Related papers: Dynamics of Protein Hydration Water
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…
We have studied the real part of the dielectric constant of water from 100 Hz to 1 MHz. We have found that there is a frequency where the dielectric constant is independent of temperature, and called this the isopermitive point. Below this…
The phase diagram of water harbours many mysteries: some of the phase boundaries are fuzzy, and the set of known stable phases may not be complete. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the…
Thermodynamic properties of the particles interacting through smooth version of Stell-Hemmer interaction were studied using Wertheim's thermodynamic perturbation theory. The temperature dependence of molar volume, heat capacity, isothermal…
Temperature plays a very important role in various biological processes like the evolution of life, as it is anticipated that early life existed in a very hot environment that eventually cooled down with time. In vitro experiments,…
We develop an approach to liquid thermodynamics based on collective modes. We perform extensive molecular dynamics simulations of noble, molecular and metallic liquids and provide the direct evidence that liquid energy and specific heat are…
In this article we investigate through molecular dynamics simulations the diffusion behavior of the TIP4P/2005 water when confined in pristine and deformed carbon nanotubes (armchair and zigzag). To analyze different diffusive mechanisms,…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
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,…
We have studied the effect of nonzero bulk viscosity with peak near the lattice QCD predicted crossover temperature $T_{co}\sim 175 MeV$ on charged particle transverse momentum spectra and elliptic flow. The Israel-Stewart theory of 2nd…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
The dynamics for molecule formation, relaxation, diffusion, and desorption on amorphous solid water is studied in a quantitative fashion. We aim at characterizing, at a quantitative level, the formation probability, stabilization, energy…
We present an inelastic neutron scattering study of liquid and solid hydrogen carried out using the wide Angular Range Chopper Spectrometer at Oak Ridge National Laboratory. From the observed dynamic structure factor, we obtained empirical…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
We report an analysis of the stretching peak appearing in the IR experimental spectra of liquid water. In the literature, ATR-IR spectroscopic measurements were repeatedly performed in a wide range of temperature and gave rise to a lively…
We report here a molecular dynamics simulation study on water and aqueous LiCl solutions confined in 1.6 nm cylindrical pores of silica to investigate a dynamical cross-over, observed earlier experimentally, wherein LiCl slows down confined…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We study the dependence of the excitation frequency of water along an isochore and an isotherm crossing the region of density anomaly. We have shown that the frequency of the longitudinal excitations demonstrated anomalous dependence on…
Freeze-out of particles in relativistic hydrodynamics is considered across a 3-dimensional space-time hypersurface. The conservation laws for time-like parts of the freeze-out hypersurface require different values of temperature, baryonic…