Efficient tight-binding Monte Carlo structural sampling of complex materials

While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte Carlo algorithm that makes use of the possibility of quickly evaluating local energies. For the thermalization of a 1000-atom configuration of {\it a}-Si, this algorithm gains about an order of magnitude in speed over standard molecular dynamics. The algorithm can easily be ported to a wide range of materials and can be dynamically optimized for a maximum efficiency.Comment: 5 pages including 3 postscript figure

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

Blimp-1-dependent and -independent natural antibody production by B-1 and B-1-derived plasma cells.

Natural antibodies contribute to tissue homeostasis and protect against infections. They are secreted constitutively without external antigenic stimulation. The differentiation state and regulatory pathways that enable continuous natural antibody production by B-1 cells, the main cellular source in mice, remain incompletely understood. Here we demonstrate that natural IgM-secreting B-1 cells in the spleen and bone marrow are heterogeneous, consisting of (a) terminally differentiated B-1-derived plasma cells expressing the transcriptional regulator of differentiation, Blimp-1, (b) Blimp-1+, and (c) Blimp-1neg phenotypic B-1 cells. Blimp-1neg IgM-secreting B-1 cells are not simply intermediates of cellular differentiation. Instead, they secrete similar amounts of IgM in wild-type and Blimp-1-deficient (PRDM-1ΔEx1A) mice. Blimp-1neg B-1 cells are also a major source of IgG3. Consequently, deletion of Blimp-1 changes neither serum IgG3 levels nor the amount of IgG3 secreted per cell. Thus, the pool of natural antibody-secreting B-1 cells is heterogeneous and contains a distinct subset of cells that do not use Blimp-1 for initiation or maximal antibody secretion

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

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

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

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

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