We use Brownian dynamics with hydrodynamic interactions to calculate both the Kirkwood (short-time) diffusivity and the long-time diffusivity of DNA chains from free solution down to channel confinement in the de Gennes regime. The Kirkwood diffusivity in confinement is always higher than the diffusivity obtained from the mean-squared displacement of the center-of-mass, as is the case in free s...

BACKGROUND Buffalo/Mna rats spontaneously develop a nephrotic syndrome (NS). We have demonstrated that this rat nephropathy recurs after renal transplantation. We studied this recurrence by kinetic analysis of graft lesions, infiltrating cells and cytokines. METHODS Kidneys from LEW.1 W rats were grafted into proteinuric Buff/Mna or healthy Wistar Furth recipients. Kidney samples were harvest...

We examine the thermodynamics of the liquid-vapor interface by direct calculation of the surface entropy, enthalpy, and free energy from extensive molecular dynamics simulations using the two-phase thermodynamics (2PT) method. Results for water, acetonitrile, cyclohexane, dimethyl sulfoxide, hexanol, N-methyl acetamide, and toluene are presented. We validate our approach by predicting the inter...

In this work, we study the influence of polymer chain length (m), based on Lennard-Jones potential, and nanoparticle (NP)-polymer interaction strength (ɛnp) on aggregation and dispersion of soft repulsive spherically structured NPs in polymer melt using coarse-grain molecular dynamics simulations. A phase diagram is proposed where transitions between different structures in the NP-polymer syste...

Our molecular-based formalism for infinitely dilute supercritical nonelectrolyte solutions is extended to electrolyte solutions by establishing rigorous connections between the microscopic behavior of the solvent around individual ionic species and their macroscopic solvation behavior. The formalism relies on the unambiguous splitting of the mixture’s properties into short-ranged ~finite! and l...

Computational Study of Volumetric Effects of Hydration Molecular Dynamics (MD) simulations were used in conjunction with the Kirkwood-Buff (KB) theory to compute partial molar volume (PMV) for solutes of various chemical natures. Simulations performed with only the Lennard-Jones (LJ) potential yield PMV for solutes which coincide with the cavity volumes derived from calculations with scaled par...

Virtually all taxa use osmolytes to protect cells against biochemical stress. Osmolytes often occur in mixtures, such as the classical combination of urea with TMAO (trimethylamine N-oxide) in cartilaginous fish or the cocktail of at least six different osmolytes in the kidney. The concentration patterns of osmolyte mixtures found in vivo make it likely that synergy between them plays an import...

Tom Kirkwood is Professor of Medicine and Director of the Institute for Ageing and Health at Newcastle University, UK. After training in mathematics and biology at the Universities of Cambridge and Oxford he first worked on the measurement of blood clotting and fibrinolytic factors. Early in his career he began an interest in the biology of ageing which he has followed since 1975. In 1977 he pu...