Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions

Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecules and their reactive collisions. In both cases, it is shown that the commonly used implementation of bimolecular reactions (i.e. the reactions of the form A + B -> C, or A + A -> C) might lead to incorrect results. Improvements of both SSAs are suggested which overcome the difficulties highlighted. In particular, a formula is presented for the smallest possible compartment size (lattice spacing) which can be correctly implemented in the first model. This implementation uses a new formula for the rate of bimolecular reactions per compartment (lattice site).Comment: 33 pages, submitted to Physical Biolog

Polarization phenomena in the reaction NN to NNpi near threshold

First calculations for spin-dependent observables of the reactions $pp \to pp\pi^0$, $pp \to pn\pi^+$ and $pp \to d\pi^+$ near threshold are presented, employing the J\"ulich model for pion production. The influence of resonant (via the excitation of the $\Delta (1232)$) and non-resonant p-wave pion production mechanisms on these observables is examined. For the reactions $pp \to pn\pi^+$ and $pp \to d\pi^+$ nice agreement of our predictions with the presently available data on spin correlation coefficents is observed whereas for $pp \to pp\pi^0$ the description of the data is less satisfying.Comment: 10 pages, 4 figure

Anisotropy in the pion angular distribution of the reaction pp -> pp pi0 at 400 MeV

The reaction pp -> pp pi0 was studied with the WASA detector at the CELSIUS storage ring. The center of mass angular distribution of the pi0 was obtained by detection of the gamma decay products together with the two outgoing protons, and found to be anisotropic with a negative second derivative slope, in agreement with the theoretical predictions from a microscopic calculation.Comment: Revtex 4 style, 5 pages 7 figures, PACS numbers:13.60.Le, 13.75.Cs, 21.45.+v, 25.10.+

Adaptive fast multipole methods on the GPU

We present a highly general implementation of fast multipole methods on graphics processing units (GPUs). Our two-dimensional double precision code features an asymmetric type of adaptive space discretization leading to a particularly elegant and flexible implementation. All steps of the multipole algorithm are efficiently performed on the GPU, including the initial phase which assembles the topological information of the input data. Through careful timing experiments we investigate the effects of the various peculiarities of the GPU architecture.Comment: Software available at http://user.it.uu.se/~stefane/freeware.htm

Measurement of Partial-Wave Contributions in pp --> pp pi^0

We report a measurement of the spin-dependent total cross section ratios delta_sigma_T/sigma_tot and delta_sigma_L/sigma_tot of the pp --> pp pi^0 reaction between 325 MeV and 400 MeV. The experiment was carried out with a polarized internal target in a storage ring. Non-vertical beam polarization was obtained by the use of solenoidal spin rotators. Near threshold, the knowledge of both spin-dependent total cross sections is sufficient to deduce the strength of certain participating partial waves, free of any model.Comment: 6 pages, 4 figure

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique

Dependence of pp->pp pi0 near Threshold on the Spin of the Colliding Nucleons

A polarized internal atomic hydrogen target and a stored, polarized beam are used to measure the spin-dependent total cross section Delta_sigma_T/sigma_tot, as well as the polar integrals of the spin correlation coefficient combination A_xx-A_yy, and the analyzing power A_y for pp-> pp pi0 at four bombarding energies between 325 and 400 MeV. This experiment is made possible by the use of a cooled beam in a storage ring. The polarization observables are used to study the contribution from individual partial waves.Comment: 6 pages, 1 table, 4 figures, corrected equations 2 and