936 research outputs found
Traveling through potential energy landscapes of disordered materials: the activation-relaxation technique
A detailed description of the activation-relaxation technique (ART) is
presented. This method defines events in the configurational energy landscape
of disordered materials, such as a-Si, glasses and polymers, in a two-step
process: first, a configuration is activated from a local minimum to a nearby
saddle-point; next, the configuration is relaxed to a new minimum; this allows
for jumps over energy barriers much higher than what can be reached with
standard techniques. Such events can serve as basic steps in equilibrium and
kinetic Monte Carlo schemes.Comment: 7 pages, 2 postscript figure
Event-based relaxation of continuous disordered systems
A computational approach is presented to obtain energy-minimized structures
in glassy materials. This approach, the activation-relaxation technique (ART),
achieves its efficiency by focusing on significant changes in the microscopic
structure (events). The application of ART is illustrated with two examples:
the structure of amorphous silicon, and the structure of Ni80P20, a metallic
glass.Comment: 4 pages, revtex, epsf.sty, 3 figure
Structural, electronic, and dynamical properties of amorphous gallium arsenide: a comparison between two topological models
We present a detailed study of the effect of local chemical ordering on the
structural, electronic, and dynamical properties of amorphous gallium arsenide.
Using the recently-proposed ``activation-relaxation technique'' and empirical
potentials, we have constructed two 216-atom tetrahedral continuous random
networks with different topological properties, which were further relaxed
using tight-binding molecular dynamics. The first network corresponds to the
traditional, amorphous, Polk-type, network, randomly decorated with Ga and As
atoms. The second is an amorphous structure with a minimum of wrong (homopolar)
bonds, and therefore a minimum of odd-membered atomic rings, and thus
corresponds to the Connell-Temkin model. By comparing the structural,
electronic, and dynamical properties of these two models, we show that the
Connell-Temkin network is energetically favored over Polk, but that most
properties are little affected by the differences in topology. We conclude that
most indirect experimental evidence for the presence (or absence) of wrong
bonds is much weaker than previously believed and that only direct structural
measurements, i.e., of such quantities as partial radial distribution
functions, can provide quantitative information on these defects in a-GaAs.Comment: 10 pages, 7 ps figures with eps
Self-organized criticality in the intermediate phase of rigidity percolation
Experimental results for covalent glasses have highlighted the existence of a
new self-organized phase due to the tendency of glass networks to minimize
internal stress. Recently, we have shown that an equilibrated self-organized
two-dimensional lattice-based model also possesses an intermediate phase in
which a percolating rigid cluster exists with a probability between zero and
one, depending on the average coordination of the network. In this paper, we
study the properties of this intermediate phase in more detail. We find that
microscopic perturbations, such as the addition or removal of a single bond,
can affect the rigidity of macroscopic regions of the network, in particular,
creating or destroying percolation. This, together with a power-law
distribution of rigid cluster sizes, suggests that the system is maintained in
a critical state on the rigid/floppy boundary throughout the intermediate
phase, a behavior similar to self-organized criticality, but, remarkably, in a
thermodynamically equilibrated state. The distinction between percolating and
non-percolating networks appears physically meaningless, even though the
percolating cluster, when it exists, takes up a finite fraction of the network.
