ArticleJournal of computational chemistry2016
SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Structural Mechanisms of Forced Unfolding of Double-Stranded Fibrin Oligomers.The journal of physical chemistry. B · 2025Article
- Improving the potency prediction for chemically modified siRNAs through insights from molecular modeling of individual sequence positions.Molecular therapy. Nucleic acids · 2025Article
- Mechanical fatigue testing in silico: Dynamic evolution of material properties of nanoscale biological particles.Acta biomaterialia · 2023Article
- Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue.Computational and structural biotechnology journal · 2022Article
- Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves.Acta biomaterialia · 2021Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
- Atomic Structural Models of Fibrin Oligomers.Structure (London, England : 1993) · 2018Article
- TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.Journal of computational chemistry · 2016Article
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5 authors.
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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.
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