1,699 research outputs found
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
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
Trypanosoma cruzi phosphomannomutase and guanosine diphosphate-mannose pyrophosphorylase ligandability assessment
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
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
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
Hydration interactions: aqueous solvent effects in electric double layers
A model for ionic solutions with an attractive short-range pair interaction
between the ions is presented. The short-range interaction is accounted for by
adding a quadratic non-local term to the Poisson-Boltzmann free energy. The
model is used to study solvent effects in a planar electric double layer. The
counter-ion density is found to increase near the charged surface, as compared
with the Poisson-Boltzmann theory, and to decrease at larger distances. The ion
density profile is studied analytically in the case where the ion distribution
near the plate is dominated only by counter-ions. Further away from the plate
the density distribution can be described using a Poisson-Boltzmann theory with
an effective surface charge that is smaller than the actual one.Comment: 11 Figures in 13 files + LaTex file. 20 pages. Accepted to Phys. Rev.
E. Corrected typos and reference
A Method to Study Relaxation of Metastable Phases: Macroscopic Mean-Field Dynamics
We propose two different macroscopic dynamics to describe the decay of
metastable phases in many-particle systems with local interactions. These
dynamics depend on the macroscopic order parameter through the restricted
free energy and are designed to give the correct equilibrium
distribution for . The connection between macroscopic dynamics and the
underlying microscopic dynamic are considered in the context of a projection-
operator formalism. Application to the square-lattice nearest-neighbor Ising
ferromagnet gives good agreement with droplet theory and Monte Carlo
simulations of the underlying microscopic dynamic. This includes quantitative
agreement for the exponential dependence of the lifetime on the inverse of the
applied field , and the observation of distinct field regions in which the
derivative of the lifetime with respect to depends differently on . In
addition, at very low temperatures we observe oscillatory behavior of this
derivative with respect to , due to the discreteness of the lattice and in
agreement with rigorous results. Similarities and differences between this work
and earlier works on finite Ising models in the fixed-magnetization ensemble
are discussed.Comment: 44 pages RevTeX3, 11 uuencoded Postscript figs. in separate file
Grundstate Properties of the 3D Ising Spin Glass
We study zero--temperature properties of the 3d Edwards--Anderson Ising spin
glass on finite lattices up to size . Using multicanonical sampling we
generate large numbers of groundstate configurations in thermal equilibrium.
Finite size scaling with a zero--temperature scaling exponent describes the data well. Alternatively, a descriptions in terms of Parisi
mean field behaviour is still possible. The two scenarios give significantly
different predictions on lattices of size .Comment: LATEX 9pages,figures upon request ,SCRI-9
Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state
An important step in a phospholipid membrane pore formation by melittin
antimicrobial peptide is a reorientation of the peptide from a surface into a
transmembrane conformation. In this work we perform umbrella sampling
simulations to calculate the potential of mean force (PMF) for the
reorientation of melittin from a surface-bound state to a transmembrane state
and provide a molecular level insight into understanding peptide and lipid
properties that influence the existence of the free energy barrier. The PMFs
were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We
observe that the free energy barrier is reduced when the P/L ratio increased.
In addition, we study the cooperative effect; specifically we investigate if
the barrier is smaller for a second melittin reorientation, given that another
neighboring melittin was already in the transmembrane state. We observe that
indeed the barrier of the PMF curve is reduced in this case, thus confirming
the presence of a cooperative effect
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