Simulations of metastable decay in two- and three-dimensional models with microscopic dynamics

We present a brief analysis of the crossover phase diagram for the decay of a metastable phase in a simple dynamic lattice-gas model of a two-phase system. We illustrate the nucleation-theoretical analysis with dynamic Monte Carlo simulations of a kinetic Ising lattice gas on square and cubic lattices. We predict several regimes in which the metastable lifetime has different functional forms, and provide estimates for the crossovers between the different regimes. In the multidroplet regime, the Kolmogorov-Johnson-Mehl-Avrami theory for the time dependence of the order-parameter decay and the two-point density correlation function allows extraction of both the order parameter in the metastable phase and the interfacial velocity from the simulation data.Comment: 14 pages, 4 figures, submitted to J. Non-Crystalline Solids, conference proceeding for IXth International Conference on the Physics of Non-Crystalline Solids, October, 199

MultiCellDS : a community-developed standard for curating microenvironment-dependent multicellular data

Exchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health

Optical properties of MgH2 measured in situ in a novel gas cell for ellipsometry/spectrophotometry

The dielectric properties of alpha-MgH2 are investigated in the photon energy range between 1 and 6.5 eV. For this purpose, a novel sample configuration and experimental setup are developed that allow both optical transmission and ellipsometric measurements of a transparent thin film in equilibrium with hydrogen. We show that alpha-MgH2 is a transparent, colour neutral insulator with a band gap of 5.6 +/- 0.1 eV. It has an intrinsic transparency of about 80% over the whole visible spectrum. The dielectric function found in this work confirms very recent band structure calculations using the GW approximation by Alford and Chou [J.A. Alford and M.Y. Chou (unpublished)]. As Pd is used as a cap layer we report also the optical properties of PdHx thin films.Comment: REVTeX4, 15 pages, 12 figures, 5 table

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

Exchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health

MultiCellDS: a standard and a community for sharing multicellular data

Cell biology is increasingly focused on cellular heterogeneity and multicellular systems. To make the fullest use of experimental, clinical, and computational efforts, we need standardized data formats, community-curated "public data libraries", and tools to combine and analyze shared data. To address these needs, our multidisciplinary community created MultiCellDS (MultiCellular Data Standard): an extensible standard, a library of digital cell lines and tissue snapshots, and support software. With the help of experimentalists, clinicians, modelers, and data and library scientists, we can grow this seed into a community-owned ecosystem of shared data and tools, to the benefit of basic science, engineering, and human health

A parameter sensitivity methodology in the context of HIV delay equation models

A sensitivity methodology for nonlinear delay systems arising in one class of cellular HIV infection models is presented. Theoretical foundations for a typical sensitivity investigation and illustrative computations are given.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46951/1/285_2004_Article_299.pd

Supplementary Material for: Spatiotemporal Dynamics of Complement C5a Production within Bacterial Extracellular Polymeric Substance

Opsonization and anaphylatoxin production are early events in the innate response to bacterial pathogens. Opsonization alone is frequently not lethal and production of anaphy-latoxins, especially C5a, allows for recruitment of cellular defenses. Complement biochemistry is extensively studied and computational models have been reported previously. However, a critical feature of complement-mediated attack is its spatial dependence: diffusion of mediators into and away from a bacterium is central to understanding C5a generation. Spatial dependence is especially important in biofilms, where diffusion limitation is crucial to bacterial counterdefense. Here we develop a model of opsonization and C5a production in the presence of a common blood-borne pathogen, <i>Staphylococcus epidermidis</i>. Our results indicate that when complement attacks a single cell, diffusion into the extracellular polymeric substance (EPS) is complete within 10 ms and that production of C5a peaks over the next 15 min. When longer diffusion lengths (as in an EPS-rich biofilm) are incorporated, diffusion limitation appears such that the intensity and duration of C5a production is increased. However, the amount of C5a produced under several likely clinical scenarios where single cells or sparse biofilms are present is below the k_D of the C5a receptor suggesting that complement activation by a single bacterium may be difficult to detect when diffusion is taken into account