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Particle Swarm Optimization (PSO) has achieved remarkable attentions for its capability to solve diverse global optimization problems. However, this method also shows several limitations. PSO easily trapped in the global optimum and often required vast computational cost when solving high dimensional problems. Therefore, we propose some modifications to overcome these issues. In this work, Differential...
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought...
How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists...
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