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Title: Systematic hierarchical coarse-graining with the inverse Monte Carlo method

We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730–3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [1] ;  [4]
  1. Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden)
  2. (Belgium)
  3. UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium)
  4. (Sweden)
Publication Date:
OSTI Identifier:
22493369
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 24; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ABUNDANCE; COMPUTER CODES; CONCENTRATION RATIO; DEGREES OF FREEDOM; DNA; FLUCTUATIONS; GRAIN SIZE; MOLECULAR DYNAMICS METHOD; MONTE CARLO METHOD; POTENTIALS; PROTEINS; SALTS; SPATIAL DISTRIBUTION