Related papers: Computing spatially resolved rotational hydration …
Computer simulations have been employed in recent years to evaluate the configurational entropy changes in model glass-forming liquids. We consider two methods, both of which involve the calculation of the `intra-basin' entropy as a means…
We report microscopic calculations of free energies and entropies for intramolecular electron transfer reactions. The calculation algorithm combines the atomistic geometry and charge distribution of a molecular solute obtained from quantum…
In this work, we design an entropy stable, finite volume approximation for the shallow water magnetohydrodynamics (SWMHD) equations. The method is novel as we design an affordable analytical expression of the numerical interface flux…
We present a simple numerical procedure for calculating the irrotational hydrodynamic flow in a helium solvation structure around a spherical solute in linear motion through superfluid helium. The calculation requires only the radial helium…
The local hydration around tetrameric Hb in its T$_0$ and R$_4$ conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the $\alpha_1 \beta_2$ and $\alpha_2…
We present and test a general-purpose code, called PPASPH, for evolving self-gravitating fluids in astrophysics, both with and without a collisionless component. In PPASPH, hydrodynamical properties are computed by using the SPH (Smoothed…
In this paper, we first develop a mathematical model for long-range, hydrophobic attraction between amphiphilic particles. The non-pairwise interactions follow from the first variation of a hydrophobic attraction domain functional. The…
Microscopic formula to describe the entropy of biomolecular solutions are derived based on the Gibbs formula of entropy, and the generalized Langevin theory combined with the RISM/3D-RISM theory. Two formula are derived: one is concerned…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
Recent calculations have shown that the linear proportionality between black hole entropy and area can be explained by performing a density matrix calculation for a massless free field theory. By applying the same formalism to an empirical…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct…
Many popular methods for the calculation of chemical potentials rely on the insertion of test particles into the target system. In the case of liquids and liquid mixtures, this procedure increases in difficulty upon increasing density or…
The smoothed particle hydrodynamics (SPH) method has been increasingly used to study fluid problems in recent years; but its computational cost can be high if high resolution is required. In this study, an adaptive resolution method based…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the…
To calculate the solvation of hydrophobic solutes we have developed the method based on the fundamental measure treatment of the density functional theory. This method allows us to carry out calculations of density profiles and the…
We perform numerical simulations to study the dynamics of the entry of hydrophobic spheres in a pool of water using ANSYS. To track the air-water interface during the translation of the sphere in the pool of water, we use the volume of…