Multi-resolution simulations of intracellular processes

Paola obtained her PhD in Material Science from "Universita' Bicohcca". In 2006 she was awarded a fellowship from the Humboldt Foundation and joined the group of Prof. Mueller-Plathe in Darmstadt, where she extended her experties toward the multiscale simulations of macromolecules. In 2008 Paola was awarded a RCUK fellowship and joined the School of Chemical Engineering and Analytical Science in the University of Manchester where since 2014 she is a Senior Lecturer. Her research is focused on using and developing state-of-art simulation techniques to predict materials properties in bulk, solutions and at interfaces.

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Professor Zaida (Zan) Luthey-Schulten is a Lycan Professor of Chemistry and the Co-Director of the NSF Center for the Physics of Living Cells at the University of Illinois at Urbana-Champaign. Her research group specializes in the development of spatially resolved stochastic cell simulations methods that are distributed through the Lattice Microbe (LM) software. Being GPU-based, LM is able to simulate cellular processes at biologically relevant length (microns), time (hours), and concentration (nM to mM) scales. The most recent applications to whole cell simulations of a minimal bacterial cell and to the functions of a genetic switch in yeast will be reported.

Ben Leimkuhler is the Professor of Applied Mathematics at the University of Edinburgh.  His work is primarily in deterministic and stochastic algorithms for scientific computing and data science, including numerical analysis, model formulation and software development.  He is known for his previous contributions to efficient molecular and particle simulation.    He is a fellow of The Alan Turing Institute, the UK’s new data-science centre, which supports his work on machine learning procedures based on stochastic differential equations.

Professor Radek Erban is a Royal Society University Research Fellow, a Professor of Mathematics at the University of Oxford and a Fellow of Merton College, Oxford. He works on the development, analysis and application of mathematical and computational methods to a broad range of real-world systems, with a focus on problems in which stochastic effects and multiscale phenomena play a key role. The main application areas include molecular-based modelling of intracellular processes (for example, actin dynamics and calcium dynamics) and studying collective behaviour of cells, animals and robots. In recent years, he focused his attention on multi-resolution methods which would enable simulation of complex intracellular processes (which take place across the whole living cell) with fine resolution of molecular dynamics. He received a European Research Council Starting Grant in 2009 and a Philip Leverhulme Prize in 2010. In Oxford, he previously held junior research fellowships at Brasenose College (2011-2014), Somerville College (2008-2011) and Linacre College (2005-2008). In Cambridge, he was also a visiting fellow of Peterhouse (2016) and a recipient of the Simons Foundation Fellowship at the Isaac Newton Institute in 2016.

Professor Samuela Pasquali holds a PhD in statistical physics from New York University. She previously worked as junior faculty at Paris Diderot University for 8 years and in 2016 she became full professor at Paris Descartes University, in the school of Pharmacy. The focus of Professor Pasquali work is the study of nucleic acids, and RNA in particular, through modelling ans simulations. Professor Pasquali is also the main developer of the coarse-grained force field HiRE-RNA for the study of large conformational changes of RNA and DNA. Since her arrival at Paris Descartes, where she joined an experimental biophysical lab, Professor Pasquali has been working at integrating experimental data into the modelling process.

Raffaello Potestio graduated in Physics from the University of Rome “La Sapienza” in 2006, with a Master Thesis on Lattice Quantum Chromodynamics under the supervision of G. Martinelli. In the same year he enrolled in a PhD course in Statistical Physics at the International School for Advanced Studies (SISSA-ISAS) in Trieste. In 2010 he defended his PhD Thesis on Coarse-grained models of protein structure and interactions, supervised by C. Micheletti. In November 2010 he entered as postdoc the group of K. Kremer at the Max Planck Institute for Polymer Research in Mainz, where in August 2013 he became Project Leader of the Statistical Mechanics of BioMolecules group.
In 2017 Raffaello Potestio was awarded an ERC Starting Grant for the VARIAMOLS project on the development and application of variable resolution modeling strategies to the computational study of large biomolecules. The project will be carried out in the Physics Department of the University of Trento, Italy, where he is enrolled as tenure track assistant professor.
Raffaello Potestio’s main research interest since during the PhD has been the development and application of coarse-grained models and coarse-graining strategies for soft matter, in particular biologically relevant systems. The two-sided, complementary goals of this approach are to understand the most fundamental and/or universal features of a system and, at the same time, to improve the computational efficiency of a simulation. He also work on the study of topologically self-entangled biopolymers, namely knotted proteins and DNA. To this end, he makes use of standard and ad hoc coarse-grained models developed specifically for the systems under examination.

Dr Vasileios Vavourakis is an Assistant Professor at the Department of Mechanical & Manufacturing Engineering, University of Cyprus (UCY), and an Honorary Senior Lecturer at the Department of Medical Physics & Biomedical Engineering, University College London (UCL). Dr Vavourakis previously worked as a Senior Research Associate and a Marie Skłodowska-Curie Fellow at UCL's Centre for Medical Image Computing, a Visiting Lecturer and Research Associate at UCY's Polytechnic School, and as a post-doctoral fellow at the Foundation for Research and Technology - Hellas. Dr Vavourakis holds a PhD in Mechanical Engineering and a Diploma in Aeronautics, awarded by the University of Patras. He is also a member of the International Association of Computational Mechanics, the UK Association for Computational Mechanics, the Technical Chamber of Greece, and the Marie Curie Alumni Association.

Professor Garegin Papoian is the Monroe Martin Professor at UMD, serving also as the Director of the Chemical Physics Graduate Program. He uses advanced computational methods to study biological processes at multiple scales, from protein functional dynamics and chromatin folding to cell-level processes, such as cell motility and other related mechanobiological phenomena. In the latter area, Professor Papoian has been developing novel analytical and simulational approaches for understanding the fundamental principles governing self-assembly and dynamics of cellular cytoskeletons comprised of actin filaments, microtubules and various other associated proteins. These complex, far-from-equilibrium mechano-chemical systems exemplify biological active matter, which is still poorly understood. Papoian group has recently developed a pioneering cytoskeletal simulation force field and associated software, MEDYAN (http://medyan.org/), which combines stochastic reaction-diffusion treatment of cellular biochemical processes with polymer physics of cytoskeletal filament network growth, emphasizing the coupling between chemistry and mechanics. The Papoian laboratory used insights gained from extensive MEDYAN simulations, to develop a general theory of elementary force dipoles that comprise contractile acto-myosin networks.

Christine Peter has studied chemistry and mathematics at the University of Freiburg, Germany. In 2003 she obtained her PhD at the ETH Zurich working on molecular dynamics simulation of biomolecular systems. Subsequently worked at the National Institutes of Health (Bethesda, USA) and the Max Planck Institute for Polymer Research (Mainz, Germany). Since 2013, she is a professor for theoretical and computational chemistry at the University of Konstanz, Germany. The group studies biological systems and biomaterials, addressing questions related to peptide and protein folding and aggregation, mineral nucleation or interactions at (bio)polymer/mineral interfaces. The research focus Iies on the development and application of hierarchical simulation approaches that systematically link models at several levels of resolution.