相关论文: Modeling and analysis of ensemble average solvatio…
In the past decade, variational implicit solvation models (VISM) have achieved great success in solvation energy predictions. However, all existing VISMs in literature lack the uniqueness of an energy minimizing solute-solvent interface and…
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…
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from…
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…
An analytical solution based on a diffuse interface model is presented for an isothermal evaporation problem under sub-saturation pressure. The macroscopic equations are derived from the free-energy method, widely recognized in the lattice…
A novel volume of fluid model (VoF) called explicit volume diffusion (EVD) is developed for the simulation of interfacial flows, including those with turbulence and primary spray atomisation. The EVD model is derived by volume averaging the…
We study the dynamics of elastic interfaces-membranes-immersed in thermally excited fluids. The work contains three components: the development of a numerical method, a purely theoretical approach, and numerical simulation. In developing a…
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…
We describe a fluctuating volume--current formulation of electromagnetic fluctuations that extends our recent work on heat exchange and Casimir interactions between arbitrarily shaped homogeneous bodies [Phys. Rev. B. 88, 054305] to…
We compare the computational performance of two modeling approaches for the flow of dilute cavitation bubbles in a liquid. The first approach is a deterministic model, for which bubbles are represented in a Lagrangian framework as advected…
The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterization of such free…
Classical eddy viscosity models add a viscosity term with turbulent viscosity coefficient developed beginning with the Kolmogorov-Prandtl parameterization. Approximations of unknown accuracy of the unknown mixing lengths and turbulent…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
A thermodynamic approach to rapid phase transformations within a diffuse interface in a binary system is developed. Assuming an extended set of independent thermodynamic variables formed by the union of the classic set of slow variables and…
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…
We present an efficient computational methodology to obtain the viscoelastic response of dilute solutions of semiflexible filaments. By considering an approach based on the fluctuation-dissipation theorem, we were able to evaluate the…
The free energetics of water density fluctuations near a surface, and the rare low-density fluctuations in particular, serve as reliable indicators of surface hydrophobicity; the easier it is to displace the interfacial waters, the more…
The vapor-liquid equilibrium (VLE) of the Mie potential, where the dispersive exponent is constant (m = 6) while the repulsive exponent n is varied between 9 and 48, is systematically investigated by molecular simulation. For systems with…
The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as…
The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…