Binary Level Set Method for Variational Implicit Solvation Model
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Publication:6074540
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 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.
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Cites work
- A PDE-based fast local level set method
- A binary level set model and some applications to Mumford-Shah image segmentation
- A diffusion-generated approach to multiphase motion
- A fourth order accurate discretization for the Laplace and heat equations on arbitrary domains, with applications to the Stefan problem
- A level set approach for computing solutions to incompressible two-phase flow
- Active contours without edges
- An efficient iterative thresholding method for image segmentation
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- An implicit interface boundary integral method for Poisson's equation on arbitrary domains
- Binary level-set shape optimization model and algorithm for volumetric modulated arc therapy in radiotherapy treatment
- Convolution-thresholding methods for interface motion
- Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations
- Large-scale simulation of normal grain growth via diffusion-generated motion.
- Level set methods and dynamic implicit surfaces
- Level-set minimization of potential controlled Hadwiger valuations for molecular solvation
- Motion of multiple junctions: A level set approach
- Short-time heat flow and functions of bounded variation in \(\mathbb R^N\)
- Threshold dynamics for networks with arbitrary surface tensions
- Threshold dynamics for the piecewise constant Mumford-Shah functional
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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