Binary Level Set Method for Variational Implicit Solvation Model

DOI10.1137/22M1508339zbMATH Open1523.65055arXiv2110.12815OpenAlexW4387335713MaRDI QIDQ6074540FDOQ6074540

Authors: Li-Tien Cheng 

Publication date: 12 October 2023

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Abstract: In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free energy of all possible interfaces separating solutes (e.g., proteins) from solvent (e.g., water). Previously, such a functional is minimized numerically by the level set method to determine the stable equilibrium conformations and solvation free energies. We vastly improve the speed by applying the binary level set method, in which the interface is approximated by a binary level set function that only takes value $pm1$ on the solute/solvent region, leading to a discrete formulation of VISM energy. The surface area is approximated by convolution of an indicator function with a compactly supported kernel. The VISM energy can be minimized by iteratively "flipping" the binary level set function in a steepest descent fashion. Numerical experiments are performed to demonstrate the accuracy and performance of our method.

Full work available at URL: https://arxiv.org/abs/2110.12815

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zbMATH Keywords

variational problemshape optimizationbinary level set methodfree boundary problemlevel set methodvariational implicit solvent model

Mathematics Subject Classification ID

Numerical optimization and variational techniques (65K10) Optimization of shapes other than minimal surfaces (49Q10) Biophysics (92C05)

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Cited In (5)

• Reservoir description using a binary level set model
• A compact coupling interface method with second-order gradient approximation for elliptic interface problems
• Level-set minimization of potential controlled Hadwiger valuations for molecular solvation
• Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models
• A constrained variational model of biomolecular solvation and its numerical implementation

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