title: SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.
abstract: Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the Cα -based protein model using the Truncated Expansion approximation (TEA) to the Rotne-Prager-Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (10(2) -10(5) residues), including biological particles (filaments, virus shells). Comparison of numerical accuracy of the TEA versus exact description of HI reveals similar results for the kinetics and thermodynamics of protein unfolding. The HI speed up and couple biomolecular transitions through cross-communication among protein domains, which result in more collective displacements of structure elements governed by more deterministic (less variable) dynamics. The force-extension/deformation spectra from nanomanipulations in silico exhibit sharper force signals that match well the experimental profiles. Hence, biomolecular simulations without HI overestimate the role of tension/stress fluctuations. Our findings establish the importance of incorporating implicit water-mediated many-body effects into theoretical modeling of dynamic processes involving biomolecules. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemistry, One University ave, University of Massachusetts, Lowell, Massachusetts, 01854.|9 Institutskiy per, Department of Control and Applied Mathematics Moscow Institute of Physics and Technology, Moscow region, 141700, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Alekseenko
authors.affiliation: Department of Chemistry, One University ave, University of Massachusetts, Lowell, Massachusetts, 01854.|9 Institutskiy per, Department of Control and Applied Mathematics Moscow Institute of Physics and Technology, Moscow region, 141700, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Kononova
authors.affiliation: 1 Universitetskaya st, Department of Information Systems Innopolis University, Innopolis, Tatarstan, 420500, Russia.|19/18, 2-nd Brestskaya st, Department of Applied Mathematics Institute of Computer Aided Design of the Russian Academy of Sciences, Moscow, 123056, Russia.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Kholodov
authors.affiliation: Department of Chemistry, One University ave, University of Massachusetts, Lowell, Massachusetts, 01854.
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Marx
authors.affiliation: Department of Chemistry, One University ave, University of Massachusetts, Lowell, Massachusetts, 01854.|9 Institutskiy per, Department of Control and Applied Mathematics Moscow Institute of Physics and Technology, Moscow region, 141700, Russia.
authors.forename: Valeri
authors.initials: V
authors.lastname: Barsegov
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D057446:Hydrodynamics; D008958:Models, Molecular; D017510:Protein Folding; D000072416:Protein Structural Elements; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012997:Solvents
keywords: GPU computing; Langevin simulations; Rotne-Prager-Yamakawa tensor; coarse-grained modeling; hydrodynamic interactions; nanomanipulation in silico