W. Maniatty, B.K. Szymanski, and T. Caraco, High-Performance Simulation of Evolutionary Aspects of Epidemics," Applied Parallel Computing, B. Kagstrom et al (eds), Papers presented at 4th Int. Workshop, PARA'98, June 16,  Home/Search Document Details and Download
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Spatial Models of Persistence in RNA Worlds: Exploring.. - William Maniatty Thomas Self-citation (Szymanski Caraco) (Correct)
....we are beginning our investigations by considering a single genotype with multiple phenotypes, and in particular we consider the simplest form, analyzing extinction trends in a system governed by the interaction between two phenotypes. This is similar to our approaches to modeling selection in [6, 13], in the future we plan to extend our approach to model mutation, and selection much like in [8] We consider two different models of selection in RNA worlds, first beginning with a two dimensional spatially explicit individual based model, and then exploring a spatially explicit aggregation based ....
....individual based model, and then exploring a spatially explicit aggregation based model. 3. 1 An Individual Based Modeling Approach The individual based model partitions a two dimensional space into a lattice of J 1 sites and synchronously advances time using uniformly sized time steps, like [6, 13]. It is assumed that RNA replicator molecules in this model have the same sequence (i.e. are of a common genotype G) and can belong to one of two phenotypes. Sites in this model are sufficiently small that they can hold at most one replicator. Uninhabited sites are partitioned into two groups, ....
W. A. Maniatry, B. K. Szymanski, and T. Caraco. High-performance simulation of evolutionary aspects of epidemics. In Proceedings of the PARA98 Workshop on Applied Parallel Computing in Lar9e Scale Industrial and Scientific Problems, volume 1541 of Lecture Notes in Computer Science, pages 322-331, Umef University, Umef Sweden, June 1998. Springer-Verlag.
High-Performance Computing Tools for Modeling Evolution.. - Maniatty, Szymanski.. Self-citation (Maniatty Szymanski Caraco) (Correct)
....fashion. We assume that mutation is modeled by a Bernoulli trial for each bit copied. 3 Model s Design and Implementation We have implemented two stepwise refinement of the TEMPEST system [13] First we allowed competition between two, genetically different strains in the system called STORM [14], next we refined STORM by allow ing genetic drift of the hosts and parasites in the system called GALE. Below we compare the implementation of GALE with that of STORM and TEMPEST. The GALE model was implemented using C and MPI. Placement of data and operations executed on a ....
....efficiently in parallel. w Denotes Regiom Echanged About A Comer i Denotes Non Overlapping Region Figure 2: Block Decomposition used in STORM The underlying model of GALE has localized interactions, so a static block data decomposition was se lected (much like in TEMPEST and STORM [13, 14]) as shown in Figure 2. To compute state transition probabilities, GALE must traverse the set of sites within the interaction neighborhood, rather than to count the number of sites in each state as TEMPEST and STORM do [13] To model reproduction, all geno types that can reach a given site must ....
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W. A. Maniatty, B. K. Szymanski, and T. Caraco. High-Performance simulation of evolutionary aspects of epidemics. In Proc. PARA98, LNCS, Springer Verlag, Berlin, Germany, 1998.
Component-based Simulation Visualization Toolkit - Huang (Correct)
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W. Maniatty, B.K. Szymanski, and T. Caraco, High-Performance Simulation of Evolutionary Aspects of Epidemics," Applied Parallel Computing, B. Kagstrom et al (eds), Papers presented at 4th Int. Workshop, PARA'98, June 16,
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