Literature DB >> 23927268

Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods.

Lili Gai1, Thomas Vogel, Katie A Maerzke, Christopher R Iacovella, David P Landau, Peter T Cummings, Clare McCabe.   

Abstract

Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ε) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results.

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Year:  2013        PMID: 23927268      PMCID: PMC4108647          DOI: 10.1063/1.4816520

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  29 in total

1.  Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.

Authors:  F Wang; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-10-17

2.  Replica exchange statistical temperature molecular dynamics algorithm.

Authors:  Jaegil Kim; John E Straub; Tom Keyes
Journal:  J Phys Chem B       Date:  2012-05-15       Impact factor: 2.991

3.  Collapse transitions in a flexible homopolymer chain: application of the Wang-Landau algorithm.

Authors:  D T Seaton; T Wüst; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-01-05

4.  Understanding the phase behavior of coarse-grained model lipid bilayers through computational calorimetry.

Authors:  Jocelyn M Rodgers; Jesper Sørensen; Frédérick J-M de Meyer; Birgit Schiøtt; Berend Smit
Journal:  J Phys Chem B       Date:  2012-01-25       Impact factor: 2.991

5.  Wang-Landau algorithm: a theoretical analysis of the saturation of the error.

Authors:  R E Belardinelli; V D Pereyra
Journal:  J Chem Phys       Date:  2007-11-14       Impact factor: 3.488

6.  Thermodynamics of peptide aggregation processes: an analysis from perspectives of three statistical ensembles.

Authors:  Christoph Junghans; Michael Bachmann; Wolfhard Janke
Journal:  J Chem Phys       Date:  2008-02-28       Impact factor: 3.488

7.  The MARTINI force field: coarse grained model for biomolecular simulations.

Authors:  Siewert J Marrink; H Jelger Risselada; Serge Yefimov; D Peter Tieleman; Alex H de Vries
Journal:  J Phys Chem B       Date:  2007-06-15       Impact factor: 2.991

8.  Generic, hierarchical framework for massively parallel Wang-Landau sampling.

Authors:  Thomas Vogel; Ying Wai Li; Thomas Wüst; David P Landau
Journal:  Phys Rev Lett       Date:  2013-05-22       Impact factor: 9.161

9.  Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling.

Authors:  Maarten G Wolf; Jaap A Jongejan; Jon D Laman; Simon W de Leeuw
Journal:  J Phys Chem B       Date:  2008-10-08       Impact factor: 2.991

10.  Scalable replica-exchange framework for Wang-Landau sampling.

Authors:  Thomas Vogel; Ying Wai Li; Thomas Wüst; David P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2014-08-05
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  1 in total

1.  Thermodynamic and conformational insights into the phase transition of a single flexible homopolymer chain using replica exchange Monte Carlo method.

Authors:  Lei Wang; Ningning Li; Shiyan Xiao; Haojun Liang
Journal:  J Mol Model       Date:  2014-06-25       Impact factor: 1.810

  1 in total

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