We apply equilibrium and nonequilibrium molecular dynamics simulations to study the dynamic properties of electrolytes in nanopores. The realistic primitive model and the restrictive primitive model widely used in the statistical mechanics of liquid-state theory are applied to model the electrolytes. The electrolytic ions are immersed in water, treated in this work as either a dielectric contin...

Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCC...

Mechanisms of bimolecular chemical reactions in solution are amenable to study on picosecond timescales, both by transient absorption spectroscopy and by computer simulation. The dynamics of exothermic reactions of CN radicals and of Cl and F atoms with organic solutes in commonly used solvents are contrasted with the corresponding dynamics in the gas phase. Many characteristics of the gas-phas...

A new approach is developed to study the dynamics of the localized process in solutions and other condensed phase systems. The approach employs a fluctuating elastic boundary (FEB) model which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions and allows for a reduction in the number of solvent m...

The microscopic connections between solvation dynamics and the experimentally measured dynamic emission Stokes shift are explored by molecular dynamics simulation using the hydrated electron as a fully quantum mechanical probe. Solvent response functions are computed using the method of spectral reconstruction at various time resolutions for both fluorescence and stimulated emission and compare...

Using NPT and NVT molecular dynamics simulation techniques, we have simulated an atomistic model of solvated Nafion in the lithium salt form, with the following three main objectives: (i) to obtain details on the local environment of the lithium cations and to assess the solvent effect on their binding, (ii) to investigate the translational and rotational motion of solvent molecules (water and ...

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to t...

A complete description of the Supercritical Antisolvent Process requires the modelling of several complex physical phenomena such as heat and mass transfer, hydrodynamic, phase equilibria of ternary mixtures, and nucleation /growth of the specie to be precipitated; moreover, the description should also account for the biphasic case, where the jet of organic solvent breaks up as droplets. As a f...