Stochastic levelset variational implicitsolvent approach to solutesolvent interfacial fluctuations
Abstract
Recent years have seen the initial success of a variational implicitsolvent model (VISM), implemented with a robust levelset method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The levelset minimization of the VISM solvation freeenergy functional of all possible solutesolvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solutesolvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic levelset method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solutesolvent interfacial force, derive the corresponding stochastic levelset equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describemore »
 Authors:
 Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006 (China)
 Department of Mathematics, University of California, San Diego, La Jolla, California 920930112 (United States)
 Soft Matter and Functional Materials, HelmholtzZentrum Berlin, 14109 Berlin, Germany and Institut für Physik, HumboldtUniversität zu Berlin, 12489 Berlin (Germany)
 Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 920930112 (United States)
 Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 920930365 (United States)
 Publication Date:
 OSTI Identifier:
 22679024
 Resource Type:
 Journal Article
 Resource Relation:
 Journal Name: Journal of Chemical Physics; Journal Volume: 145; Journal Issue: 5; Other Information: (c) 2016 Author(s); Country of input: International Atomic Energy Agency (IAEA)
 Country of Publication:
 United States
 Language:
 English
 Subject:
 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; COMPUTERIZED SIMULATION; CONFORMATIONAL CHANGES; DIELECTRIC MATERIALS; FLUCTUATIONS; FREE ENERGY; MOLECULAR DYNAMICS METHOD; NUMERICAL DATA; SOLUTES; SOLVENTS
Citation Formats
Zhou, Shenggao, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, Sun, Hui, Cheng, LiTien, Dzubiella, Joachim, Li, Bo, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, and McCammon, J. Andrew. Stochastic levelset variational implicitsolvent approach to solutesolvent interfacial fluctuations. United States: N. p., 2016.
Web. doi:10.1063/1.4959971.
Zhou, Shenggao, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, Sun, Hui, Cheng, LiTien, Dzubiella, Joachim, Li, Bo, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, & McCammon, J. Andrew. Stochastic levelset variational implicitsolvent approach to solutesolvent interfacial fluctuations. United States. doi:10.1063/1.4959971.
Zhou, Shenggao, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, Sun, Hui, Cheng, LiTien, Dzubiella, Joachim, Li, Bo, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu, and McCammon, J. Andrew. Sun .
"Stochastic levelset variational implicitsolvent approach to solutesolvent interfacial fluctuations". United States.
doi:10.1063/1.4959971.
@article{osti_22679024,
title = {Stochastic levelset variational implicitsolvent approach to solutesolvent interfacial fluctuations},
author = {Zhou, Shenggao, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu and Sun, Hui and Cheng, LiTien and Dzubiella, Joachim and Li, Bo, Email: sgzhou@suda.edu.cn, Email: bli@math.ucsd.edu and McCammon, J. Andrew},
abstractNote = {Recent years have seen the initial success of a variational implicitsolvent model (VISM), implemented with a robust levelset method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The levelset minimization of the VISM solvation freeenergy functional of all possible solutesolvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solutesolvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic levelset method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solutesolvent interfacial force, derive the corresponding stochastic levelset equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the freeenergy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the interplate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicitsolvent approach.},
doi = {10.1063/1.4959971},
journal = {Journal of Chemical Physics},
number = 5,
volume = 145,
place = {United States},
year = {Sun Aug 07 00:00:00 EDT 2016},
month = {Sun Aug 07 00:00:00 EDT 2016}
}

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