2,130 research outputs found
Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation
Parallelism of tight-binding molecular dynamics simulations is presented by
means of the order-N electronic structure theory with the Wannier states,
recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is
tested for silicon nanocrystals of more than millions atoms with the
transferable tight-binding Hamiltonian. The efficiency of parallelism is
perfect, 98.8 %, and the method is the most suitable to parallel computation.
The elapse time for a system of atoms is 3.0 minutes by a
computer system of 64 processors of SGI Origin 3800. The calculated results are
in good agreement with the results of the exact diagonalization, with an error
of 2 % for the lattice constant and errors less than 10 % for elastic
constants.Comment: 5 pages, 3 figure
An Empirical Charge Transfer Potential with Correct Dissociation Limits
The empirical valence bond (EVB) method [J. Chem. Phys. 52, 1262 (1970)] has
always embodied charge transfer processes. The mechanism of that behavior is
examined here and recast for use as a new empirical potential energy surface
for large-scale simulations. A two-state model is explored. The main features
of the model are: (1) Explicit decomposition of the total system electron
density is invoked; (2) The charge is defined through the density decomposition
into constituent contributions; (3) The charge transfer behavior is controlled
through the resonance energy matrix elements which cannot be ignored; and (4) A
reference-state approach, similar in spirit to the EVB method, is used to
define the resonance state energy contributions in terms of "knowable"
quantities. With equal validity, the new potential energy can be expressed as a
nonthermal ensemble average with a nonlinear but analytical charge dependence
in the occupation number. Dissociation to neutral species for a gas-phase
process is preserved. A variant of constrained search density functional theory
is advocated as the preferred way to define an energy for a given charge.Comment: Submitted to J. Chem. Phys. 11/12/03. 14 pages, 8 figure
Nucleation and Bulk Crystallization in Binary Phase Field Theory
We present a phase field theory for binary crystal nucleation. In the
one-component limit, quantitative agreement is achieved with computer
simulations (Lennard-Jones system) and experiments (ice-water system) using
model parameters evaluated from the free energy and thickness of the interface.
The critical undercoolings predicted for Cu-Ni alloys accord with the
measurements, and indicate homogeneous nucleation. The Kolmogorov exponents
deduced for dendritic solidification and for "soft-impingement" of particles
via diffusion fields are consistent with experiment.Comment: 4 pages, 4 figures, accepted to PR
Results of two multi-chord stellar occultations by dwarf planet (1) Ceres
We report the results of two multi-chord stellar occultations by the dwarf
planet (1) Ceres that were observed from Brazil on 2010 August 17, and from the
USA on 2013 October 25. Four positive detections were obtained for the 2010
occultation, and nine for the 2013 occultation. Elliptical models were adjusted
to the observed chords to obtain Ceres' size and shape. Two limb fitting
solutions were studied for each event. The first one is a nominal solution with
an indeterminate polar aspect angle. The second one was constrained by the pole
coordinates as given by Drummond et al. Assuming a Maclaurin spheroid, we
determine an equatorial diameter of 972 6 km and an apparent oblateness
of 0.08 0.03 as our best solution. These results are compared to all
available size and shape determinations for Ceres made so far, and shall be
confirmed by the NASA's Dawn space mission.Comment: 9 pages, 6 figures. Accepted for publication in MNRA
Singularities and Topology of Meromorphic Functions
We present several aspects of the "topology of meromorphic functions", which
we conceive as a general theory which includes the topology of holomorphic
functions, the topology of pencils on quasi-projective spaces and the topology
of polynomial functions.Comment: 21 pages, 1 figur
Renormalization group approach to multiscale modelling in materials science
Dendritic growth, and the formation of material microstructure in general,
necessarily involves a wide range of length scales from the atomic up to sample
dimensions. The phase field approach of Langer, enhanced by optimal asymptotic
methods and adaptive mesh refinement, copes with this range of scales, and
provides an effective way to move phase boundaries. However, it fails to
preserve memory of the underlying crystallographic anisotropy, and thus is
ill-suited for problems involving defects or elasticity. The phase field
crystal (PFC) equation-- a conserving analogue of the Hohenberg-Swift equation
--is a phase field equation with periodic solutions that represent the atomic
density. It can natively model elasticity, the formation of solid phases, and
accurately reproduces the nonequilibrium dynamics of phase transitions in real
materials. However, the PFC models matter at the atomic scale, rendering it
unsuitable for coping with the range of length scales in problems of serious
interest. Here, we show that a computationally-efficient multiscale approach to
the PFC can be developed systematically by using the renormalization group or
equivalent techniques to derive appropriate coarse-grained coupled phase and
amplitude equations, which are suitable for solution by adaptive mesh
refinement algorithms
Thermodynamic Behavior of a Model Covalent Material Described by the Environment-Dependent Interatomic Potential
Using molecular dynamics simulations we study the thermodynamic behavior of a
single-component covalent material described by the recently proposed
Environment-Dependent Interatomic Potential (EDIP). The parameterization of
EDIP for silicon exhibits a range of unusual properties typically found in more
complex materials, such as the existence of two structurally distinct
disordered phases, a density decrease upon melting of the low-temperature
amorphous phase, and negative thermal expansion coefficients for both the
crystal (at high temperatures) and the amorphous phase (at all temperatures).
