Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotati...
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Continuing on recent computational and experimental work on jammed packings of hard ellipsoids [Donev et al., Science 303, 990 (2004)] we consider jamming in packings of smooth strictly convex nonspherical hard parti...
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Continuing on recent computational and experimental work on jammed packings of hard ellipsoids [Donev et al., Science 303, 990 (2004)] we consider jamming in packings of smooth strictly convex nonspherical hard particles. We explain why an isocounting conjecture, which states that for large disordered jammed packings the average contact number per particle is twice the number of degrees of freedom per particle (Z¯=2df), does not apply to nonspherical particles. We develop first- and second-order conditions for jamming and demonstrate that packings of nonspherical particles can be jammed even though they are underconstrained (hypoconstrained, Z¯<2df). We apply an algorithm using these conditions to computer-generated hypoconstrained ellipsoid and ellipse packings and demonstrate that our algorithm does produce jammed packings, even close to the sphere point. We also consider packings that are nearly jammed and draw connections to packings of deformable (but stiff) particles. Finally, we consider the jamming conditions for nearly spherical particles and explain quantitatively the behavior we observe in the vicinity of the sphere point.
Using inverse statistical-mechanical optimization techniques, we have discovered isotropic pair interaction potentials with strongly repulsive cores that cause the tetrahedrally coordinated diamond and wurtzite lattic...
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Using inverse statistical-mechanical optimization techniques, we have discovered isotropic pair interaction potentials with strongly repulsive cores that cause the tetrahedrally coordinated diamond and wurtzite lattices to stabilize, as evidenced by lattice sums, phonon spectra, positive-energy defects, and self-assembly in classical molecular dynamics simulations. These results challenge conventional thinking that such open lattices can only be created via directional covalent interactions observed in nature. Thus, our discovery adds to fundamental understanding of the nature of the solid state by showing that isotropic interactions enable the self-assembly of open crystal structures with a broader range of coordination number than previously thought. Our work is important technologically because of its direct relevance generally to the science of self-assembly and specifically to photonic crystal fabrication.
Concentrated bacterial suspensions spontaneously develop transient spatiotemporal patterns of coherent locomotion whose correlation lengths greatly exceed the size of individual organisms. Continuum models have indica...
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Concentrated bacterial suspensions spontaneously develop transient spatiotemporal patterns of coherent locomotion whose correlation lengths greatly exceed the size of individual organisms. Continuum models have indicated that a state of uniform swimming order is linearly unstable at finite wavelengths, but have not addressed the nonlinear dynamics of the coherent state, with its biological implications for mixing, transport, and intercellular communication. We investigate a specific model incorporating hydrodynamic interactions in thin-film geometries and show by numerical studies that it displays large scale persistently recurring vortices, as actually observed.
High-energy photon detectors are often made thick in order to improve their photon-detection efficiency. To avoid issues of parallax and increased signal variance that result from random interaction depth, we must det...
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High-energy photon detectors are often made thick in order to improve their photon-detection efficiency. To avoid issues of parallax and increased signal variance that result from random interaction depth, we must determine the 3D interaction position in the imaging detector. With this goal in mind, we examine a method of calibrating response statistics of a thick-detector gamma camera to produce a maximum- likelihood estimate of 3D interaction position. We parameterize the mean detector response as a function of 3D position and estimate the parameters by maximizing their likelihood given prior knowledge of the path-length distribution and a complete list of camera signals for an ensemble of gamma-ray interactions. Demonstrating this calibration method with simulated gamma-camera data, we show that the resulting calibration is accurate and can be used to produce unbiased estimates of 3D interaction position.
Heterogeneous materials abound in nature and man-made situations. Examples include porous media, biological materials, and composite materials. Diverse and interesting properties exhibited by these materials result fr...
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Heterogeneous materials abound in nature and man-made situations. Examples include porous media, biological materials, and composite materials. Diverse and interesting properties exhibited by these materials result from their complex microstructures, which also make it difficult to model the materials. Yeong and Torquato [Phys. Rev. E 57, 495 (1998)] introduced a stochastic optimization technique that enables one to generate realizations of heterogeneous materials from a prescribed set of correlation functions. In this first part of a series of two papers, we collect the known necessary conditions on the standard two-point correlation function S2(r) and formulate a conjecture. In particular, we argue that given a complete two-point correlation function space, S2(r) of any statistically homogeneous material can be expressed through a map on a selected set of bases of the function space. We provide examples of realizable two-point correlation functions and suggest a set of analytical basis functions. We also discuss an exact mathematical formulation of the (re)construction problem and prove that S2(r) cannot completely specify a two-phase heterogeneous material alone. Moreover, we devise an efficient and isotropy-preserving construction algorithm, namely, the lattice-point algorithm to generate realizations of materials from their two-point correlation functions based on the Yeong-Torquato technique. Subsequent analysis can be performed on the generated images to obtain desired macroscopic properties. These developments are integrated here into a general scheme that enables one to model and categorize heterogeneous materials via two-point correlation functions. We will mainly focus on basic principles in this paper. The algorithmic details and applications of the general scheme are given in the second part of this series of two papers.
While short-term population dynamical consequences of harvesting havebeen studied for a long time,it is only recently that the potentiallyimportant ensuing evolutionary responses have started to receive *** now,most s...
While short-term population dynamical consequences of harvesting havebeen studied for a long time,it is only recently that the potentiallyimportant ensuing evolutionary responses have started to receive *** now,most studies of harvesting induced evolutionhave focused on a single species in isolation,leaving potentially important coevolutionary interactions *** present a model for the origin and evolution of size-structured food webs based on Lotka-Volterra ***-dependent interactions and small mutations in body size leads to food webs with three to four trophic *** subjecting the resulting communities to various harvesting regimes,the consequences for population dynamics and evolutionary dynamics are analyzed.
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