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

Dendritic Actin Filament Nucleation Causes Traveling Waves and Patches

The polymerization of actin via branching at a cell membrane containing nucleation-promoting factors is simulated using a stochastic-growth methodology. The polymerized-actin distribution displays three types of behavior: a) traveling waves, b) moving patches, and c) random fluctuations. Increasing actin concentration causes a transition from patches to waves. The waves and patches move by a treadmilling mechanism which does not require myosin II. The effects of downregulation of key proteins on actin wave behavior are evaluated.Comment: 10 pages, 4 figure

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

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

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

Effect of Crack Blunting on Subsequent Crack Propagation

Theories of toughness of materials depend on an understanding of the characteristic instabilities of the crack tip, and their possible interactions. In this paper we examine the effect of dislocation emission on subsequent cleavage of a crack and on further dislocation emission. The work is an extension of the previously published Lattice Greens Function methodology. We have developed a Cavity Greens Function describing a blunt crack and used it to study the effect of crack blunting under a range of different force laws. As the crack is blunted, we find a small but noticeable increase in the crack loading needed to propagate the crack. This effect may be of importance in materials where a dislocation source near the crack tip in a brittle material causes the crack to absorb anti-shielding dislocations, and thus cause a blunting of the crack. It is obviously also relevant to cracks in more ductile materials where the crack itself may emit dislocations.Comment: LaTeX, 8 pages, 4 Postscript figures included as uuencoded gzipped tar file. To appear in Mat. Res. Soc. Symp. Proc. Also available at http://nils.wustl.edu/schiotz/papers/MRS-Fall-95.htm

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