Structural differences between the two disordered phases also lead to a
first-order transition between them, which suggests the existence of a second
critical point, as is believed to exist for amorphous forms of frozen water.
For EDIP-Si, however, the unusual behavior is associated not only with the open
nature of tetrahedral bonding but also with a competition between four-fold
(covalent) and five-fold (metallic) coordination. The unusual behavior of the
model and its unique ability to simulation the liquid/amorphous transition on
molecular-dynamics time scales make it a suitable prototype for fundamental
studies of anomalous thermodynamics in disordeered systems.Comment: 48 pages (double-spaced), 13 figure
Elastic moduli, dislocation core energy and melting of hard disks in two dimensions
Elastic moduli and dislocation core energy of the triangular solid of hard
disks of diameter are obtained in the limit of vanishing dislocation-
antidislocation pair density, from Monte Carlo simulations which incorporates a
constraint, namely that all moves altering the local connectivity away from
that of the ideal triangular lattice are rejected. In this limit, we show that
the solid is stable against all other fluctuations at least upto densities as
low as . Our system does not show any phase transition so
diverging correlation lengths leading to finite size effects and slow
relaxations do not exist. The dislocation pair formation probability is
estimated from the fraction of moves rejected due to the constraint which
yields, in turn, the core energy E_c and the (bare) dislocation fugacity y.
Using these quantities, we check the relative validity of first order and
Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) melting scenarios and obtain
numerical estimates of the typical expected transition densities and pressures.
We conclude that a KTHNY transition from the solid to a hexatic phase preempts
the solid to liquid first order transition in this system albeit by a very
small margin, easily masked by crossover effects in unconstrained
``brute-force'' simulations with small number of particles.Comment: 17 pages, 8 figure
Inhibition of Nox2 Oxidase Activity Ameliorates Influenza A Virus-Induced Lung Inflammation
Influenza A virus pandemics and emerging anti-viral resistance highlight the urgent need for novel generic pharmacological strategies that reduce both viral replication and lung inflammation. We investigated whether the primary enzymatic source of inflammatory cell ROS (reactive oxygen species), Nox2-containing NADPH oxidase, is a novel pharmacological target against the lung inflammation caused by influenza A viruses. Male WT (C57BL/6) and Nox2−/y mice were infected intranasally with low pathogenicity (X-31, H3N2) or higher pathogenicity (PR8, H1N1) influenza A virus. Viral titer, airways inflammation, superoxide and peroxynitrite production, lung histopathology, pro-inflammatory (MCP-1) and antiviral (IL-1β) cytokines/chemokines, CD8+ T cell effector function and alveolar epithelial cell apoptosis were assessed. Infection of Nox2−/y mice with X-31 virus resulted in a significant reduction in viral titers, BALF macrophages, peri-bronchial inflammation, BALF inflammatory cell superoxide and lung tissue peroxynitrite production, MCP-1 levels and alveolar epithelial cell apoptosis when compared to WT control mice. Lung levels of IL-1β were ∼3-fold higher in Nox2−/y mice. The numbers of influenza-specific CD8+DbNP366+ and DbPA224+ T cells in the BALF and spleen were comparable in WT and Nox2−/y mice. In vivo administration of the Nox2 inhibitor apocynin significantly suppressed viral titer, airways inflammation and inflammatory cell superoxide production following infection with X-31 or PR8. In conclusion, these findings indicate that Nox2 inhibitors have therapeutic potential for control of lung inflammation and damage in an influenza strain-independent manner
Protective role of vitamin B6 (PLP) against DNA damage in Drosophila models of type 2 diabetes
Growing evidence shows that improper intake of vitamin B6 increases cancer risk and several studies indicate that diabetic patients have a higher risk of developing tumors. We previously demonstrated that in Drosophila the deficiency of Pyridoxal 5' phosphate (PLP), the active form of vitamin B6, causes chromosome aberrations (CABs), one of cancer prerequisites, and increases hemolymph glucose content. Starting from these data we asked if it was possible to provide a link between the aforementioned studies. Thus, we tested the effect of low PLP levels on DNA integrity in diabetic cells. To this aim we generated two Drosophila models of type 2 diabetes, the first by impairing insulin signaling and the second by rearing flies in high sugar diet. We showed that glucose treatment induced CABs in diabetic individuals but not in controls. More interestingly, PLP deficiency caused high frequencies of CABs in both diabetic models demonstrating that hyperglycemia, combined to reduced PLP level, impairs DNA integrity. PLP-depleted diabetic cells accumulated Advanced Glycation End products (AGEs) that largely contribute to CABs as α-lipoic acid, an AGE inhibitor, rescued not only AGEs but also CABs. These data, extrapolated to humans, indicate that low PLP levels, impacting on DNA integrity, may be considered one of the possible links between diabetes and cancer
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