Related papers: An Analysis of the Thermodynamics of Hydrophobic S…
Smoothed particle hydrodynamics (SPH) is typically used for barotropic fluids, where the pressure depends only on the local mass density. Here, we show how to incorporate the entropy into the SPH, so that the pressure can also depend on the…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like…
Thermodynamic multi-component solution solidification approach to liquid-to-glass transition is proposed and actual mechanisms underlying vitrification, other than viscous slowdown, are identified. Due to polydisperse aggregation in liquid…
Hydrodynamic transport coefficients may be evaluated from first principles in a weakly coupled scalar field theory at arbitrary temperature. In a theory with cubic and quartic interactions, the infinite class of diagrams which contribute to…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
A central aim of multiscale modeling is to use results from the Schr\"odinger Equation to predict phenomenology on length scales that far exceed those of typical molecular correlations. In this work, we present a new approach rooted in…
Water near hydrophobic surfaces is like that at a liquid-vapor interface, where fluctuations in water density are substantially enhanced compared to that in bulk water. Here we use molecular simulations with specialized sampling techniques…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Diffuse-interface theory provides a foundation for the modeling and simulation of microstructure evolution in a very wide range of materials, and for the tracking/capturing of dynamic interfaces between different materials on larger scales.…
We show that for any liquid or solid with strong correlation between its $NVT$ virial and potential-energy equilibrium fluctuations, the temperature is a product of a function of excess entropy per particle and a function of density,…
We investigate the equation of state, diffusion coefficient, and structural order of a family of spherically-symmetric potentials consisting of a hard core and a linear repulsive ramp. This generic potential has two characteristic length…
The most accepted origin for the water anomalous behavior is the phase transition between two liquids (LLPT) in the supercooled regime connected to the glassy first order phase transition at lower temperatures. Two length scales potentials…
We propose a systematic expansion method which is applied to freely evolving granular fluids contained in sufficiently small systems. Restricting ourselves to small systems, we show that there exists a small parameter which characterizes a…
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of…
We present a theory of nonionic solutes in a mixture solvent composed of water-like and alcohol-like species. First, we show relationship among the solvation chemical potential, the partial volumes $v_i$, the Kirkwood-Buff integrals, the…
Colloidal gels are out-of-equilibrium structures, made up of a rarefied network of colloidal particles. Comparing experiments to numerical simulations, with hydrodynamic interactions switched off, we demonstrate the crucial role of the…
We use a coarse grained solvent model to study the self assembly of two nano-scale hydrophobic particles in water. We show how solvent degrees of freedom are involved in the process. By using tools of transition path sampling, we elucidate…
We propose a particle-based method to simulate thin-film fluid that jointly facilitates aggressive surface deformation and vigorous tangential flows. We build our dynamics model from the surface tension driven Navier-Stokes equation with…
Quantifying wettability at the nanoscale remains challenging, as macroscopic contact-angle measurements fail to capture the molecular interactions that define hydrophilic and hydrophobic behavior. We derive an analytical relation linking…