Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU

DOI10.1016/J.JCP.2022.111673OpenAlexW4304943231MaRDI QIDQ2099725

Shuang Liu, Hsiao-Bing Cheng, Zirui Zhang, Bo Li, Li-Tien Cheng

Publication date: 18 November 2022

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2208.05524

zbMATH Keywords

binary level-set methodCoulomb-field approximationGPU implementationmolecular mechanical interactionsvariational implicit-solvent explicit-solute model

Mathematics Subject Classification ID

Numerical methods for partial differential equations, initial value and time-dependent initial-boundary value problems (65Mxx) Miscellaneous topics in partial differential equations (35Rxx) Parabolic equations and parabolic systems (35Kxx)

Uses Software

• LS-VISM

Cites Work

• Level-set minimization of potential controlled Hadwiger valuations for molecular solvation
• Geometric and potential driving formation and evolution of biomolecular surfaces
• Efficient algorithms for diffusion-generated motion by mean curvature
• Convolution-generated motion as a link between cellular automata and continuum pattern dynamics
• An efficient iterative thresholding method for image segmentation
• Kernels with prescribed surface tension \& mobility for threshold dynamics schemes
• A binary level set model and some applications to Mumford-Shah image segmentation
• A variant of the level set method and applications to image segmentation
• Convolution-thresholding methods for interface motion

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