Literature DB >> 27698046

Multiscale simulation of molecular processes in cellular environments.

Mara Chiricotto1, Fabio Sterpone1, Philippe Derreumaux1, Simone Melchionna2.   

Abstract

We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
© 2016 The Author(s).

Keywords:  cellular compartments; lattice Boltzmann; molecular dynamics; multiscale

Mesh:

Substances:

Year:  2016        PMID: 27698046      PMCID: PMC5052736          DOI: 10.1098/rsta.2016.0225

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  45 in total

1.  Computer simulations aimed at structure prediction of supersecondary motifs in proteins.

Authors:  F Forcellino; P Derreumaux
Journal:  Proteins       Date:  2001-11-01

2.  Sampling the self-assembly pathways of KFFE hexamers.

Authors:  Guanghong Wei; Normand Mousseau; Philippe Derreumaux
Journal:  Biophys J       Date:  2004-09-17       Impact factor: 4.033

3.  Anomalous diffusion of proteins due to molecular crowding.

Authors:  Daniel S Banks; Cécile Fradin
Journal:  Biophys J       Date:  2005-08-19       Impact factor: 4.033

4.  Crowding and confinement effects on protein diffusion in vivo.

Authors:  Michael C Konopka; Irina A Shkel; Scott Cayley; M Thomas Record; James C Weisshaar
Journal:  J Bacteriol       Date:  2006-09       Impact factor: 3.490

Review 5.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution.

Authors:  Matej Praprotnik; Luigi Delle Site; Kurt Kremer
Journal:  Annu Rev Phys Chem       Date:  2008       Impact factor: 12.703

Review 6.  Branched chain mechanism of polymerization and ultrastructure of prion protein amyloid fibrils.

Authors:  Ilia V Baskakov
Journal:  FEBS J       Date:  2007-07-06       Impact factor: 5.542

7.  Fiber-dependent amyloid formation as catalysis of an existing reaction pathway.

Authors:  Amy M Ruschak; Andrew D Miranker
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-17       Impact factor: 11.205

8.  Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species.

Authors:  Wei Song; Guanghong Wei; Normand Mousseau; Philippe Derreumaux
Journal:  J Phys Chem B       Date:  2008-03-15       Impact factor: 2.991

Review 9.  Crowding effects on diffusion in solutions and cells.

Authors:  James A Dix; A S Verkman
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

Review 10.  Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences.

Authors:  Huan-Xiang Zhou; Germán Rivas; Allen P Minton
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

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  6 in total

1.  Bridging the gaps at the physics-chemistry-biology interface.

Authors:  P V Coveney; J P Boon; S Succi
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-11-13       Impact factor: 4.226

2.  Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Authors:  Rommie E Amaro; Adrian J Mulholland
Journal:  Nat Rev Chem       Date:  2018-04-11       Impact factor: 34.035

3.  Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.

Authors:  Phuong Hoang Nguyen; Pierre Tufféry; Philippe Derreumaux
Journal:  Methods Mol Biol       Date:  2022

4.  Intradimer forces and their implication for conformations of von Willebrand factor multimers.

Authors:  Aleksey V Belyaev
Journal:  Biophys J       Date:  2021-01-30       Impact factor: 4.033

5.  Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.

Authors:  Michael Feig; Isseki Yu; Po-Hung Wang; Grzegorz Nawrocki; Yuji Sugita
Journal:  J Phys Chem B       Date:  2017-07-12       Impact factor: 2.991

6.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.

Authors:  Astrid F Brandner; Stepan Timr; Simone Melchionna; Philippe Derreumaux; Marc Baaden; Fabio Sterpone
Journal:  Sci Rep       Date:  2019-11-11       Impact factor: 4.379

  6 in total

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