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Position: PhD studentship in Theoretical Biophysics
Institution: University College London
Department: UCL Physics and Astronomy
Location: London, United Kingdom
Duties: The successful candidate will gain expertise in theoretical and computational modeling in biophysics as well as acquire a broad knowledge of soft matter physics, cell biology and statistical mechanics. You will be trained as a multidisciplinary scientist working collaboratively as part of a research team. The goal of our research is to understand the mechanisms by which living cells, tissues, and organisms sense and transmit physical forces, change shapes, grow, self-replicate and adapt to environmental changes. We integrate methods from statistical physics, soft matter physics and systems biology to develop quantitative theoretical models across different spatiotemporal scales and across different levels of biological organisation
Requirements: The successful applicant should have (or expect to achieve) at least the equivalent of a UK upper second class MSci or Master’s degree (or equivalent) in Physics, Biophysics, Applied Mathematics, Chemistry or a relevant subject. Candidates should have a strong background in physics, mathematics, experience with programming, and knowledge of biological systems. Candidates should also have excellent written and verbal communication. Previous exposure to research at the interface of physics and biology is desirable
   
Text: PhD studentship in Theoretical Biophysics, - Ref:1774451 Click here to go back to search results Apply Now UCL Department / Division UCL Physics and Astronomy Location of position London Duration of Studentship 4 years Stipend ?17,050 per annum Vacancy Information A 4-year fully funded PhD position in Theoretical Biophysics is available from January 2019 to work under the supervision of Dr. Shiladitya Banerjee. Studentship Description We are pleased to invite applications for a fully funded 4-year PhD studentship in the area of Theoretical and Computational Biophysics at the University College London (UCL). The studentship will be based at the Department of Physics and Astronomy and the Institute for the Physics of Living Systems (IPLS) at UCL. IPLS is a cross-faculty institute with a mission to promote interdisciplinary research at the interface of physics and biology for a fundamental understanding of the complex behaviors of living systems. The proposed project will be carried out in the research group of Dr. Shiladitya Banerjee. The research group uses techniques and methods from theoretical physics and applied mathematics to develop quantitative models of biological processes essential for regulating cell physiology and development. We seek to recruit a highly motivated and bright PhD student who will contribute towards the understanding of how unicellular bacteria can adapt their growth and morphologies to proliferate in the presence of antibiotics. To this end, we will integrate theory and experimental data analysis to understand how changes in cell morphologies regulate their fitness for proliferation under perturbations that challenge cell survival. In particular, our model will combine techniques in soft matter physics with the knowledge of cell biology, to predict how bacterial cells adapt their growth and morphologies to resist antibiotics. The project is funded by the Royal Society. What scientific questions will you investigate? Living matter operates far from equilibrium, constantly consuming and dissipating energy to perform their defining tasks of growth, self-replication, and adaptation to diverse environmental conditions. Over the past two decades, general physical principles governing the dynamics of non-equilibrium systems have emerged. How these principles apply to the regulation of vital biological processes remains poorly understood. The goal of the proposed research is to develop a simple and general biophysical model for uncovering the mechanisms underlying out-of-equilibrium adaptation of living cells to perturbations that challenge their survival. To this end, we will use unicellular bacteria as our model systems. Bacterial growth and shapes are determined by the peptidoglycan cell wall, a rigid protein-based structure that can withstand high amounts of osmotic pressure while driving cell elongation. We seek to investigate how alterations in cell wall mechanical properties and resultant shape changes determine cellular fitness for proliferation in diverse environments. This is important for understanding how bacterial cells can adapt their mechanical and biochemical properties to proliferate in the presence of antibiotics that target its protein biosynthesis. To this end, we propose a novel framework in which theoretical modelling and experimental data are integrated to dissect how the coupling between cell geometry, growth, and division dynamics promote adaptive response to applied perturbations in the growth media. Our theoretical framework for predicting cellular growth and