Search Results - "Stochastic simulation algorithm"

Quantifying Parameter Interdependence in Stochastic Discrete Models of Biochemical Systems by Gholami, Samaneh, Ilie, Silvana

“…Stochastic modeling of biochemical processes at the cellular level has been the subject of intense research in recent years…”
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Mathematical Modeling in Systems Biology

“…The reprint presents a collection of systems biology-related topics and new studies that utilize computational, mathematical, and systems-oriented approaches…”
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Stochastic Simulation of Imperfect Mixing in Free Radical Polymerization by Hernandez, Hugo F, Tauer, Klaus

“…A modified algorithm for the stochastic simulation of chemical reactions subject to mass transfer limitation (imperfect mixing) is presented…”
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Noise-induced entrainment of the circadian clock by thermoperiods in tomato: A computational approach by Huang, Ting, Lv, Hengmin, Shu, Yiting, Luo, Jian, Yu, Linxuan, Chen, Bing, Sun, Xin, Hou, Xilin, You, Xiong, Zhang, Tonghua

“… Model simulations by the stochastic simulation algorithm showed warm temperatures resulting in an advanced phase…”
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SGN Sim, a Stochastic Genetic Networks Simulator by Ribeiro, Andre S., Lloyd-Price, Jason

“…) where transcription and translation are modeled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA…”
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Noisy attractors and ergodic sets in models of gene regulatory networks by Ribeiro, Andre S., Kauffman, Stuart A.

“… of “ergodic set” as a set of states from which the system, once entering, does not leave when subject to internal noise, first, using the Boolean network model, we show that if all nodes of states on attractors…”
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A low-rank complexity reduction algorithm for the high-dimensional kinetic chemical master equation by Einkemmer, Lukas, Mangott, Julian, Prugger, Martina

“…). This approach, compared to the commonly used stochastic simulation algorithm (SSA, a Monte Carlo method…”
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A Practicable Method of Tuning the Noise Intensity at Protein Level by Lo, Shih-Chiang, You, Chao-Xuan, Shu, Che-Chi

“…The expression of genes is inevitably subject to intracellular noise. Noise, for some regulatory networks, is constructive but detrimental to many others…”
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A Performance-Based Wind Engineering Framework for Engineered Building Systems Subject to Hurricanes by Ouyang, Zhicheng, Spence, Seymour M.J.

“…Over the past decade, significant research efforts have been dedicated to the development of performance-based wind engineering (PBWE). Notwithstanding these…”
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CellLine, a stochastic cell lineage simulator by Ribeiro, Andre S., Charlebois, Daniel A., Lloyd-Price, Jason

“… Each cell's dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time delayed reactions…”
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General network reliability problem and its efficient solution by Subset Simulation by Zuev, Konstantin M., Wu, Stephen, Beck, James L.

“…Complex technological networks designed for distribution of some resource or commodity are a pervasive feature of modern society. Moreover, the dependence of…”
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Predicting Multivariate Insurance Loss Payments Under the Bayesian Copula Framework by Zhang, Yanwei, Dukic, Vanja

“… We derive a full Bayesian stochastic simulation algorithm that can estimate parameters in this class of models…”
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Stochastic simulations of the Schnakenberg model with spatial inhomogeneities using reactive multiparticle collision dynamics by Sayyidmousavi, Alireza, Rohlf, Katrin

“…A numerically efficient globally averaged number density approach is used to simulate a reaction-diffusion system using a particle-based stochastic simulation algorithm called reactive multiparticle collision (RMPC) dynamics…”
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A kinetic Monte Carlo simulation study of inositol 1,4,5-trisphosphate receptor (IP3R) calcium release channel by Haeri, H.H., Hashemianzadeh, S.M., Monajjemi, M.

“… Because of the limitations of this approach we have used a stochastic simulation algorithm (SSA) presented by Gillespie…”
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Design Parameters for Granzyme-Mediated Cytotoxic Lymphocyte Target-Cell Killing and Specificity by Woodsworth, Daniel J, Dunsing, Valentin, Coombs, Daniel

“… Due to its central role in lymphocyte biology, as well as its implication in a host of pathologies from cancer to autoimmunity, the granzyme-perforin pathway has been the subject of extensive investigation…”
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Stochastic simulation algorithms for query networks by Cousins, S B, Frisse, M E, Chen, W, Mead, C N

“… Stochastic simulation algorithms allow one to compute approximations of probability values in a reasonable amount of time…”
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A low-rank complexity reduction algorithm for the high-dimensional kinetic chemical master equation by Einkemmer, Lukas, Mangott, Julian, Prugger, Martina

“…). This approach, compared to the commonly used stochastic simulation algorithm (SSA, a Monte Carlo method…”
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Confidence from uncertainty - A multi-target drug screening method from robust control theory by Luni, Camilla, Shoemaker, Jason E, Sanft, Kevin R, Petzold, Linda R, Doyle, Francis J

“…Background Robustness is a recognized feature of biological systems that evolved as a defence to environmental variability. Complex diseases such as diabetes,…”
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Stochastic diffusion model of heterogeneous populations by Zakharyan, Armen

“…Kolmogorov's first and second equations in partial differential equations can be used to find solutions of transition probabilities in simple systems; while…”
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Stochastic Modeling in Systems Biology by Jinzhi Lei

“…Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology…”
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