Literature DB >> 16912812

Calculation of the Entropy of Lattice Polymer Models from Monte Carlo Trajectories.

Ronald P White1, Jason Funt, Hagai Meirovitch.   

Abstract

While lattice models are used extensively for macromolecules (synthetic polymers proteins, etc), calculation of the absolute entropy, S, and the free energy, F, from a given Monte Carlo (MC) trajectory is not straightforward. Recently we have developed the hypothetical scanning MC (HSMC) method for calculating S and F of fluids. Here we extend HSMC to self-avoiding walks on a square lattice and discuss its wide applicability to complex polymer lattice models. HSMC is independent of existing techniques and thus constitutes an independent research tool; it provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation.

Entities:  

Year:  2005        PMID: 16912812      PMCID: PMC1540743          DOI: 10.1016/j.cplett.2005.06.002

Source DB:  PubMed          Journal:  Chem Phys Lett        ISSN: 0009-2614            Impact factor:   2.328


  9 in total

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Journal:  Int J Pept Protein Res       Date:  1975

2.  Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.

Authors:  Yang Zhang; Jeffrey Skolnick
Journal:  Biophys J       Date:  2004-10       Impact factor: 4.033

Review 3.  Free energy via molecular simulation: applications to chemical and biomolecular systems.

Authors:  D L Beveridge; F M DiCapua
Journal:  Annu Rev Biophys Biophys Chem       Date:  1989

4.  Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2004-12-08       Impact factor: 3.488

5.  Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides.

Authors:  Srinath Cheluvaraja; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2005-02-01       Impact factor: 3.488

6.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

Authors:  Y Duan; P A Kollman
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728

7.  Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-12

Review 8.  Computer simulation of the free energy of peptides with the local states method: analogues of gonadotropin releasing hormone in the random coil and stable states.

Authors:  H Meirovitch; S C Koerber; J E Rivier; A T Hagler
Journal:  Biopolymers       Date:  1994-07       Impact factor: 2.505

9.  Nanoscale self-assembly of multiblock copolymer chains into rods.

Authors:  Yves Termonia
Journal:  Biomacromolecules       Date:  2004 Nov-Dec       Impact factor: 6.988

  9 in total
  5 in total

1.  Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2005-12-01       Impact factor: 3.488

2.  Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force.

Authors:  Srinath Cheluvaraja; Hagai Meirovitch
Journal:  J Phys Chem B       Date:  2005-11-24       Impact factor: 2.991

3.  Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2006-05-28       Impact factor: 3.488

4.  Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.

Authors:  Hagai Meirovitch
Journal:  J Mol Recognit       Date:  2010 Mar-Apr       Impact factor: 2.137

5.  Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing.

Authors:  Wade F Zeno; Upayan Baul; Wilton T Snead; Andre C M DeGroot; Liping Wang; Eileen M Lafer; D Thirumalai; Jeanne C Stachowiak
Journal:  Nat Commun       Date:  2018-10-08       Impact factor: 14.919

  5 in total

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