154 research outputs found
Theory of continuum percolation I. General formalism
The theoretical basis of continuum percolation has changed greatly since its
beginning as little more than an analogy with lattice systems. Nevertheless,
there is yet no comprehensive theory of this field. A basis for such a theory
is provided here with the introduction of the Potts fluid, a system of
interacting -state spins which are free to move in the continuum. In the limit, the Potts magnetization, susceptibility and correlation functions
are directly related to the percolation probability, the mean cluster size and
the pair-connectedness, respectively. Through the Hamiltonian formulation of
the Potts fluid, the standard methods of statistical mechanics can therefore be
used in the continuum percolation problem.Comment: 26 pages, Late
Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation
The phase behavior of charged rods in the presence of inter-rod linkers is
studied theoretically as a model for the equilibrium behavior underlying the
organization of actin filaments by linker proteins in the cytoskeleton. The
presence of linkers in the solution modifies the effective inter-rod
interaction and can lead to inter-filament attraction. Depending on the
system's composition and physical properties such as linker binding energies,
filaments will either orient perpendicular or parallel to each other, leading
to network-like or bundled structures. We show that such a system can have one
of three generic phase diagrams, one dominated by bundles, another by networks,
and the third containing both bundle and network-like phases. The first two
diagrams can be found over a wide range of interaction energies, while the
third occurs only for a narrow range. These results provide theoretical
understanding of the classification of linker proteins as bundling proteins or
crosslinking proteins. In addition, they suggest possible mechanisms by which
the cell may control cytoskeletal morphology.Comment: 17 pages, 3 figure
Exact solution of a one-dimensional continuum percolation model
I consider a one dimensional system of particles which interact through a
hard core of diameter \si and can connect to each other if they are closer
than a distance . The mean cluster size increases as a function of the
density until it diverges at some critical density, the percolation
threshold. This system can be mapped onto an off-lattice generalization of the
Potts model which I have called the Potts fluid, and in this way, the mean
cluster size, pair connectedness and percolation probability can be calculated
exactly. The mean cluster size is S = 2 \exp[ \rho (d -\si)/(1 - \rho \si)] -
1 and diverges only at the close packing density \rho_{cp} = 1 / \si . This
is confirmed by the behavior of the percolation probability. These results
should help in judging the effectiveness of approximations or simulation
methods before they are applied to higher dimensions.Comment: 21 pages, Late
The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience
With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscienceâs Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line
Disease Ontology: a backbone for disease semantic integration
The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ICD, NCI's thesaurus, SNOMED CT and OMIM disease-specific terms and identifiers. The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g. IDO, Cell line ontology, NIFSTD ontology, Experimental Factor Ontology, Influenza Ontology), and as an ontological cross mappings resource between DO, MeSH and OMIM (e.g. GeneWiki). The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease. The next iteration of the DO web browser will integrate DO's extended relations and logical definition representation along with these biomedical resource cross-mappings
Theory of continuum percolation III. Low density expansion
We use a previously introduced mapping between the continuum percolation
model and the Potts fluid (a system of interacting s-states spins which are
free to move in the continuum) to derive the low density expansion of the pair
connectedness and the mean cluster size. We prove that given an adequate
identification of functions, the result is equivalent to the density expansion
derived from a completely different point of view by Coniglio et al. [J. Phys A
10, 1123 (1977)] to describe physical clustering in a gas. We then apply our
expansion to a system of hypercubes with a hard core interaction. The
calculated critical density is within approximately 5% of the results of
simulations, and is thus much more precise than previous theoretical results
which were based on integral equations. We suggest that this is because
integral equations smooth out overly the partition function (i.e., they
describe predominantly its analytical part), while our method targets instead
the part which describes the phase transition (i.e., the singular part).Comment: 42 pages, Revtex, includes 5 EncapsulatedPostscript figures,
submitted to Phys Rev
Transitions in the Horizontal Transport of Vertically Vibrated Granular Layers
Motivated by recent advances in the investigation of fluctuation-driven
ratchets and flows in excited granular media, we have carried out experimental
and simulational studies to explore the horizontal transport of granular
particles in a vertically vibrated system whose base has a sawtooth-shaped
profile. The resulting material flow exhibits novel collective behavior, both
as a function of the number of layers of particles and the driving frequency;
in particular, under certain conditions, increasing the layer thickness leads
to a reversal of the current, while the onset of transport as a function of
frequency occurs gradually in a manner reminiscent of a phase transition. Our
experimental findings are interpreted here with the help of extensive, event
driven Molecular Dynamics simulations. In addition to reproducing the
experimental results, the simulations revealed that the current may be reversed
as a function of the driving frequency as well. We also give details about the
simulations so that similar numerical studies can be carried out in a more
straightforward manner in the future.Comment: 12 pages, 18 figure
Generalized model for dynamic percolation
We study the dynamics of a carrier, which performs a biased motion under the
influence of an external field E, in an environment which is modeled by dynamic
percolation and created by hard-core particles. The particles move randomly on
a simple cubic lattice, constrained by hard-core exclusion, and they
spontaneously annihilate and re-appear at some prescribed rates. Using
decoupling of the third-order correlation functions into the product of the
pairwise carrier-particle correlations we determine the density profiles of the
"environment" particles, as seen from the stationary moving carrier, and
calculate its terminal velocity, V_c, as the function of the applied field and
other system parameters. We find that for sufficiently small driving forces the
force exerted on the carrier by the "environment" particles shows a
viscous-like behavior. An analog Stokes formula for such dynamic percolative
environments and the corresponding friction coefficient are derived. We show
that the density profile of the environment particles is strongly
inhomogeneous: In front of the stationary moving carrier the density is higher
than the average density, , and approaches the average value as an
exponential function of the distance from the carrier. Past the carrier the
local density is lower than and the relaxation towards may
proceed differently depending on whether the particles number is or is not
explicitly conserved.Comment: Latex, 32 pages, 4 ps-figures, submitted to PR
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework
The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is âhiddenâ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community
Biology-driven approaches to prevent and treat relapse of myeloid neoplasia after allogeneic hematopoietic stem cell transplantation
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