed in a sealed vessel with the PCM wax. The student will be responsible for performing an initial analysis of the required water-flow rates, thermal loading and calculating the mass of wax needed. The student will then propose the dimensions of the design and specification for a mechanical stirrer. Based on the calculations of the student a prototype will be constructed. The student will be responsible for proposing a testing methodology for the existing water-supply in the lab and then the new stabilised prototype. Skills Required & Training Offered This internship is intended as a taster experience of the working style of a PhD student. A basic knowledge of thermodynamics would be advantageous, although tuition can be provided. This project will emphasise independent working but in a fully supportive environment. Project management and time management will be done in professional research-project style, and the student will be expected to keep laboratory notes and produce typed summary reports as would be done by a PhD student. Again training and advice in scientific writing and note taking will be provided by the onsite team.


www.tcd.ie/crann/aml

Location of lab: Advanced Microscopy Laboratory, Unit 27/29 Trinity Enterprise Campus, Grand Canal Dock, Dublin 2

Working hours:

http://www.tcd.ie/crann/aml

Number of Weeks offered: Flexible, between 8 and 12, but can be negotiated. Previous students have done a 6+1+6 format with a weeks break in the middle for travelling.

Hours per week: Standard office hours so ≈37.5, but working hours may be flexible around experimental requirements.

Earliest Start Date possible: 13th May 2019



Proposer details:


Name: Marta Martins


Website: https://www.tcd.ie/Microbiology/research/


Student required:


Basic microbiology and immunology techniques

Study level (3rd year, 4th year) 4th year

Any other requirements: Dedicated and responsible


Brief job description: (please include (1) type of work, (2) what student should hope to achieve at end of the process, (3) who will supervise student on daily basis (post-doc etc.)) (1) Type of work. The student will work with human macrophages and Ca2+-channel modulators. This will involve the study of the role that these compounds have in the differentiation and metabolism of M1 vs. M2 human macrophages. The work conducted by the student will contribute to understand the intracellular effect of selected Ca2+-channel modulators on the activation of M1 and M2 macrophages and their subsequent impact on the killing of phagocytosed bacteria. This study in healthy macrophages using Ca2+-channel modulators will be important to generate basic knowledge about the metabolism of human macrophages when activated. This will be extremely important to help advance knowledge for the future efficacious therapy of macrophages infected by multidrug resistant bacteria. Additionally, the results from this study can impact on the treatment of multidrug resistant bacteria helping to overcome the increase of antibiotic resistance. (2) What the student should hope to achieve at end of the process. The student will be trained in basic microbiology and immunology techniques. The student will also acquire training in working in a level 2-biosafety laboratory and with more advanced techniques, such as flow cytometry. Additionally, the student will be challenged on a day-to-day basis regarding input to the experiments and analysis of the research results. The student will be integrated in the day routine of the research, including presenting his results at lab meetings that take place every week in the Martins’s Research Group in Antimicrobial Resistance and Host modulation. The student will also have the opportunity to attend lab meetings from

other research groups in the department of Microbiology that can contribute to deepen his/her knowledge in microbiology. At the end of the project the student will be given the opportunity to give a seminar in the department of Microbiology as part of this project which will test the student’s ability to prepare an oral presentation as well as to answer questions from his/her peers. (3) Supervision. The student will be supervised by the P.I. Marta Martins and closely supervised on a laboratory daily basis by one Post-Doc. Dr. Luiza Pieta (Martins’s lab).


https://www.tcd.ie/Microbiology/research/marta-martins/

Location of lab: Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin

Working hours:

Number of Weeks offered: 9 weeks

Hours per week: 30

Earliest Start Date possible: 10th June 2019 (flexible)

Latest End Date possible: 9th August 2019 (flexible)


Proposer details:

Title: Research Fellow

Name: Charlotte Callaghan, PhD


Website: https://www.researchgate.net/profile/Charlotte_Callaghan


Prof. Shane O’Mara

Student required:


No specific training necessary, this summer research internship is to offer an opportunity to an undergraduate student considering a career scientific research.

