相关论文: A new approach to constrained total variation solv…

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…

ariational implicit solvation models (VISM) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is…

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…

This paper characterizes sharp solute-solvent interfaces in hydrophobic environments, and there are three major ingredients. The first is the variational implicit solvent model (VISM) which establishes the free energy functional of…

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…

Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…

Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key…

A variational model to simultaneously treat Stress-Driven Rearrangement Instabilities, such as boundary discontinuities, internal cracks, external filaments, edge delamination, wetting, and brittle fractures, is introduced. The model is…

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…

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},…

Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…

In this article, we introduce the concept of energy-variational solutions for a large class of systems of nonlinear evolutionary partial differential equations. Under certain convexity assumptions, the existence of such solutions can be…

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in…

A new diffuse interface model for a two-phase flow of two incompressible fluids with different densities is introduced using methods from rational continuum mechanics. The model fulfills local and global dissipation inequalities and is also…

To reduce the carbon footprint of computing and stabilize electricity grids, there is an increasing focus on approaches that align the power usage of IT infrastructure with the availability of clean energy. Unfortunately, research on…

The variational multiscale (VMS) formulation formally segregates the evolution of the coarse-scales from the fine-scales. VMS modeling requires the approximation of the impact of the fine scales in terms of the coarse scales. In linear…

We consider a continuum mechanical model of cell invasion through thin membranes. The model consists of a transmission problem for cell volume fraction complemented with continuity of stresses and mass flux across the surfaces of the…

The dynamics of compressible liquid-vapor flow depends sensitively on the microscale behavior at the phase boundary. We consider a sharp-interface approach, and propose a multiscale model to describe liquid-vapor flow accurately, without…

The adsorption behavior of ions at liquid-vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of…

We map molecular dynamics simulations of fluid-fluid interfaces onto mesoscale continuum theories for partially miscible fluids. Unlike most previous work, we examine not only the interface order parameter and density profiles, but also the…