2,206 research outputs found
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
- …