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In this paper we examine the different formulations of Gillespie's stochastic simulation algorithm (SSA) [D. Gillespie, J. Phys. Chem. 81, 2340 (1977)] with respect to computational efficiency, and propose an optimization to improve the efficiency of the direct method. Based on careful timing studies and an analysis of the time-consuming operations, we(More)
TOR is the target of the immunosuppressant rapamycin and a key regulator of cell growth. It modulates diverse cellular processes in the cytoplasm and nucleus, including the expression of amino acid transporters, ribosomal RNAs and ribosomal proteins. Despite considerable recent progress, little is known about the spatial and temporal regulation of TOR(More)
The RNA splicing endonuclease cleaves two phosphodiester bonds within folded precursor RNAs during intron removal, producing the functional RNAs required for protein synthesis. Here we describe at a resolution of 2.85 angstroms the structure of a splicing endonuclease from Archaeglobus fulgidus bound with a bulge-helix-bulge RNA containing a noncleaved and(More)
In this paper, we present an efficient algorithm to predict the probability distribution of the circuit delay while accounting for spatial correlations. We exploit the structure of the covariance matrix to decouple the correlated variables to independent ones in linear-time, as opposed to conventional techniques which have a cubic-time complexity.(More)
Event-related brain potentials (ERPs) were measured when 18 Chinese subjects performed a dilemma decision task. During this task, subjects were required to decide who to rescue when two relatives (FN-FN, e.g., father and mother) or two strangers (SN-SN: stranger A and stranger B) were buried in the debris after a great earthquake. All subjects had(More)
Traditional deterministic approaches for simulation of chemically reacting systems fail to capture the randomness inherent in such systems at scales common in intracellular biochemical processes. In this manuscript, we briefly review the state of the art in discrete stochastic and multiscale algorithms for simulation of biochemical systems and we present(More)
Intracellular lipopolysaccharide from Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, Shigella flexneri, and Burkholderia thailandensis activates mouse caspase-11, causing pyroptotic cell death, interleukin-1β processing, and lethal septic shock. How caspase-11 executes these downstream signalling events is largely unknown. Here(More)
The inhibition of inappropriate behaviors is important for adaptive living in changing environments. The present study investigated gender-related behavioral inhibitory control by recording event-related potentials for standard and deviant stimuli while subjects performed a standard/deviant distinction task by accurately pressing different keys within 1000(More)
The small number of some reactant molecules in biological systems formed by living cells can result in dynamical behavior which cannot be captured by traditional determin-istic models. In such a problem, a more accurate simulation can be obtained with discrete stochastic simulation (Gillespie's stochastic simulation algorithm – SSA). Many stochastic(More)