752 research outputs found
Local Simulation Algorithms for Coulombic Interactions
We consider dynamically constrained Monte-Carlo dynamics and show that this
leads to the generation of long ranged effective interactions. This allows us
to construct a local algorithm for the simulation of charged systems without
ever having to evaluate pair potentials or solve the Poisson equation. We
discuss a simple implementation of a charged lattice gas as well as more
elaborate off-lattice versions of the algorithm. There are analogies between
our formulation of electrostatics and the bosonic Hubbard model in the phase
approximation. Cluster methods developed for this model further improve the
efficiency of the electrostatics algorithm.Comment: Proceedings Statphys22 10 page
Modifications of turbulence and turbulent transport associated with a bias-induced confinement transition in LAPD
Azimuthal flow is driven in the edge of the Large Plasma Device (LAPD) [W.
Gekelman, {\itshape et. al}, Rev. Sci. Instr. {\bfseries 62}, 2875 (1991)]
through biasing a section of the vacuum vessel relative to the plasma source
cathode. As the applied bias exceeds a threshold, a transition in radial
particle confinement is observed, evidenced by a dramatic steepening in the
density profile, similar to the L- to H-mode transition in toroidal confinement
devices. The threshold behavior and dynamic behavior of radial transport is
related to flow penetration and the degree of spatial overlap between the flow
shear and density gradient profiles. An investigation of the changes in
turbulence and turbulent particle transport associated with the confinement
transition is presented. Two-dimensional cross-correlation measurements show
that the spatial coherence of edge turbulence in LAPD changes significantly
with biasing. The azimuthal correlation in the turbulence increases
dramatically, while the radial correlation length is little altered. Turbulent
amplitude is reduced at the transition, particularly in electric field
fluctuations, but the dominant change observed is in the cross-phase between
density and electric field fluctuations. The changes in cross-phase lead to a
suppression and then apparent reversal of turbulent particle flux as the
threshold is exceeded.Comment: 11 pages, 13 figures, accepted for publication in Physics of Plasmas
(to appear Jan 2009 issue
Comment on "Elasticity Model of a Supercoiled DNA Molecule"
We perform simulations to numerically study the writhe distribution of a
stiff polymer. We compare with analytic results of Bouchiat and Mezard (PRL 80
1556- (1998); cond-mat/9706050).Comment: 1 page, 1 figure revtex
Modification of turbulent transport with continuous variation of flow shear in the Large Plasma Device
Continuous control over azimuthal flow and shear in the edge of the Large
Plasma Device (LAPD) has been achieved using a biasable limiter which has
allowed a careful study of the effect of flow shear on pressure-gradient-driven
turbulence and transport in LAPD. LAPD rotates spontaneously in the ion
diamagnetic direction (IDD); positive limiter bias first reduces, then
minimizes (producing a near-zero shear state), and finally reverses the flow
into the electron diamagnetic direction (EDD). Degradation of particle
confinement is observed in the minimum shearing state and reduction in
turbulent particle flux is observed with increasing shearing in both flow
directions. Near-complete suppression of turbulent particle flux is observed
for shearing rates comparable to the turbulent autocorrelation rate measured in
the minimum shear state. Turbulent flux suppression is dominated by amplitude
reduction in low-frequency (kHz) density fluctuations. An increase in
fluctuations for the highest shearing states is observed with the emergence of
a coherent mode which does not lead to net particle transport. The variations
of density fluctuations are fit well with power-laws and compare favorably to
simple models of shear suppression of transport.Comment: 10 pages, 5 figures; Submitted to Phys. Rev. Let
Energy gaps in quantum first-order mean-field-like transitions: The problems that quantum annealing cannot solve
We study first-order quantum phase transitions in models where the mean-field
traitment is exact, and the exponentially fast closure of the energy gap with
the system size at the transition. We consider exactly solvable ferromagnetic
models, and show that they reduce to the Grover problem in a particular limit.
