942 research outputs found
Non-equilibrium statistical mechanics of classical nuclei interacting with the quantum electron gas
Kinetic equations governing time evolution of positions and momenta of atoms
in extended systems are derived using quantum-classical ensembles within the
Non-Equilibrium Statistical Operator Method (NESOM). Ions are treated
classically, while their electrons quantum mechanically; however, the
statistical operator is not factorised in any way and no simplifying
assumptions are made concerning the electronic subsystem. Using this method, we
derive kinetic equations of motion for the classical degrees of freedom (atoms)
which account fully for the interaction and energy exchange with the quantum
variables (electrons). Our equations, alongside the usual Newtonian-like terms
normally associated with the Ehrenfest dynamics, contain additional terms,
proportional to the atoms velocities, which can be associated with the
electronic friction. Possible ways of calculating the friction forces which are
shown to be given via complicated non-equilibrium correlation functions, are
discussed. In particular, we demonstrate that the correlation functions are
directly related to the thermodynamic Matsubara Green's functions, and this
relationship allows for the diagrammatic methods to be used in treating
electron-electron interaction perturbatively when calculating the correlation
functions. This work also generalises previous attempts, mostly based on model
systems, of introducing the electronic friction into Molecular Dynamics
equations of atoms.Comment: 18 page
Magnetic friction due to vortex fluctuation
We use Monte Carlo and molecular dynamics simulation to study a magnetic
tip-sample interaction. Our interest is to understand the mechanism of heat
dissipation when the forces involved in the system are magnetic in essence. We
consider a magnetic crystalline substrate composed of several layers
interacting magnetically with a tip. The set is put thermally in equilibrium at
temperature T by using a numerical Monte Carlo technique. By using that
configuration we study its dynamical evolution by integrating numerically the
equations of motion. Our results suggests that the heat dissipation in this
system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure
Class of dilute granular Couette flows with uniform heat flux
In a recent paper [F. Vega Reyes et al., Phys. Rev. Lett. 104, 028001 (2010)]
we presented a preliminary description of a special class of steady Couette
flows in dilute granular gases. In all flows of this class the viscous heating
is exactly balanced by inelastic cooling. This yields a uniform heat flux and a
linear relationship between the local temperature and flow velocity. The class
(referred to as the LTu class) includes the Fourier flow of ordinary gases and
the simple shear flow of granular gases as special cases. In the present paper
we provide further support for this class of Couette flows by following four
different routes, two of them being theoretical (Grad's moment method of the
Boltzmann equation and exact solution of a kinetic model) and the other two
being computational (molecular dynamics and Monte Carlo simulations of the
Boltzmann equation). Comparison between theory and simulations shows a very
good agreement for the non-Newtonian rheological properties, even for quite
strong inelasticity, and a good agreement for the heat flux coefficients in the
case of Grad's method, the agreement being only qualitative in the case of the
kinetic model.Comment: 15 pages, 10 figures; v2: change of title plus some other minor
change
The Knudsen temperature jump and the Navier-Stokes hydrodynamics of granular gases driven by thermal walls
Thermal wall is a convenient idealization of a rapidly vibrating plate used
for vibrofluidization of granular materials. The objective of this work is to
incorporate the Knudsen temperature jump at thermal wall in the Navier-Stokes
hydrodynamic modeling of dilute granular gases of monodisperse particles that
collide nearly elastically. The Knudsen temperature jump manifests itself as an
additional term, proportional to the temperature gradient, in the boundary
condition for the temperature. Up to a numerical pre-factor of order unity,
this term is known from kinetic theory of elastic gases. We determine the
previously unknown numerical pre-factor by measuring, in a series of molecular
dynamics (MD) simulations, steady-state temperature profiles of a gas of
elastically colliding hard disks, confined between two thermal walls kept at
different temperatures, and comparing the results with the predictions of a
hydrodynamic calculation employing the modified boundary condition. The
modified boundary condition is then applied, without any adjustable parameters,
to a hydrodynamic calculation of the temperature profile of a gas of inelastic
hard disks driven by a thermal wall. We find the hydrodynamic prediction to be
in very good agreement with MD simulations of the same system. The results of
this work pave the way to a more accurate hydrodynamic modeling of driven
granular gases.Comment: 7 pages, 3 figure
Molecular dynamics simulation of polymer helix formation using rigid-link methods
Molecular dynamics simulations are used to study structure formation in
