The sweeping rate in diffusion-mediated reactions on dust grain surfaces

A prominent chemical reaction in interstellar clouds is the formation of molecular hydrogen by recombination, which essentially takes place on dust grain surfaces. Analytical approaches to model such a system have hitherto neglected the spatial aspects of the problem by employing a simplistic version of the sweeping rate of reactants. We show how these aspects can be accounted for by a consistent definition of the sweeping rate, and calculate it exactly for a spherical grain. Two regimes can be identified: Small grains, on which two reactants almost surely meet, and large grains, where this is very unlikely. We compare the true sweeping rate to the conventional approximation and find a characteristic reduction in both regimes, most pronounced for large grains. These effects can be understood heuristically using known results from the analysis of two-dimensional random walks. We finally examine the influence of using the true sweeping rate in the calculation of the efficiency of hydrogen recombination: For fixed temperature, the efficiency can be reduced considerably, and relative to that, small grains gain in importance, but the temperature window in which recombination is efficient is not changed substantially.Comment: 10 pages, 6 figure

Specification of spatial relationships in directed graphs of cell signaling networks

Graph theory provides a useful and powerful tool for the analysis of cellular signaling networks. Intracellular components such as cytoplasmic signaling proteins, transcription factors and genes are connected by links, representing various types of chemical interactions that result in functional consequences. However, these graphs lack important information regarding the spatial distribution of cellular components. The ability of two cellular components to interact depends not only on their mutual chemical affinity but also on co-localization to the same subcellular region. Localization of components is often used as a regulatory mechanism to achieve specific effects in response to different receptor signals. Here we describe an approach for incorporating spatial distribution into graphs, and for the development of mixed graphs where links are specified by mutual chemical affinity as well as colocalization. We suggest that such mixed graphs will provide more accurate descriptions of functional cellular networks and their regulatory capabilities and aid in the development of large-scale predictive models of cellular behavior

The formation of H_2 and HD with the master equation approach

The formation of H2 and HD molecules on interstellar dust grains is studied using rate equation and master equation models. Rate equations are used in the analysis of laboratory experiments which examine the formation of molecular hydrogen on astrophysically relevant surfaces. However, under interstellar conditions, rate equations are not suitable for the calculation of reaction rates on dust-grain surfaces. Due to the low flux and the sub-micron size of the grains, the populations of H and D atoms on a single grain are likely to be small. In this case the reaction rates are dominated by fluctuations and should be calculated using stochastic methods. The rate of molecular hydrogen formation in interstellar clouds is evaluated using the master equation, taking into account the distribution of grain sizes.Comment: 10 pages, 2 figures. IAU symposium 231 conference proceeding

An "All Possible Steps" Approach to the Accelerated Use of Gillespie's Algorithm

Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by D. Gillespie about three decades ago [D.T. Gillespie, J. Phys. Chem. {\bf 81}, 2340, (1977)]. Since then, intensive work has been done to make the algorithm more efficient in terms of running time. All accelerated versions of the algorithm are aimed at minimizing the running time required to produce a stochastic trajectory in state space. In these simulations, a necessary condition for reliable statistics is averaging over a large number of simulations. In this study I present a new accelerating approach which does not alter the stochastic algorithm, but reduces the number of required runs. By analysis of collected data I demonstrate high precision levels with fewer simulations. Moreover, the suggested approach provides a good estimation of statistical error, which may serve as a tool for determining the number of required runs.Comment: Accepted for publication at the Journal of Chemical Physics. 19 pages, including 2 Tables and 4 Figure

Reaction Kinetics in a Tight Spot

The standard analysis of reaction networks based on deterministic rate equations fails in confined geometries, commonly encountered in fields such as astrochemistry, thin film growth and cell biology. In these systems the small reactant population implies anomalous behavior of reaction rates, which can be accounted for only by following the full distribution of reactant numbers