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.

Sergio Pantano graduated in Physics from the University of San Luis, Argentina and received his Masters and PhD from the Scuola Internazionale Superiore di Studi Avanzati (SISSA, Italy) in 2001, where he became interested in computational biology. In 2004 he was appointed as independent researcher at the Venetian Institute for Molecular Medicine (Padua, Italy) and as PI at the Institut Pasteur de Montevideo in 2007, where he currently leads the group of Biomolecular Simulations. Dr Pantano has applied a variety of structural bioinformatics and simulation methods to the study of molecular systems of biomedical relevance. His group pioneered the development of coarse-grained models for molecular dynamics simulations of biological systems in South America and has created the SIRAH force field for coarse grained and multiscale simulations. His main interests are currently the rational design of biosensors and dynamics of virus-like particles.

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.

Carla Molteni is Professor of Physics at King's College London. She is an expert in atomistic simulations applied to materials and biological systems, and works at the interface of physics with chemistry, materials science and biology. Before joining King's, she held an EPSRC Advanced Research Fellow at the Cavendish Laboratory, University of Cambridge, and a College Research Fellowship at New Hall (now Murray Edwards College). She was previously a postdoctoral researcher at the Max Planck Institut fuer Festkoerperforschung in Stuttgart (Germany) and a EU Human Capital & Mobility Postdoctoral Fellow at the Cavendish Laboratory. She obtained her Laurea and PhD in Physics at the University of Milan (Italy).

Paolo Carloni obtained his PhD in Chemistry (majoring in computational biophysics) at the University of Florence in 1993 supervised by Lucia Banci, Pier Luigi Orioli (University of Florence, Italy) and Michele Parrinello (then IBM Zurich Research Laboratory, Switzerland). Currently, he is a full professor in Theoretical Biophysics at RWTH Aachen and Director of the 'Computational Biomedicine' Institute (IAS-5 / INM-9) and co-director of INM-11 at Forschungszentrum Jülich. His research focuses on molecular simulations and bioinformatics approaches to molecular biophysics, molecular medicine and structural genomics. He has published more than 240 papers, one edited book. He has given more than one hundred fifty seminars and colloquia delivered throughout the world at the major universities, research and industrial laboratories and professional meetings. In addition, he has organized a dozen of international conferences. Paolo Carloni is a member of the Editorial Advisory Board for the Journals: Proteins: Structure, Function, Bioinformatics and PlosONE. Moreover, he is a member of the PRACE Scientific Steering Committee and the JARA-HPC (Jülich Aachen Research Alliance focusing on high performance computing) initiative. Over the years his research has been funded by several grants provided by the Regione Friuli Venezia Giulia, the Italian University Ministry, the Italian Institute of Technology, the HFSP, pharmaceutical and food companies (Illy, Glaxo, Layline Genomics), the National Institute for the Physics of Matter, the German Science Foundation DFG, the German Federal Ministry for Education and Research BMBF and the European Commission.

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.

Dr Julija Zavadlav is a Postdoctoral Associate at ETH, Zürich, Switzerland. Dr Zavadlav obtained her PhD in Physics from the University of Ljubljana, Slovenia in 2015. While she was a PhD student (2011-2015) she was employed by the National Institute of Chemistry, Ljubljana, Slovenia. Since 2016 Jilija has been a part of the Computational Science & Engineering group at ETH, Zürich, Switzerland. In 2017 she has received the ETH Postdoctoral Fellowship. Her research interest is focused on multiscale simulation methods, Bayesian Uncertainty Quantification, and molecular modelling of soft and biological matter.

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.

After a number of postdoctoral positions at various Universities in the UK and USA, Dr Nerukh worked as a senior research associate at Department of Chemistry, Cambridge University, UK, before accepting permanent position at Aston University as a lecturer. Dr Nerukh work has led to the development of an original numerical method for Bohmian quantum dynamics and fundamentally new approaches for the complex dynamics of classical molecular systems that applies state of the art mathematical theory of complexity of dynamical systems. His most recent research includes the development of multiscale hybrid Molecular Dynamics / Hydrodynamics framework for modelling large biomolecular systems at several spatial and temporal scales simultaneously. Such systems include all-atom models of entire viruses in solution. He has published over 50 papers and is PI or co-Pi on ten major grants.

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Dr Sarah A Harris obtained her first degree in Physics. She obtained a PhD from the Nottingham School of Pharmacy where she modelled drug-DNA interactions with Molecular Dynamics Simulations, and then moved to the Condensed Matter and Materials Physics group at University College London to work on Classical Nucleation Theory for her postdoctoral research project. As a lecturer in Biological Physics in Physics and Astronomy at Leeds, she now uses high performance supercomputing to model the physical properties of biological macromolecules, and to understand how these impart biological function. Current projects use atomistic computational models of proteins and nucleic acids to understand how dynamics and flexibility affect molecular recognition and how the shape and information content of DNA is influenced by supercoiling and packing within complex topologies. To understand the role of super-macromolecular organisation at the mesoscale, she is working with a multidisciplinary team or researchers from Mathematics, Physics and Biology at Leeds to construct a novel continuum mechanics model of proteins, known as Fluctuating Finite Element Analysis. She sits on the UK-wide committee for the Computational Collaborative Project for Biomolecular Simulation (CCPBioSim) and teaches undergraduate courses in Statistical Mechanics and Classical Thermodynamics.