Literature DB >> 21341830

An improved coarse-grained model of solvation and the hydrophobic effect.

Patrick Varilly1, Amish J Patel, David Chandler.   

Abstract

We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.

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Year:  2011        PMID: 21341830      PMCID: PMC3077811          DOI: 10.1063/1.3532939

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


  49 in total

1.  Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding.

Authors:  D M Huang; D Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2000-07-18       Impact factor: 11.205

Review 2.  Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids.

Authors:  John D Weeks
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

3.  Self-consistent treatment of repulsive and attractive forces in nonuniform liquids.

Authors: 
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4.  Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions.

Authors:  Jianhan Chen; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2007-02-09       Impact factor: 15.419

5.  Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.

Authors:  Nikolaos K Voulgarakis; Jhih-Wei Chu
Journal:  J Chem Phys       Date:  2009-04-07       Impact factor: 3.488

6.  Quantifying water density fluctuations and compressibility of hydration shells of hydrophobic solutes and proteins.

Authors:  Sapna Sarupria; Shekhar Garde
Journal:  Phys Rev Lett       Date:  2009-07-17       Impact factor: 9.161

7.  Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations.

Authors:  Rahul Godawat; Sumanth N Jamadagni; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-25       Impact factor: 11.205

Review 8.  Parallel tempering: theory, applications, and new perspectives.

Authors:  David J Earl; Michael W Deem
Journal:  Phys Chem Chem Phys       Date:  2005-12-07       Impact factor: 3.676

9.  Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

Authors:  Manoj V Athawale; Gaurav Goel; Tuhin Ghosh; Thomas M Truskett; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

10.  Water dynamics and dewetting transitions in the small mechanosensitive channel MscS.

Authors:  Andriy Anishkin; Sergei Sukharev
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

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  15 in total

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Journal:  J Biol Chem       Date:  2017-08-04       Impact factor: 5.157

2.  Extended surfaces modulate hydrophobic interactions of neighboring solutes.

Authors:  Amish J Patel; Patrick Varilly; Sumanth N Jamadagni; Hari Acharya; Shekhar Garde; David Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-10       Impact factor: 11.205

3.  Pathways to dewetting in hydrophobic confinement.

Authors:  Richard C Remsing; Erte Xi; Srivathsan Vembanur; Sumit Sharma; Pablo G Debenedetti; Shekhar Garde; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-22       Impact factor: 11.205

4.  Understanding the role of hydrogen bonds in water dynamics and protein stability.

Authors:  Valentino Bianco; Svilen Iskrov; Giancarlo Franzese
Journal:  J Biol Phys       Date:  2011-10-01       Impact factor: 1.365

5.  Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions.

Authors:  Jeffrey K Weber; Vijay S Pande
Journal:  J Chem Phys       Date:  2013-02-28       Impact factor: 3.488

6.  Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.

Authors:  Boris Ni; Andrij Baumketner
Journal:  J Chem Phys       Date:  2013-02-14       Impact factor: 3.488

7.  The hydrophobic effect, and fluctuations: The long and the short of it.

Authors:  Erte Xi; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2016-04-14       Impact factor: 11.205

8.  Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.

Authors:  Shenggao Zhou; Hui Sun; Li-Tien Cheng; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2016-08-07       Impact factor: 3.488

9.  Spontaneous recovery of superhydrophobicity on nanotextured surfaces.

Authors:  Suruchi Prakash; Erte Xi; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-02       Impact factor: 11.205

10.  Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation.

Authors:  Suriyanarayanan Vaikuntanathan; Grant Rotskoff; Alexander Hudson; Phillip L Geissler
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-08       Impact factor: 11.205

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