1,716 research outputs found
Estimation of microscopic averages from metadynamics
With the help of metadynamics it is possible to calculate efficiently the
free energy of systems displaying high energy barriers as a function of few
selected "collective variables". In doing this, the contribution of all the
other degrees of freedom ("microscopic" variables) is averaged out and, thus,
lost. In the following, it is shown that it is possible to calculate the
thermal average of these microscopic degrees of freedom during the
metadynamics, not loosing this piece of information
Monovalent counterion distributions at highly charged water interfaces: Proton-transfer and Poisson-Boltzmann theory
Surface sensitive synchrotron-X-ray scattering studies reveal the
distributions of monovalent ions next to highly charged interfaces. A lipid
phosphate (dihexadecyl hydrogen-phosphate) was spread as a monolayer at the
air-water interface, containing CsI at various concentrations. Using anomalous
reflectivity off and at the Cs resonance, we provide, for the first
time, spatial counterion distributions (Cs) next to the negatively charged
interface over a wide range of ionic concentrations. We argue that at low salt
concentrations and for pure water the enhanced concentration of hydroniums
HO at the interface leads to proton-transfer back to the phosphate
group by a high contact-potential, whereas high salt concentrations lower the
contact-potential resulting in proton-release and increased surface
charge-density. The experimental ionic distributions are in excellent agreement
with a renormalized-surface-charge Poisson-Boltzmann theory without fitting
parameters or additional assumptions
Targeted free energy perturbation
A generalization of the free energy perturbation identity is derived, and a
computational strategy based on this result is presented. A simple example
illustrates the efficiency gains that can be achieved with this method.Comment: 8 pages + 1 color figur
Monte Carlo simulations of the screening potential of the Yukawa one-component plasma
A Monte Carlo scheme to sample the screening potential H(r) of Yukawa plasmas
notably at short distances is presented. This scheme is based on an importance
sampling technique. Comparisons with former results for the Coulombic
one-component plasma are given. Our Monte Carlo simulations yield an accurate
estimate of H(r) as well for short range and long range interparticle
distances.Comment: to be published in Journal of Physics A: Mathematical and Genera
Free energies of crystalline solids: a lattice-switch Monte Carlo method
We present a method for the direct evaluation of the difference between the
free energies of two crystalline structures, of different symmetry. The method
rests on a Monte Carlo procedure which allows one to sample along a path,
through atomic-displacement-space, leading from one structure to the other by
way of an intervening transformation that switches one set of lattice vectors
for another. The configurations of both structures can thus be sampled within a
single Monte Carlo process, and the difference between their free energies
evaluated directly from the ratio of the measured probabilities of each. The
method is used to determine the difference between the free energies of the fcc
and hcp crystalline phases of a system of hard spheres.Comment: 5 pages Revtex, 3 figure
Equilibrium Sampling From Nonequilibrium Dynamics
We present some applications of an Interacting Particle System (IPS)
methodology to the field of Molecular Dynamics. This IPS method allows several
simulations of a switched random process to keep closer to equilibrium at each
time, thanks to a selection mechanism based on the relative virtual work
induced on the system. It is therefore an efficient improvement of usual
non-equilibrium simulations, which can be used to compute canonical averages,
free energy differences, and typical transitions paths
Model of a fluid at small and large length scales and the hydrophobic effect
We present a statistical field theory to describe large length scale effects
induced by solutes in a cold and otherwise placid liquid. The theory divides
space into a cubic grid of cells. The side length of each cell is of the order
of the bulk correlation length of the bulk liquid. Large length scale states of
the cells are specified with an Ising variable. Finer length scale effects are
described with a Gaussian field, with mean and variance affected by both the
large length scale field and by the constraints imposed by solutes. In the
absence of solutes and corresponding constraints, integration over the Gaussian
field yields an effective lattice gas Hamiltonian for the large length scale
field. In the presence of solutes, the integration adds additional terms to
this Hamiltonian. We identify these terms analytically. They can provoke large
length scale effects, such as the formation of interfaces and depletion layers.
We apply our theory to compute the reversible work to form a bubble in liquid
water, as a function of the bubble radius. Comparison with molecular simulation
results for the same function indicates that the theory is reasonably accurate.
Importantly, simulating the large length scale field involves binary arithmetic
only. It thus provides a computationally convenient scheme to incorporate
explicit solvent dynamics and structure in simulation studies of large
molecular assemblies
Monte Carlo simulation and global optimization without parameters
We propose a new ensemble for Monte Carlo simulations, in which each state is
assigned a statistical weight , where is the number of states with
smaller or equal energy. This ensemble has robust ergodicity properties and
gives significant weight to the ground state, making it effective for hard
optimization problems. It can be used to find free energies at all temperatures
and picks up aspects of critical behaviour (if present) without any parameter
tuning. We test it on the travelling salesperson problem, the Edwards-Anderson
spin glass and the triangular antiferromagnet.Comment: 10 pages with 3 Postscript figures, to appear in Phys. Rev. Lett
An equation-free computational approach for extracting population-level behavior from individual-based models of biological dispersal
The movement of many organisms can be described as a random walk at either or
both the individual and population level. The rules for this random walk are
based on complex biological processes and it may be difficult to develop a
tractable, quantitatively-accurate, individual-level model. However, important
problems in areas ranging from ecology to medicine involve large collections of
individuals, and a further intellectual challenge is to model population-level
behavior based on a detailed individual-level model. Because of the large
number of interacting individuals and because the individual-level model is
complex, classical direct Monte Carlo simulations can be very slow, and often
of little practical use. In this case, an equation-free approach may provide
effective methods for the analysis and simulation of individual-based models.
In this paper we analyze equation-free coarse projective integration. For
analytical purposes, we start with known partial differential equations
describing biological random walks and we study the projective integration of
these equations. In particular, we illustrate how to accelerate explicit
numerical methods for solving these equations. Then we present illustrative
kinetic Monte Carlo simulations of these random walks and show a decrease in
computational time by as much as a factor of a thousand can be obtained by
exploiting the ideas developed by analysis of the closed form PDEs. The
illustrative biological example here is chemotaxis, but it could be any random
walker which biases its movement in response to environmental cues.Comment: 30 pages, submitted to Physica
Multicanonical Hybrid Monte Carlo: Boosting Simulations of Compact QED
We demonstrate that substantial progress can be achieved in the study of the
phase structure of 4-dimensional compact QED by a joint use of hybrid Monte
Carlo and multicanonical algorithms, through an efficient parallel
implementation. This is borne out by the observation of considerable speedup of
tunnelling between the metastable states, close to the phase transition, on the
Wilson line. We estimate that the creation of adequate samples (with order 100
flip-flops) becomes a matter of half a year's runtime at 2 Gflops sustained
performance for lattices of size up to 24^4.Comment: 15 pages, 8 figure
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