5,416 research outputs found
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Multiscale and inhomogeneous molecular systems are challenging topics in the
field of molecular simulation. In particular, modeling biological systems in
the context of multiscale simulations and exploring material properties are
driving a permanent development of new simulation methods and optimization
algorithms. In computational terms, those methods require parallelization
schemes that make a productive use of computational resources for each
simulation and from its genesis. Here, we introduce the heterogeneous domain
decomposition approach which is a combination of an heterogeneity sensitive
spatial domain decomposition with an \textit{a priori} rearrangement of
subdomain-walls. Within this approach, the theoretical modeling and
scaling-laws for the force computation time are proposed and studied as a
function of the number of particles and the spatial resolution ratio. We also
show the new approach capabilities, by comparing it to both static domain
decomposition algorithms and dynamic load balancing schemes. Specifically, two
representative molecular systems have been simulated and compared to the
heterogeneous domain decomposition proposed in this work. These two systems
comprise an adaptive resolution simulation of a biomolecule solvated in water
and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure
Interacting Growth Walk on a honeycomb lattice
The Interacting Growth Walk (IGW) is a kinetic algorithm proposed recently
for generating long, compact, self avoiding walks. The growth process in IGW is
tuned by the so called growth temperature . On a square
lattice and at , IGW is attrition free and hence grows indefinitely. In
this paper we consider IGW on a honeycomb lattice. We take contact energy, see
text, as . We show that IGW at
() is identical to Interacting Self Avoiding Walk (ISAW) at
(). Also IGW at ()
corresponds to ISAW at (). For other
temperatures we need to introduce a statistical weight factor to a walk of the
IGW ensemble to make correspondence with the ISAW ensemble.Comment: 3 pages, 1 figure, REVTEX fil
Exciton doublet in the Mott-Hubbard LiCuVO insulator identified by spectral ellipsometry
Spectroscopic ellipsometry was used to study the dielectric function of
LiCuVO, a compound comprised of chains of edge-sharing CuO
plaquettes, in the spectral range (0.75 - 6.5) eV at temperatures (7-300) K.
For photon polarization along the chains, the data reveal a weak but
well-resolved two-peak structure centered at 2.15 and 2.95 eV whose spectral
weight is strongly enhanced upon cooling near the magnetic ordering
temperature. We identify these features as an exciton doublet in the
Mott-Hubbard gap that emerges as a consequence of the Coulomb interaction
between electrons on nearest and next-nearest neighbor sites along the chains.
Our results and methodology can be used to address the role of the long-range
Coulomb repulsion for compounds with doped copper-oxide chains and planes.Comment: 4 pages with 4 figures and EPAPS supplementary online material (3
pages with 4 figures), accepted in Phys. Rev. Let
Irreversible Processes in a Universe modelled as a mixture of a Chaplygin gas and radiation
The evolution of a Universe modelled as a mixture of a Chaplygin gas and
radiation is determined by taking into account irreversible processes. This
mixture could interpolate periods of a radiation dominated, a matter dominated
and a cosmological constant dominated Universe. The results of a Universe
modelled by this mixture are compared with the results of a mixture whose
constituents are radiation and quintessence. Among other results it is shown
that: (a) for both models there exists a period of a past deceleration with a
present acceleration; (b) the slope of the acceleration of the Universe
modelled as a mixture of a Chaplygin gas with radiation is more pronounced than
that modelled as a mixture of quintessence and radiation; (c) the energy
density of the Chaplygin gas tends to a constant value at earlier times than
the energy density of quintessence does; (d) the energy density of radiation
for both mixtures coincide and decay more rapidly than the energy densities of
the Chaplygin gas and of quintessence.Comment: 8 pages, 1 figure, to be published in GR
Ground state of two unlike charged colloids: An analogy with ionic bonding
In this letter, we study the ground state of two spherical macroions of
identical radius, but asymmetric bare charge ((Q_{A}>Q_{B})). Electroneutrality
of the system is insured by the presence of the surrounding divalent
counterions. Using Molecular Dynamics simulations within the framework of the
primitive model, we show that the ground state of such a system consists of an
overcharged and an undercharged colloid. For a given macroion separation the
stability of these ionized-like states is a function of the difference
((\sqrt{N_{A}}-\sqrt{N_{B}})) of neutralizing counterions (N_{A}) and (N_{B}).
Furthermore the degree of ionization, or equivalently, the degree of
overcharging, is also governed by the distance separation of the macroions. The
natural analogy with ionic bonding is briefly discussed.Comment: published versio
Band filling and interband scattering effects in MgB: C vs Al doping
We argue, based on band structure calculations and Eliashberg theory, that
the observed decrease of of Al and C doped MgB samples can be
understood mainly in terms of a band filling effect due to the electron doping
by Al and C. A simple scaling of the electron-phonon coupling constant
by the variation of the density of states as function of electron
doping is sufficient to capture the experimentally observed behavior. Further,
we also explain the long standing open question of the experimental observation
of a nearly constant gap as function of doping by a compensation of the
effect of band filling and interband scattering. Both effects together generate
a nearly constant gap and shift the merging point of both gaps to higher
doping concentrations, resolving the discrepancy between experiment and
theoretical predictions based on interband scattering only.Comment: accepted by PR
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