ArticleJournal of computational physics2011
Multiscale molecular dynamics using the matched interface and boundary method.
Article in Journal of computational physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- A DNN Biophysics Model with Topological and Electrostatic Features.Journal of chemical information and modeling · 2026Article
- Calculation of solvation force in molecular dynamics simulation by deep-learning method.Biophysical journal · 2024Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- MLIMC: Machine Learning-Based Implicit-Solvent Monte Carlo.Chinese journal of chemical physics · 2021Article
- Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation.Journal of computational physics · 2020Article
- DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme.Frontiers in molecular biosciences · 2019Article
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- Numerical interpretation of molecular surface field in dielectric modeling of solvation.Journal of computational chemistry · 2017Article
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.Journal of computational chemistry · 2017Article
- Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.Scientific reports · 2016Article
- Matched Interface and Boundary Method for Elasticity Interface Problems.Journal of computational and applied mathematics · 2015Article
- Second order Method for Solving 3D Elasticity Equations with Complex Interfaces.Journal of computational physics · 2015Article
- Multidimensional persistence in biomolecular data.Journal of computational chemistry · 2015Article
- MIB Galerkin method for elliptic interface problems.Journal of computational and applied mathematics · 2014Article
- A Galerkin formulation of the MIB method for three dimensional elliptic interface problems.Computers & mathematics with applications (Oxford, England : 1987) · 2014Article
- Persistent homology analysis of protein structure, flexibility, and folding.International journal for numerical methods in biomedical engineering · 2014Article
- Multiscale geometric modeling of macromolecules I: Cartesian representation.Journal of computational physics · 2014Article
- Multiscale Multiphysics and Multidomain Models I: Basic Theory.Journal of theoretical & computational chemistry · 2013Article
- Multiscale multiphysics and multidomain models--flexibility and rigidity.The Journal of chemical physics · 2013Article
- Multiscale geometric modeling of macromolecules II: Lagrangian representation.Journal of computational chemistry · 2013Article
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2 authors.
Funding
Abstract
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.