We point out both similarities and differences between the intermediate phase
and the critical point of ordinary percolation models without
self-organization. Our results are consistent with an interpretation of recent
experiments on the pressure dependence of Raman frequencies in chalcogenide
glasses in terms of network homogeneity.Comment: 20 pages, 18 figure
Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus
This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory
Crater lake cichlids individually specialize along the benthic-limnetic axis
A common pattern of adaptive diversification in freshwater fishes is the repeated evolution of elongated open water (limnetic) species and high-bodied shore (benthic) species from generalist ancestors. Studies on phenotype-diet correlations have suggested that population-wide individual specialization occurs at an early evolutionary and ecological stage of divergence and niche partitioning. This variable restricted niche use across individuals can provide the raw material for earliest stages of sympatric divergence. We investigated variation in morphology and diet as well as their correlations along the benthic-limnetic axis in an extremely young Midas cichlid species, Amphilophus tolteca, endemic to the Nicaraguan crater lake Asososca Managua. We found that A. tolteca varied continuously in ecologically relevant traits such as body shape and lower pharyngeal jaw morphology. The correlation of these phenotypes with niche suggested that individuals are specialized along the benthic-limnetic axis. No genetic differentiation within the crater lake was detected based on genotypes from 13 microsatellite loci. Overall, we found that individual specialization in this young crater lake species encompasses the limnetic- as well as the benthic macro-habitat. Yet there is no evidence for any diversification within the species, making this a candidate system for studying what might be the early stages preceding sympatric divergence
Self-organization with equilibration: a model for the intermediate phase in rigidity percolation
Recent experimental results for covalent glasses suggest the existence of an
intermediate phase attributed to the self-organization of the glass network
resulting from the tendency to minimize its internal stress. However, the exact
nature of this experimentally measured phase remains unclear. We modify a
previously proposed model of self-organization by generating a uniform sampling
of stress-free networks. In our model, studied on a diluted triangular lattice,
an unusual intermediate phase appears, in which both rigid and floppy networks
have a chance to occur, a result also observed in a related model on a Bethe
lattice by Barre et al. [Phys. Rev. Lett. 94, 208701 (2005)]. Our results for
the bond-configurational entropy of self-organized networks, which turns out to
be only about 2% lower than that of random networks, suggest that a
self-organized intermediate phase could be common in systems near the rigidity
percolation threshold.Comment: 9 pages, 6 figure
Drug treatment of malaria infections can reduce levels of protection transferred to offspring via maternal immunity
Maternally transferred immunity can have a fundamental effect on the ability of offspring to deal with infection. However, levels of antibodies in adults can vary both quantitatively and qualitatively between individuals and during the course of infection. How infection dynamics and their modification by drug treatment might affect the protection transferred to offspring remains poorly understood. Using the rodent malaria parasite Plasmodium chabaudi, we demonstrate that curing dams part way through infection prior to pregnancy can alter their immune response, with major consequences for offspring health and survival. In untreated maternal infections, maternally transferred protection suppressed parasitaemia and reduced pup mortality by 75 per cent compared with pups from naïve dams. However, when dams were treated with anti-malarial drugs, pups received fewer maternal antibodies, parasitaemia was only marginally suppressed, and mortality risk was 25 per cent higher than for pups from dams with full infections. We observed the same qualitative patterns across three different host strains and two parasite genotypes. This study reveals the role that within-host infection dynamics play in the fitness consequences of maternally transferred immunity. Furthermore, it highlights a potential trade-off between the health of mothers and offspring suggesting that anti-parasite treatment may significantly affect the outcome of infection in newborns
Simulation study of the inhomogeneous Olami-Feder-Christensen model of earthquakes
Statistical properties of the inhomogeneous version of the
Olami-Feder-Christensen (OFC) model of earthquakes is investigated by numerical
simulations. The spatial inhomogeneity is assumed to be dynamical. Critical
features found in the original homogeneous OFC model, e.g., the
Gutenberg-Richter law and the Omori law are often weakened or suppressed in the
presence of inhomogeneity, whereas the characteristic features found in the
original homogeneous OFC model, e.g., the near-periodic recurrence of large
events and the asperity-like phenomena persist.Comment: Shortened from the first version. To appear in European Physical
Journal
Towards device-size atomistic models of amorphous silicon
The atomic structure of amorphous materials is believed to be well described
by the continuous random network model. We present an algorithm for the
generation of large, high-quality continuous random networks. The algorithm is
a variation of the "sillium" approach introduced by Wooten, Winer, and Weaire.
By employing local relaxation techniques, local atomic rearrangements can be
tried that scale almost independently of system size. This scaling property of
the algorithm paves the way for the generation of realistic device-size atomic
networks.Comment: 7 pages, 3 figure
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