829 research outputs found
Symplectic quaternion scheme for biophysical molecular dynamics
Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space
First-principles molecular-dynamics simulations of a hydrous silica melt: Structural properties and hydrogen diffusion mechanism
We use {\it ab initio} molecular dynamics simulations to study a sample of
liquid silica containing 3.84 wt.% HO.We find that, for temperatures of
3000 K and 3500 K,water is almost exclusively dissolved as hydroxyl groups, the
silica network is partially broken and static and dynamical properties of the
silica network change considerably upon the addition of water.Water molecules
or free O-H groups occur only at the highest temperature but are not stable and
disintegrate rapidly.Structural properties of this system are compared to those
of pure silica and sodium tetrasilicate melts at equivalent temperatures. These
comparisons confirm the picture of a partially broken tetrahedral network in
the hydrous liquid and suggest that the structure of the matrix is as much
changed by the addition of water than it is by the addition of the same amount
(in mole %) of sodium oxide. On larger length scales, correlations are
qualitatively similar but seem to be more pronounced in the hydrous silica
liquid. Finally, we study the diffusion mechanisms of the hydrogen atoms in the
melt. It turns out that HOSi triclusters and SiO dangling bonds play a
decisive role as intermediate states for the hydrogen diffusion.Comment: 25 pages, 18 figures. submitte
Molecular dynamics in shape space and femtosecond vibrational spectroscopy of metal clusters
We introduce a method of molecular dynamics in shape space aimed at metal
clusters. The ionic degrees of freedom are described via a dynamically
deformable jellium with inertia parameters derived from an incompressible,
irrotational flow. The shell correction method is used to calculate the
electronic potential energy surface underlying the dynamics. Our finite
temperature simulations of Ag_14 and its ions, following the negative to
neutral to positive scheme, demonstrate the potential of pump and probe
ultrashort laser pulses as a spectroscopy of cluster shape vibrations.Comment: Latex/Revtex, 4 pages with 3 Postscript figure
Colored-noise thermostats \`a la carte
Recently, we have shown how a colored-noise Langevin equation can be used in
the context of molecular dynamics as a tool to obtain dynamical trajectories
whose properties are tailored to display desired sampling features. In the
present paper, after having reviewed some analytical results for the stochastic
differential equations forming the basis of our approach, we describe in detail
the implementation of the generalized Langevin equation thermostat and the
fitting procedure used to obtain optimal parameters. We discuss in detail the
simulation of nuclear quantum effects, and demonstrate that, by carefully
choosing parameters, one can successfully model strongly anharmonic solids such
as neon. For the reader's convenience, a library of thermostat parameters and
some demonstrative code can be downloaded from an on-line repository
Diffusion and viscosity in a supercooled polydisperse system
We have carried out extensive molecular dynamics simulations of a supercooled
polydisperse Lennard-Jones liquid with large variations in temperature at a
fixed pressure. The particles in the system are considered to be polydisperse
both in size and mass. The temperature dependence of the dynamical properties
such as the viscosity () and the self-diffusion coefficients () of
different size particles is studied. Both viscosity and diffusion coefficients
show super-Arrhenius temperature dependence and fit well to the well-known
Vogel-Fulcher-Tammann (VFT) equation. Within the temperature range
investigated, the value of the Angell's fragility parameter (D )
classifies the present system into a strongly fragile liquid. The critical
temperature for diffusion () increases with the size of the
particles. The critical temperature for viscosity () is larger than
that for the diffusion and a sizeable deviations appear for the smaller size
particles implying a decoupling of translational diffusion from viscosity in
deeply supercooled liquid. Indeed, the diffusion shows markedly non-Stokesian
behavior at low temperatures where a highly nonlinear dependence on size is
observed. An inspection of the trajectories of the particles shows that at low
temperatures the motions of both the smallest and largest size particles are
discontinuous (jump-type). However, the crossover from continuous Brownian to
large length hopping motion takes place at shorter time scales for the smaller
size particles.Comment: Revtex4, 7 pages, 8 figure
An extended-phase-space dynamics for the generalized nonextensive thermostatistics
We apply a variant of the Nose-Hoover thermostat to derive the Hamiltonian of
a nonextensive system that is compatible with the canonical ensemble of the
generalized thermostatistics of Tsallis. This microdynamical approach provides
a deterministic connection between the generalized nonextensive entropy and
power law behavior. For the case of a simple one-dimensional harmonic
oscillator, we confirm by numerical simulation of the dynamics that the
distribution of energy H follows precisely the canonical q-statistics for
different values of the parameter q. The approach is further tested for
classical many-particle systems by means of molecular dynamics simulations. The
results indicate that the intrinsic nonlinear features of the nonextensive
formalism are capable to generate energy fluctuations that obey anomalous
probability laws. For q<1 a broad distribution of energy is observed, while for
q>1 the resulting distribution is confined to a compact support.Comment: 4 pages, 5 figure
Kapitza Resistance between Few-Layer Graphene and Water: Liquid Layering Effects
The Kapitza resistance (RK) between few-layer graphene (FLG) and water was studied using molecular dynamics simulations. The R_K was found to depend on the number of the layers in the FLG though, surprisingly, not on the water block thickness. This distinct size dependence is attributed to the large difference in the phonon mean free path between the FLG and water. Remarkably, R_K is strongly dependent on the layering of water adjacent to the FLG, exhibiting an inverse proportionality relationship to the peak density of the first water layer, which is consistent with better acoustic phonon matching between FLG and water. These findings suggest novel ways to engineer the thermal transport properties of solid–liquid interfaces by controlling and regulating the liquid layering at the interface
Effects of pressure on diffusion and vacancy formation in MgO from non-empirical free-energy integrations
The free energies of vacancy pair formation and migration in MgO were
computed via molecular dynamics using free-energy integrations and a
non-empirical ionic model with no adjustable parameters. The intrinsic
diffusion constant for MgO was obtained at pressures from 0 to 140 GPa and
temperatures from 1000 to 5000 K. Excellent agreement was found with the zero
pressure diffusion data within experimental error. The homologous temperature
model which relates diffusion to the melting curve describes well our high
pressure results within our theoretical framework.Comment: 4 pages, latex, 1 figure, revtex, submitted to PR
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