Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of (irreversible) expected coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the ``coarse molecular dynamics'' approach, we combine multiple short (0.5-ps) replica simulations to map the free energy surface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000 ps) rate of interconversion between the two stable configurational basins corresponding to the alpha-helical and extended minima.Comment: The article has been submitted to "The Journal of Chemical Physics.

O stars effective temperature and HII regions ionization parameter gradients in the Galaxy

Extensive photoionization model grids are computed for single star HII regions using stellar atmosphere models from the WM-basic code. Mid-IR emission line intensities are predicted and diagnostic diagrams of [NeIII]/[NeII] and [SIV]/[SIII] excitation ratio are build, taking into account the metallicities of both the star and the HII region. The diagrams are used in conjunction with galactic HII region observations obtained with the ISO Observatory to determine the effective temperature Teff of the exciting O stars and the mean ionization parameter U. Teff and U are found to increase and decrease, respectively, with the metallicity of the HII region represented by the [Ne/Ne_sol] ratio. No evidence is found for gradients of Teff or U with galactocentric distance Rgal. The observed excitation sequence with Rgal is mainly due to the effect of the metallicity gradient on the spectral ionizing shape, upon which the effect of an increase in Teff with Z is superimposed. We show that not taking properly into account the effect of metallicity on the ionizing shape of the stellar atmosphere would lead to an apparent decrease of Teff with Z and an increase of Teff with Rgal.Comment: Accepted in Ap

Coarse Nonlinear Dynamics and Metastability of Filling-Emptying Transitions: Water in Carbon Nanotubes

Using a Coarse-grained Molecular Dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling/emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise to tubes that are empty, water-filled, or fluctuate between these two long-lived metastable states. The corresponding coarse-grained free energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations.Comment: 4 pages, 3 figures; accepted versio

Density-Dependent Analysis of Nonequilibrium Paths Improves Free Energy Estimates II. A Feynman-Kac Formalism

The nonequilibrium fluctuation theorems have paved the way for estimating equilibrium thermodynamic properties, such as free energy differences, using trajectories from driven nonequilibrium processes. While many statistical estimators may be derived from these identities, some are more efficient than others. It has recently been suggested that trajectories sampled using a particular time-dependent protocol for perturbing the Hamiltonian may be analyzed with another one. Choosing an analysis protocol based on the nonequilibrium density was empirically demonstrated to reduce the variance and bias of free energy estimates. Here, we present an alternate mathematical formalism for protocol postprocessing based on the Feynmac-Kac theorem. The estimator that results from this formalism is demonstrated on a few low-dimensional model systems. It is found to have reduced bias compared to both the standard form of Jarzynski's equality and the previous protocol postprocessing formalism.Comment: 21 pages, 5 figure

Molecular Realism in Default Models for Information Theories of Hydrophobic Effects

This letter considers several physical arguments about contributions to hydrophobic hydration of inert gases, constructs default models to test them within information theories, and gives information theory predictions using those default models with moment information drawn from simulation of liquid water. Tested physical features include: packing or steric effects, the role of attractive forces that lower the solvent pressure, and the roughly tetrahedral coordination of water molecules in liquid water. Packing effects (hard sphere default model) and packing effects plus attractive forces (Lennard-Jones default model) are ineffective in improving the prediction of hydrophobic hydration free energies of inert gases over the previously used Gibbs and flat default models. However, a conceptually simple cluster Poisson model that incorporates tetrahedral coordination structure in the default model is one of the better performers for these predictions. These results provide a partial rationalization of the remarkable performance of the flat default model with two moments in previous applications. The cluster Poisson default model thus will be the subject of further refinement.Comment: 5 pages including 3 figure

The marketing of major league soccer

For the past six years, Major League Soccer has tried to penetrate American homes with its brand of soccer. Television advertisements and in-house surveys have been made to encourage people to view soccer as a spectator sport. The league, though, has been on decline since its first year and the question still remains why soccer has a hard time being a spectator sport in America. This study examined how Youth Soccer parents perceive the league. The author went to various Youth Soccer games and registrations and used an intercept survey of the soccer parents. The parents were asked if they had ever heard of Major League Soccer, where did they hear about it and ways to improve the league for spectators. They also answered questions on their child\u27s favorite soccer player and sports hero to determine if the league is having success in marketing players. Most of the parents have heard of Major League Soccer and agreed that the games should be on the television more often. Many of them acknowledge that a team that\u27s closer in proximity to them would draw more attention from the youth soccer parents