771 research outputs found
Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
We present a new adaptive resolution technique for efficient particle-based
multiscale molecular dynamics (MD) simulations. The presented approach is
tailor-made for molecular systems where atomistic resolution is required only
in spatially localized domains whereas a lower mesoscopic level of detail is
sufficient for the rest of the system. Our method allows an on-the-fly
interchange between a given molecule's atomic and coarse-grained level of
description, enabling us to reach large length and time scales while spatially
retaining atomistic details of the system. The new approach is tested on a
model system of a liquid of tetrahedral molecules. The simulation box is
divided into two regions: one containing only atomistically resolved
tetrahedral molecules, the other containing only one particle coarse-grained
spherical molecules. The molecules can freely move between the two regions
while changing their level of resolution accordingly. The coarse-grained and
the atomistically resolved systems have the same statistical properties at the
same physical conditions.Comment: 17 pages, 11 figures, 5 table
Static and Dynamic Critical Behavior of a Symmetrical Binary Fluid: A Computer Simulation
A symmetrical binary, A+B Lennard-Jones mixture is studied by a combination
of semi-grandcanonical Monte Carlo (SGMC) and Molecular Dynamics (MD) methods
near a liquid-liquid critical temperature . Choosing equal chemical
potentials for the two species, the SGMC switches identities () to generate well-equilibrated configurations of the system on
the coexistence curve for and at the critical concentration, ,
for . A finite-size scaling analysis of the concentration susceptibility
above and of the order parameter below is performed, varying the
number of particles from N=400 to 12800. The data are fully compatible with the
expected critical exponents of the three-dimensional Ising universality class.
The equilibrium configurations from the SGMC runs are used as initial states
for microcanonical MD runs, from which transport coefficients are extracted.
Self-diffusion coefficients are obtained from the Einstein relation, while the
interdiffusion coefficient and the shear viscosity are estimated from
Green-Kubo expressions. As expected, the self-diffusion constant does not
display a detectable critical anomaly. With appropriate finite-size scaling
analysis, we show that the simulation data for the shear viscosity and the
mutual diffusion constant are quite consistent both with the theoretically
predicted behavior, including the critical exponents and amplitudes, and with
the most accurate experimental evidence.Comment: 35 pages, 13 figure
Critical Dynamics in a Binary Fluid: Simulations and Finite-size Scaling
We report comprehensive simulations of the critical dynamics of a symmetric
binary Lennard-Jones mixture near its consolute point. The self-diffusion
coefficient exhibits no detectable anomaly. The data for the shear viscosity
and the mutual-diffusion coefficient are fully consistent with the asymptotic
power laws and amplitudes predicted by renormalization-group and mode-coupling
theories {\it provided} finite-size effects and the background contribution to
the relevant Onsager coefficient are suitably accounted for. This resolves a
controversy raised by recent molecular simulations.Comment: 4 pages, 4 figure
Water adsorption on amorphous silica surfaces: A Car-Parrinello simulation study
A combination of classical molecular dynamics (MD) and ab initio
Car-Parrinello molecular dynamics (CPMD) simulations is used to investigate the
adsorption of water on a free amorphous silica surface. From the classical MD
SiO_2 configurations with a free surface are generated which are then used as
starting configurations for the CPMD.We study the reaction of a water molecule
with a two-membered ring at the temperature T=300K. We show that the result of
this reaction is the formation of two silanol groups on the surface. The
activation energy of the reaction is estimated and it is shown that the
reaction is exothermic.Comment: 12 pages, 6 figures, to be published in J. Phys.: Condens. Matte
NOTES: WOODPECKER FORAGE AVAILABILITY IN HABI- TAT DISTURBANCES OF THE BLACK HILLS
Habitat disturbance events are critical to ecological systems in which some bird species have become specialized. The vegetation community, reduced competition, ability to avoid predators, nest-site characteristics, and forage opportunities within a disturbed ecosystem are all aspects that make it desirable for selection by particular species (Svärdson 1949, Cody 1981, Martin 1998). Specifically, avian species rely on the forest conditions created by fire, insects, and disease (Brawn et al. 2001, Hunter et al. 2001, Devictor et al. 2008). In the Black Hills National Forest (BHNF) of South Dakota,two major types of natural disturbances include wildfires and mountain pine beetle (Dendroctonus ponderosae; MPB) infestations. Dead trees (snags) created by these disturbances attract a suite of insects and wildlife species. Bark beetles (Family: Curculionidae, Scolytinae) and wood borer beetles (Families: Buprestidae and Cerambycidae) are of particular importance to black-backed woodpeckers (Picoides arcticus; BBWO) because they feed almost exclusively on the larvae of these insects (Beal 1911, Murphy and Lehnhausen 1998, Hutto 2006, Bonnot et al. 2008, Bonnot et al. 2009). Black-backed woodpeckers are of key interest to resource management agencies due to their habitat specialization needs and the management activities like wildfire salvage logging and pre-thinning that occur in these disturbance areas (Hutto 1995, 2006). These management activities potentially reduce nest site and food availability for BBWOs and, as a result, they were recently petitioned for protection under the Endangered Species Act (Hanson et al. 2012). Following a fire event or insect infestation, the relative probability of using trees affected by the disturbance increases over surrounding healthy trees (Rota 2013). As a result, we were interested in understanding the food that is available to the woodpeckers following these forest disturbances
Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: I. Statics
Molecular dynamics simulations were conducted to investigate the structural
properties of melts of nonconcatenated ring polymers and compared to melts of
linear polymers. The longest rings were composed of N=1600 monomers per chain
which corresponds to roughly 57 entanglement lengths for comparable linear
polymers. For the rings, the radius of gyration squared was found to scale as N
to the 4/5 power for an intermediate regime and N to the 2/3 power for the
larger rings indicating an overall conformation of a crumpled globule. However,
almost all beads of the rings are "surface beads" interacting with beads of
other rings, a result also in agreement with a primitive path analysis
performed in the following paper (DOI: 10.1063/1.3587138). Details of the
internal conformational properties of the ring and linear polymers as well as
their packing are analyzed and compared to current theoretical models.Comment: 15 pages, 14 figure
Curvature Dependence of Surface Free Energy of Liquid Drops and Bubbles: A Simulation Study
We study the excess free energy due to phase coexistence of fluids by Monte
Carlo simulations using successive umbrella sampling in finite LxLxL boxes with
periodic boundary conditions. Both the vapor-liquid phase coexistence of a
simple Lennard-Jones fluid and the coexistence between A-rich and B-rich phases
of a symmetric binary (AB) Lennard-Jones mixture are studied, varying the
density rho in the simple fluid or the relative concentration x_A of A in the
binary mixture, respectively. The character of phase coexistence changes from a
spherical droplet (or bubble) of the minority phase (near the coexistence
curve) to a cylindrical droplet (or bubble) and finally (in the center of the
miscibility gap) to a slab-like configuration of two parallel flat interfaces.
