Related papers: Computing spatially resolved rotational hydration …
The entropies of molecules in solution are routinely calculated using gas phase formulae. It is assumed that, because implicit solvation models are fitted to reproduce free energies, this is sufficient for modeling reactions in solution.…
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…
The spatial resolution of extensive thermodynamic functions is discussed. A physical definition of the spatial resolution based on a spatial analogy of partial molar quantities is advocated, which is shown to be consistent with how…
We have developed a method to calculate the hydration of hydrophobic solutes by the fundamental measure theory. This method allows us to carry out calculations of the density profile and the hydration energy for hydrophobic molecules. An…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
We discuss differences in simulation results that arise between the use of either the thermal energy or the entropy as an independent variable in smoothed particle hydrodynamics (SPH). In this context, we derive a new version of SPH that…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Solvent plays an important role in the relative motion of nanoscopic bodies, and the study of such phenomena can help elucidate the mechanism of hydrophobic assembly, as well as the influence of solvent-mediated effects on in vivo motion in…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
In this paper we present solutions to three short comings of Smoothed Particles Hydrodynamics (SPH) encountered in previous work when applying it to Giant Impacts. First we introduce a novel method to obtain accurate SPH representations of…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
The extraction of inhomogeneous 3-dimensional densities around tagged solutes from molecular simulations is known to have a very high computational cost because this is traditionally performed by collecting histograms, with each discrete…
A new computational method is presented to resolve hydrodynamic interactions acting on solid particles immersed in incompressible host fluids. In this method, boundaries between solid particles and host fluids are replaced with a continuous…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
Smoothed Particle Hydrodynamics (SPH) is a popular numerical technique developed for simulating complex fluid flows. Among its key ingredients is the use of nonlocal integral relaxations to local differentiations. Mathematical analysis of…
Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a…
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of…