Study level (3rd year, 4th year) Minimum of 3rd year study

Any other requirements: Knowledge of molecular biology or neuroscience is desirable



Project Title: The Opioid System as the Brain’s Interface between Cognition and Motivation Major depressive disorder (MDD), which comprises a biologically heterogeneous diagnosis, affects approximately 350 million people worldwide at any point in time. Given the shortcomings of available antidepressants in terms of response and remission rates current research focusses on the generation of novel antidepressants with different mechanisms of action. There has been a renewed interest in opioid modulators for the treatment of MDD for patients that don’t respond well to standard therapy [1]. However, the role of individual opioid receptors in regulating mood and motivation remains unclear. The traineeship offered here will allow the student to take ownership of a small project which is part of a larger scale research programme investigating the role of opioid receptors in regulating mood and motivation [2]. Within this project, we explore the function of mu, kappa and delta opioid receptors in mediating mood and motivational behaviours in the interferon-alpha (INF-α)-induced depression model and the Wistar Kyoto (WKY) rat.

Specifically, the student project offered here will investigate the complex relationship between mu opioid receptors and IFN-α in the nucleus accumbens (NAc) prefrontal cortex and hippocampus, brain regions which are associated with mediation of motivation and cognitive behaviour. Further, the project will allow for investigation of synaptogenesis, synaptic connections between neurons, which is altered in depressive states [3]. We are developing novel immunhistological techniques to demonstrate receptor-ligand co-localisation and utilizing flow cytometry techniques to examine alterations in synaptogenesis in the NAc, prefrontal cortex and hippocampus. (1) The student will develop understanding of the scientific process and acquire basic and advanced laboratory techniques, including immunofluorescence and flow cytometry. (2) From the student’s perspective, they will take ownership of a piece of research, improving confidence in the lab and helping to develop future research ideas. They will learn to work as part of a research team, and improve on transferable skills including presentations and scientific writing. (3) Students will be supervised by Charlotte Callaghan, research fellow at TCD. References 1. Lutz, P.E. and B.L. Kieffer, Opioid receptors: distinct roles in mood disorders. Trends Neurosci,

2013. 36(3): p. 195-206. 2. Callaghan, C.K., et al., Antidepressant-like effects of 3-carboxamido seco-nalmefene (3CS-

nalmefene), a novel opioid receptor modulator, in a rat IFN-alpha-induced depression model. Brain Behav Immun, 2017.

3. Dale, E., B. Bang-Andersen, and C. Sanchez, Emerging mechanisms and treatments for depression beyond SSRIs and SNRIs. Biochem Pharmacol, 2015. 95(2): p. 81-97.


https://www.tcd.ie/Neuroscience/partners/PI%20Profiles/Shane_ OMara2.php

Location of lab: Trinity College Institute of Neuroscience

Working hours:


Hours per week: 35



https://www.tcd.ie/Neuroscience/partners/PI%20Profiles/Shane_


Proposer details:


Name: Kim McKelvey


Website: Mckelveylab.com


Student required:


Experience in nanoscience or physical chemistry or electrochemistry





Carbon dioxide reduction at single redox-active enzymes

Increasing greenhouse gas emissions, generated from the burning of fossils fuels, has resulted in the release of large amounts of carbon dioxide (CO2) into the atmosphere. This is causing global warming and climate change. However, it is possible to capture CO2 and reuse it to make useful liquid fuel products, thus reducing atmospheric CO2 concentrations at the same time as generating a commercially useful product. However, this process is challenging due to the kinetics of CO2 reduction and the thermodynamic stability of CO2. One novel approach is to use redox active enzymes, extracted from biological sources, to catalyse the electrochemical reduction of CO2. Redox active enzymes are highly efficient electrocatalysts that operated under mild conditions, and therefore offer a commercially viable path for reducing atmospheric CO2 concentrations.