Extending the analysis of M. Schrader, P. Virnau, and K. Binder [Phys. Rev. E
79, 061104 (2009)], we extract the surface free energy gamma (R) of both
spherical and cylindrical droplets and bubbles in the vapor-liquid case, and
present evidence that for R -> Infinity the leading order (Tolman) correction
for droplets has sign opposite to the case of bubbles, consistent with the
Tolman length being independent on the sign of curvature. For the symmetric
binary mixture the expected non-existence of the Tolman length is confirmed. In
all cases {and for a range of radii} R relevant for nucleation theory, gamma(R)
deviates strongly from gamma (Infinity) which can be accounted for by a term of
order gamma(Infinity)/gamma(R)-1 ~ 1/R^2. Our results for the simple
Lennard-Jones fluid are also compared to results from density functional theory
and we find qualitative agreement in the behavior of gamma(R) as well as in the
sign and magnitude of the Tolman length.Comment: 25 pages, submitted to J. Chem. Phy
Radiating dipoles in photonic crystals
The radiation dynamics of a dipole antenna embedded in a Photonic Crystal are
modeled by an initially excited harmonic oscillator coupled to a non--Markovian
bath of harmonic oscillators representing the colored electromagnetic vacuum
within the crystal. Realistic coupling constants based on the natural modes of
the Photonic Crystal, i.e., Bloch waves and their associated dispersion
relation, are derived. For simple model systems, well-known results such as
decay times and emission spectra are reproduced. This approach enables direct
incorporation of realistic band structure computations into studies of
radiative emission from atoms and molecules within photonic crystals. We
therefore provide a predictive and interpretative tool for experiments in both
the microwave and optical regimes.Comment: Phys. Rev. E, accepte
Energy landscape of a Lennard-Jones liquid: Statistics of stationary points
Molecular dynamics simulations are used to generate an ensemble of saddles of
the potential energy of a Lennard-Jones liquid. Classifying all extrema by
their potential energy u and number of unstable directions k, a well defined
relation k(u) is revealed. The degree of instability of typical stationary
points vanishes at a threshold potential energy, which lies above the energy of
the lowest glassy minima of the system. The energies of the inherent states, as
obtained by the Stillinger-Weber method, approach the threshold energy at a
temperature close to the mode-coupling transition temperature Tc.Comment: 4 RevTeX pages, 6 eps figures. Revised versio
Phase separation of an asymmetric binary fluid mixture confined in a nanoscopic slit pore: Molecular-dynamics simulations
As a generic model system of an asymmetric binary fluid mixture, hexadecane
dissolved in carbon dioxide is considered, using a coarse-grained bead-spring
model for the short polymer, and a simple spherical particle with Lennard-Jones
interactions for the carbon dioxide molecules. In previous work, it has been
shown that this model reproduces the real phase diagram reasonable well, and
also the initial stages of spinodal decomposition in the bulk following a
sudden expansion of the system could be studied. Using the parallelized
simulation package ESPResSo on a multiprocessor supercomputer, phase separation
of thin fluid films confined between parallel walls that are repulsive for both
types of molecules are simulated in a rather large system (1356 x 1356 x 67.8
A^3, corresponding to about 3.2 million atoms). Following the sudden system
expansion, a complicated interplay between phase separation in the directions
perpendicular and parallel to the walls is found: in the early stages the
hexadecane molecules accumulate mostly in the center of the slit pore, but as
the coarsening of the structure in the parallel direction proceeds, the
inhomogeneity in the perpendicular direction gets much reduced. Studying then
the structure factors and correlation functions at fixed distances from the
wall, the densities are essentially not conserved at these distances, and hence
the behavior differs strongly from spinodal decomposition in the bulk. Some of
the characteristic lengths show a nonmonotonic variation with time, and simple
coarsening described by power-law growth is only observed if the domain sizes
are much larger than the film thickness.Comment: accepted for publication in PR
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