Related papers: Machine-Learned Molecular Surface and Its Applicat…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the…
Potential Energy Surfaces (PESs) are an indispensable tool to investigate, characterise and understand chemical and biological systems in the gas and condensed phases. Advances in Machine Learning (ML) methodologies have led to the…
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104},…
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning…
The accurate description of molecule-surface interactions requires a detailed knowledge of the underlying potential-energy surface (PES). Recently, neural networks (NNs) have been shown to be an efficient technique to accurately interpolate…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
We train an equivariant machine learning model to predict energies and forces for a real-world study of hydrogen combustion under conditions of finite temperature and pressure. This challenging case for reactive chemistry illustrates that…
The level-set method is a popular interface tracking method in two-phase flow simulations. An often-cited reason for using it is that the method naturally handles topological changes in the interface, e.g. merging drops, due to the implicit…
Atomistic simulations of electrochemical interfaces remain challenging due to the long time scales required to adequately sample the structure of the electric double layer. The emergence of efficient, short-range machine learning…
Dynamics of flexible molecules are often determined by an interplay between local chemical bond fluctuations and conformational changes driven by long-range electrostatics and van der Waals interactions. This interplay between interactions…
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties,…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
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…