A molecular dynamics study of the depletion of water (drying) around a single and between two hydrophobic nanoscale oblate plates in explicit water as a function of the distance of separation between them, their size, and the strength of the attraction between the plates and the water molecules is presented. A simple macroscopic thermodynamic model based on Young's law successfully predicts dry...

The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the electronic correlation and treat a large number of hydrogen atoms, allowing a r...

We show that arbitrary phase space vector fields can be used to generate phase functions whose ensemble averages give the thermodynamic temperature. We describe conditions for the validity of these functions in periodic boundary systems and the Molecular Dynamics (MD) ensemble, and test them with a short-ranged potential MD simulation. 05.20.-y 05.20.Gd Typeset using REVTEX 1

Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics. Two newly implemented simulation techniques, parallel replica dynamics and replica exch...

We investigate the response of bulk liquid water to a temperature gradient using nonequilibrium molecular dynamics simulations. It is shown that the thermal gradient polarizes water in the direction of the gradient, leading to a non-negligible electrostatic field whose origin lies in the water reorientation under nonequilibrium conditions. The dependence of the magnitude of the electrostatic fi...

The biochemical cycle of a molecular motor provides the essential link between its thermodynamics and kinetics. The thermodynamics of the cycle determine the motor's ability to perform mechanical work, whilst the kinetics of the cycle govern its stochastic behaviour. We concentrate here on tightly coupled, processive molecular motors, such as kinesin and myosin V, which hydrolyse one molecule o...

Based on the previous article 'Cellular Thermodynamics' (2004) by Joe Wolfe Article contents • Introduction • Equilibrium • Steady state • Heat, light, photons and 'useful energy' • Macroscopic and microscopic views • Distribution of molecules and energy: low energy vs. high entropy • Reaction rates and equilibria • Enthalpy • Gibbs free energy • Other equilibria • The chemical potential • Surf...

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the the...

Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is unstructured. We obtain significant differences in their binding behavior. The stable sequence has rigid docking as its preferred binding mode, while the uns...

Using the five-site transferable intermolecular potential (TIP5P) we perform molecular dynamics simulations to investigate the relationship between the excess entropy and anomalies of water. We find that the two-body excess entropy is an ideal quantity to predict the regions of structural, dynamic, and thermodynamic anomalies of water in its pressure-temperature and density-temperature phase di...