8,627 research outputs found
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
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
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
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
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