We compute the coefficient in the exponential closure of the gap using an
instantonic approach, and discuss the (dire) consequences for quantum
annealing.Comment: 6 pages, 3 figure
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers
In this paper, we have studied, within a discrete WLC model, the spatial
constraints in magnetic tweezers used in single molecule experiments. Two
elements are involved: first, the fixed plastic slab on which is stuck the
initial strand, second, the magnetic bead which pulls (or twists) the attached
molecule free end. We have shown that the bead surface can be replaced by its
tangent plane at the anchoring point, when it is close to the bead south pole
relative to the force. We are led to a model with two parallel repulsive
plates: the fixed anchoring plate and a fluctuating plate, simulating the bead,
in thermal equilibrium with the system. The bead effect is a slight upper shift
of the elongation, about four times smaller than the similar effect induced by
the fixed plate. This rather unexpected result, has been qualitatively
confirmed within the soluble Gaussian model. A study of the molecule elongation
versus the countour length exhibits a significant non-extensive behaviour. The
curve for short molecules (with less than 2 kbp) is well fitted by a straight
line, with a slope given by the WLC model, but it does not go through the
origin. The non-extensive offset gives a 15% upward shift to the elongation of
a 2 kbp molecule stretched by a 0.3 pN force.Comment: 28 pages, 6 figures An explanatory figure has been added. The
physical interpretation of the results has been made somewhat more
transparen
Simulation of a semiflexible polymer in a narrow cylindrical pore
The probability that a randomly accelerated particle in two dimensions has
not yet left a simply connected domain after a time decays as
for long times. The same quantity also determines the
confinement free energy per unit length of a
semiflexible polymer in a narrow cylindrical pore with cross section . From simulations of a randomly accelerated particle we estimate the
universal amplitude of for both circular and rectangular cross
sections.Comment: 10 pages, 2 eps figure
Entropic Elasticity of Double-Strand DNA Subject to Simple Spatial Constraints
The aim of the present paper is the study of the entropic elasticity of the
dsDNA molecule, having a cristallographic length L of the order of 10 to 30
persistence lengths A, when it is subject to spatial obstructions. We have not
tried to obtain the single molecule partition function by solving a
Schodringer-like equation. We prefer to stay within a discretized version of
the WLC model with an added one-monomer potential, simulating the spatial
constraints. We derived directly from the discretized Boltzmann formula the
transfer matrix connecting the partition functions relative to adjacent
"effective monomers". We have plugged adequate Dirac delta-functions in the
functional integral to ensure that the monomer coordinate and the tangent
vector are independent variables. The partition function is, then, given by an
iterative process which is both numerically efficient and physically
transparent. As a test of our discretized approach, we have studied two
configurations involving a dsDNA molecule confined between a pair of parallel
plates.Comment: The most formal developments of Section I have been moved into an
appendix and replaced by a direct derivation of the transfer matrix used in
the applications. of Section II. Two paragraphs and two figures have been
added to clarify the physical interpretation of the result
Two-point microrheology and the electrostatic analogy
The recent experiments of Crocker et al. suggest that microrheological
measurements obtained from the correlated fluctuations of widely-separatedprobe
particles determine the rheological properties of soft, complex materials more
accurately than do the more traditional particle autocorrelations. This
presents an interesting problem in viscoelastic dynamics. We develop an
important, simplifing analogy between the present viscoelastic problem and
classical electrostatics. Using this analogy and direct calculation we analyze
both the one and two particle correlations in a viscoelastic medium in order to
explain this observation
Local Simulation Algorithms for Coulomb Interaction
Long ranged electrostatic interactions are time consuming to calculate in
molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic
framework for simulating charged particles which modifies the dynamics so as to
allow equilibration using a local Hamiltonian. The method introduces an
auxiliary field with constrained dynamics so that the equilibrium distribution
is determined by the Coulomb interaction. We demonstrate the efficiency of the
method by simulating a simple, charged lattice gas.Comment: Last figure changed to improve demonstration of numerical efficienc
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