Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves

We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same material, it is possible for the first time to test competing angular functions, expose inconsistencies in the basic assumption of a cluster expansion, and extract general features of covalent bonding. We test our methods on silicon, and provide the direct evidence that the Tersoff-type bond order formalism correctly describes coordination dependence. For bond-bending forces, we obtain skewed angular functions that favor small angles, unlike existing models. As a proof-of-principle demonstration, we derive a Si interatomic potential which exhibits comparable accuracy to existing models.Comment: 4 pages revtex (twocolumn, psfig), 3 figures. Title and some wording (but no content) changed since original submission on 24 April 199

Branching, Capping, and Severing in Dynamic Actin Structures

Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to study steady-state network morphology. In bulk, we identify several scaling regimes in severing and branching protein concentrations and find that the coupling between severing and branching is optimally exploited for conditions {\it in vivo}. Near the leading edge, we find qualitative agreement with the {\it in vivo} morphology.Comment: 4 pages, 2 figure

Order-N Density-Matrix Electronic-Structure Method for General Potentials

A new order-N method for calculating the electronic structure of general (non-tight-binding) potentials is presented. The method uses a combination of the ``purification''-based approaches used by Li, Nunes and Vanderbilt, and Daw, and a representation of the density matrix based on ``travelling basis orbitals''. The method is applied to several one-dimensional examples, including the free electron gas, the ``Morse'' bound-state potential, a discontinuous potential that mimics an interface, and an oscillatory potential that mimics a semiconductor. The method is found to contain Friedel oscillations, quantization of charge in bound states, and band gap formation. Quantitatively accurate agreement with exact results is found in most cases. Possible advantages with regard to treating electron-electron interactions and arbitrary boundary conditions are discussed.Comment: 13 pages, REVTEX, 7 postscript figures (not quite perfect

Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Collective vibrational states with fast iterative QRPA method

An iterative method we previously proposed to compute nuclear strength functions is developed to allow it to accurately calculate properties of individual nuclear states. The approach is based on the quasi-particle-random-phase approximation (QRPA) and uses an iterative non-hermitian Arnoldi diagonalization method where the QRPA matrix does not have to be explicitly calculated and stored. The method gives substantial advantages over conventional QRPA calculations with regards to the computational cost. The method is used to calculate excitation energies and decay rates of the lowest lying 2+ and 3- states in Pb, Sn, Ni and Ca isotopes using three different Skyrme interactions and a separable gaussian pairing force.Comment: 10 pages, 11 figure

Band-overlap metallization of BaS, BaSe and BaTe

The insulator-metal transition volumes for BaS, BaSe, and BaTe are calculated for the first time, using the self-consistent augmented spherical wave technique. The metallized transition volumes are smaller than those corresponding to the NaCl yields CsCl structural transitions, but, 10 to 15% larger than those obtained by the Herzfeld dielectric theory. The calculated equilibrium energy gaps in the NaCl structure underestimate the measured ones by 50 to 60%

Solid-Liquid Phase Diagrams for Binary Metallic Alloys: Adjustable Interatomic Potentials

We develop a new approach to determining LJ-EAM potentials for alloys and use these to determine the solid-liquid phase diagrams for binary metallic alloys using Kofke's Gibbs-Duhem integration technique combined with semigrand canonical Monte Carlo simulations. We demonstrate that it is possible to produce a wide-range of experimentally observed binary phase diagrams (with no intermetallic phases) by reference to the atomic sizes and cohesive energies of the two elemental materials. In some cases, it is useful to employ a single adjustable parameter to adjust the phase diagram (we provided a good choice for this free parameter). Next, we perform a systematic investigation of the effect of relative atomic sizes and cohesive energies of the elements on the binary phase diagrams. We then show that this approach leads to good agreement with several experimental binary phase diagrams. The main benefit of this approach is not the accurately reproduction of experimental phase diagrams, but rather to provide a method by which material properties can be continuously changed in simulations studies. This is one of the keys to the use of atomistic simulations to understand mechanisms and properties in a manner not available to experiment