simple model polymer chains that are subject to excluded volume and torsional
interactions. The changing conformations exhibited by chains of different
lengths under gradual cooling are followed until each reaches a state from
which no further change is possible. The interactions are chosen so that the
true ground state is a helix, and a high proportion of simulation runs succeed
in reaching this state; the fraction that manage to form defect-free helices is
a function of both chain length and cooling rate. In order to demonstrate
behavior analogous to the formation of protein tertiary structure, additional
attractive interactions are introduced into the model, leading to the
appearance of aligned, antiparallel helix pairs. The simulations employ a
computational approach that deals directly with the internal coordinates in a
recursive manner; this representation is able to maintain constant bond lengths
and angles without the necessity of treating them as an algebraic constraint
problem supplementary to the equations of motion.Comment: 15 pages, 14 figure
Exciton correlations in coupled quantum wells and their luminescence blue shift
In this paper we present a study of an exciton system where electrons and
holes are confined in double quantum well structures. The dominating
interaction between excitons in such systems is a dipole - dipole repulsion. We
show that the tail of this interaction leads to a strong correlation between
excitons and substantially affects the behavior of the system. Making use of
qualitative arguments and estimates we develop a picture of the exciton -
exciton correlations in the whole region of temperature and concentration where
excitons exist. It appears that at low concentration degeneracy of the excitons
is accompanied with strong multi-particle correlation so that the system cannot
be considered as a gas. At high concentration the repulsion suppresses the
quantum degeneracy down to temperatures that could be much lower than in a Bose
gas with contact interaction. We calculate the blue shift of the exciton
luminescence line which is a sensitive tool to observe the exciton - exciton
correlations.Comment: 27 pages in PDF and DVI format, 8 figure
Effect of bond lifetime on the dynamics of a short-range attractive colloidal system
We perform molecular dynamics simulations of short-range attractive colloid
particles modeled by a narrow (3% of the hard sphere diameter) square well
potential of unit depth. We compare the dynamics of systems with the same
thermodynamics but different bond lifetimes, by adding to the square well
potential a thin barrier at the edge of the attractive well. For permanent
bonds, the relaxation time diverges as the packing fraction
approaches a threshold related to percolation, while for short-lived bonds, the
-dependence of is more typical of a glassy system. At intermediate
bond lifetimes, the -dependence of is driven by percolation at low
, but then crosses over to glassy behavior at higher . We also
study the wavevector dependence of the percolation dynamics.Comment: Revised; 9 pages, 9 figure
Generalized quantum cumulant dynamics
A means of unifying some semiclassical models of computational chemistry is presented; these include quantized Hamiltonian dynamics, quantal cumulant dynamics, and semiclassical Moyal dynamics (SMD). A general method for creating the infinite hierarchy of operator dynamics in the Heisenberg picture is derived together with a general method for truncation (or closure) of that series, and in addition, we provide a simple link to the phase space methods of SMD. Operator equations of arbitrary order may be created readily, avoiding the tedious algebra identified previously. Truncation is based on a simple recurrence formula which is related to, but avoids the more complex contractions of, Wick's theorem. This generalized method is validated against a number of trial problems considered using the previous methods. We also touch on some of the limitations involved using such methods, noting, in particular, that any truncation will lead to a state which is in some sense unphysical. Finally, we briefly introduce our quantum algebra package QuantAL which provides an automated method for the generation of the required equation set, the initial conditions for all variables from any start, and all the higher order approximations necessary for truncation of the series, at essentially arbitrary order
Statistical Properties of Contact Maps
A contact map is a simple representation of the structure of proteins and
other chain-like macromolecules. This representation is quite amenable to
numerical studies of folding. We show that the number of contact maps
corresponding to the possible configurations of a polypeptide chain of N amino
acids, represented by (N-1)-step self avoiding walks on a lattice, grows
exponentially with N for all dimensions D>1. We carry out exact enumerations in
D=2 on the square and triangular lattices for walks of up to 20 steps and
investigate various statistical properties of contact maps corresponding to
such walks. We also study the exact statistics of contact maps generated by
walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.
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