In a typically electrocatalytic device for CO2 reduction millions of redox active enzymes are immobilized on an electrode surface where they work in unison to reduce CO2. However, each redox active enzyme operates as an individual electrocatalytic centre, reducing CO2 at


rates that depend on local environment surrounding the enzyme as well as the individual enzymes structure. We want to measure CO2 reduction at a single redox active enzyme, understanding how a single enzyme operates in isolation.

The students should expect to be working in a nanoelectrochemistry lab, making very precise electrochemical measurements on single enzymes. The student will use micrometre and nanometre scale electrodes to isolate the very small (pico or femto ampere) scale electrochemical currents generated from a single redox active enzyme. We will focus on carbonic anhydrase, a highly active CO2 reduction enzyme that converts CO2 to bicarbonate. We will use an electrochemical collision technique to isolate the electrochemical response from a single enzyme based on the collision of the enzyme with a small surface area electrode. The student will prepare enzyme samples (from commercially availed enzymes sources), undertake nanoscale electrochemical measurements, and analyse experimental electrochemical data.

Aim: Make the first measurement of the electrocatalytic CO2 reduction activity of a single carbonic anhydrase enzyme.

The student will be supervised by PhD student Marc Brunet Cabré, as well as Assistant Professor Kim McKelvey.


www.mckelveylab.com

Location of lab: B306, TBSI, Trinity College Dublin, Dublin, Ireland

Working hours:


Hours per week: 40

Earliest Start Date possible: 20th May

Latest End Date possible: 23rd August


Proposer details:

Title: Professor

Name: Maeve Caldwell


Website: https://www.tcd.ie/medicine/physiology/staff/


Student required:


It would be useful if the student could use a pipette and be familiar with aseptic technique for cell culture work.

Study level (3rd year, 4th year) Preferably 4th year




The student would be supervised by and work with a final year PhD student in my lab. S/he will learn how to culture stem cells, neurons and astrocytes. The student will learn how to carry out a number of techniques including quantitative PCR, immunocytochemistry and ELISA. S/he will also learn fluorescent microscopy and how that can be utilised to generate quantitative data. In addition, s/he will learn how to carry out statistical analysis on their data.


https://www.tcd.ie/medicine/physiology/

Location of lab: Trinity College Institute for Neuroscience

Working hours:


Hours per week: 35-40

Earliest Start Date possible: Early to mid June


Latest End Date possible: Mid August.


Proposer details:

Title: Professor

Name: Yvonne Buckley


Website: https://www.tcd.ie/Zoology/people/buckleyy


Student required:

Specify any previous training / experience the student should have: Basic understanding of ecology through relevant modules in degree programme: Biological sciences, Botany, Zoology, Environmental Sciences etc

Study level (3rd year, 4th year) 3rd and 4th year

Any other requirements: Willingness/ability to work outdoors and in potentially inclement weather



Student will be required to carry out laboratory and field-based data collection as part of international, multi-disciplinary, collaborative research projects (NutNet & Plantpopnet) seeking to understand the drivers of animal and plant population processes. The student will gain vital experience in fundamental ecology, field work in the floristically diverse Burren National Park and laboratory methods, species identification, data handling (collection, cleaning and coding) and some statistical analysis. Supervision will be provided by Prof. Yvonne Buckley and Alain Finn, Research Assistant in the Buckley Lab. Approx. 2-3 weeks of field work in Dublin, Cork and Clare are included in this internship.


https://www.tcd.ie/Zoology/research/groups/buckley/

Location of lab: Department of Zoology, TCD

Working hours:


Hours per week: 30

Earliest Start Date possible: 01/06/2019

Latest End Date possible: 30/09/2019

offer of training form summer 2019 - naughton fellowships · 2019-12-04 · offer of training form...

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