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Challenges Across Large-Scale Biomolecular and Polymer Simulations

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Challenges Across Large-Scale Biomolecular and Polymer Simulations Challenges across Large-Scale Biomolecular and Polymer Simulations February 21, 2017 - February 24, 2017 CECAM-AT Ivan Coluzza University of Vienna, Austria Samuela Pasquali Paris Descartes University, France Barbara Capone University of Vienna, Austria Christoph Dellago University of Vienna, Austria Tamar Schlick New York University, USA 1 Description The goal of this workshop is to bring together scientists who study large scale molecular systems both in the biological world and those from the polymer science community. This workshop aims to bring broad-minded scientists interested in these challenges to discuss state-of-the-art approaches and issues with the goal of advancing structural biophysics and applied fields. By discussing various approaches and ways to integrate knowledge on multiple scales, we hope to build a community to advance this important field. The increase in computer power in tandem with algorithmic and force-field improvements are opening opportunities for modeling large biomolecular systems as never before. Yet, many challenges in modeling and simulations of such complex systems, in realistic environments, require innovations to make the necessary experimental connections and develop new theories and mechanistic details of the associated processes. The workshop that we propose will follow and build upon the first workshop organized in Telluride (June 14-18, 2015) by Tamar Schlick and Klaus Schulten entitled "Challenges in Simulating Large-Scale Biomolecular Complexes", by focusing on the following subjects: - Large scale simulations with respect to time and system size. We will include recent advances in atomistic force-fields and technological advances in algorithms and hardware that make possible simulations on the millisecond time scales for systems composed of millions of atoms, such as large solvated biomolecules. - Quantitative coarse-grained models going toward multi scale approaches. We will highlight the development of models beyond atomistic with different resolution tailored to the problem under investigation. Such approaches are essential for addressing problems that are still out of reach by atomistic simulations, even with the best hardware and algorithms. Moreover, some collective phenomena and statistical properties of the systems emerge more naturally from a representation of the systems focusing only on the relevant degrees of freedom, approximating specific details. - Bridging the gap between polymer physics and large biomolecular systems. We aim to unite two communities where complementary approaches are developed for the study of large molecular systems both on theory, simulation algorithms and experimental techniques. Several examples already show that the overlap between these communities can provide high impact results, including chromatin and RNA modeling. All these areas will be represented by scientists with either a theoretical or experimental background. In the latter case, we will aim to bring experimentalists with modeling experience as well. All the above-mentioned subjects are crucial for the further development of large scale molecular simulations. However, scientists from such distant disciplines rarely have the chance to come together and exchange their point of view on the common problem of large molecular simulations. With this workshop, we intend to create a long-lasting discussion table that in the future will be the base of an established common effort for the design of self-assembling systems both biological and artificial. The workshop will start the 21st of February at 14:30 and end the 24th at 12:45. The venue for the meeting is: https://goo.gl/maps/qJqQJtxgNXG2 Key references [1] T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung, and X. Xiao, Quarterly Reviews of Biophysics 44, 191 (2011). [2] J. H. Konnert and W. A. Hendrickson, Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography 36, 344 (1980). [3] A. Jack and M. Levitt, Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography 34, 931 (1978). [4] A. Warshel and M. Levitt, Journal of molecular biology 103, 227 (1976). [5] J. A. McCammon, B. R. Gelin, and M. Karplus, Nature 267, 585 (1977). [6] J. C. Phillips, R. Braun, W. Wang, J. 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