shape regulation will combine concepts and tools from soft matter physics, statistical mechanics and bacterial cell biology, to develop a physical model for growing cell wall structures that is coupled to cell ?decision-making? rules for division and size control. We will use this model to study how single bacterial cells harness the feedback between cell shape and growth rate to adapt to environmental changes. In particular, we will investigate the mechanisms of fitness recovery in rod-shaped bacteria in the presence antibiotics that inhibit ribosomes and cell wall biosynthesis. We will compare our model predictions against high-throughput experimental measurements of bacterial cell shape and growth on varying growth media (including antibiotics). This integrated approach provides a framework for uncovering the mechanisms by which cells maintains their fitness in varying environments, and to determine the energy cost of feedback control mechanisms that elicit adaptive cellular response. The theoretical framework we propose can be extended to predict a broad range of cellular response to applied stress, without detailed knowledge of the underlying biochemical pathways. What training will you receive? The successful candidate will gain expertise in theoretical and computational modeling in biophysics as well as acquire a broad knowledge of soft matter physics, cell biology and statistical mechanics. You will be trained as a multidisciplinary scientist working collaboratively as part of a research team. About our lab The goal of our research is to understand the mechanisms by which living cells, tissues, and organisms sense and transmit physical forces, change shapes, grow, self-replicate and adapt to environmental changes. We integrate methods from statistical physics, soft matter physics and systems biology to develop quantitative theoretical models across different spatiotemporal scales and across different levels of biological organisation. Our approach is highly cross-disciplinary and is performed in close collaboration with experimental laboratories around the world. See lab webpage for details: http://shiladitya-banerjee.com Selected Recent Publications - Seara, D.S., et al (2018). Entropy Production Rate is Maximized in Non-Contractile Actomyosin. Nature Communications. arXiv:1840.04232. - Schaumann, E.N., Staddon, M.F., Gardel, M.L., Banerjee, S. (2018). Force localization modes in dynamic epithelial colonies. Molecular Biology of the Cell, mbc.E18050336. 
 - Freedman, S.L., Banerjee, S., Hocky, G.M., Dinner, A.R. (2017). A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks.. Biophysical Journal, 113 (2), 448-460. 
 - Banerjee, S., et al (2017). Biphasic growth dynamics control cell division in Caulobacter crescentus. Nature Microbiology, 2:17116, 1-6. - Linsmeier, I., et al (2016). Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility. Nature Communications, 7:12615, 1-6. 
 - Banerjee, S., Scherer, N.F., Dinner, A.R. (2016). Shape dynamics of growing cell walls. Soft Matter, 12 (14), 3442-3450. Person Specification The successful applicant should have (or expect to achieve) at least the equivalent of a UK upper second class MSci or Master?s degree (or equivalent) in Physics, Biophysics, Applied Mathematics, Chemistry or a relevant subject. Candidates should have a strong background in physics, mathematics, experience with programming, and knowledge of biological systems. Candidates should also have excellent written and verbal communication. Previous exposure to research at the interface of physics and biology is desirable. Eligibility Please refer to the following website for eligibility criteria: https://www.ucl.ac.uk/physics-astronomy/study/phd The earliest start date is 7 January 2019. The studentship will cover all university fees and includes funds for maintenance at the standard UK rate and for participation in international conferences and workshops. If you have any queries about this studentship, please contact Dr. Shiladitya Banerjee ( shiladitya.banerjee@ucl.ac.uk ) Please submit applications in the following format: ?A CV, including full details of all University course grades to date. ?Contact details for two academic or professional referees (at least one academic). ?A personal statement (750 words maximum) outlining (i) your academic excellence, (ii) suitability for the project with reference to the criteria in the person specification, (iii) what you hope to achieve from the PhD and (iv) your research experience to-date. Please include a contact telephone number and an email address where you can be easily reached. References will be taken up for all short-listed candidates. Please send electronic applications to shiladitya.banerjee@ucl.ac.uk Only shortlisted candidates will be contacted. Contact name Shiladitya Banerjee Contact details shiladitya.banerjee@ucl.ac.uk UCL Taking Action for Equality Closing Date 20 Dec 2018 Latest time for the submission of applications 23:59 Interview date tbc Apply Now
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