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Showing 1 to 11 of 11 for “"Gillespie algorithm"”.
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Algebraic Methods for Modeling Gene Regulatory Networks
… such as stochastic differential equations and Gillespie algorithm simulations. Within the discrete setting, a framework that incorporates propensity probabilities for activation and degradation is presented. This approach allows a finer analysis of discrete models and provides a natural setup …
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Stochastic modelling of gene regulation with microRNAs
… are shown to be excellent approximations to the Gillespie Algorithm.
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Stochastic Simulation and System Identification of large Signal Transduction Networks in Cells
… reactions occur. Therefore, a stochastic hybrid algorithm is developed by combining the exact Gillespie algorithm with a system of stochastic differential equations. This enables stochastically accurate and highly efficient simulations for large reaction systems and for any other kind of Markov …
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Collective dynamics of evolving populations and their strategies with application to medicine
… results with stochastic simulations using the Gillespie algorithm. Finally, we estimate the range of parameters that delineate the various steady states of our model. In the second project, we present a mean field model for the phase diagram of a community of micro- organisms, interacting …
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A Gillespie-Type Algorithm for Particle Based Stochastic Model on Lattice
… I propose a general stochastic simulation algorithm for particle based lattice model using the concepts of Gillespie's stochastic simulation algorithm, which was originally designed for well-stirred systems. I describe the details about this method and analyze its complexity compared with …
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Handling External Events Efficiently in Gillespie's Stochastic Simulation Algorithm
Gillespie's Stochastic Simulation Algorithm (SSA) provides an elegant simulation approach for simulating models composed of coupled chemical reactions. Although this approach can be used to describe a wide variety biological, chemical, and ecological systems, often systems have external behaviors …
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A Stochastic Model for The Transmission Dynamics of Toxoplasma Gondii
… and stochastic model by us. A stochastic algorithm due to Gillespie, based on the chemical master equation, is introduced. A compartment-based model and a Smoluchowski equation model are described to simulate the diffusion of hosts. The parameter analyses are conducted based on the …
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Accelerating Finite State Projection through General Purpose Graphics Processing
The finite state projection algorithm provides modelers a new way of directly solving the chemical master equation. The algorithm utilizes the matrix exponential function, and so the algorithm’s performance suffers when it is applied to large problems. Other work has been done to reduce the size of …
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Mathematical models of daphnia epidemics
Disease ecology studies the interactions among hosts, pathogens, and the environment and how these shape the spread of disease. These interactions can be quite complex and lead to fascinating dynamics. Our system of study, Daphnia has a lot of interesting and complex features that can be analyzed …
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How bacteria tune mixed positive/negative feedback loops to generate diverse gene expression dynamics
Bacteria are constantly sensing their environment, and must respond as it changes. Some of their most common systems for sensing and responding to change are alternative sigma factors. These are a type of transcription factor, and unique in that they integrate into the RNA polymerase molecule …
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On the coupling of noisy processes in biology to produce functional phenotypic variability
Noise is ubiquitous in biology. Recent studies have demonstrated that both gene expression and physiological processes, such as growth, can be noisy. The cell-to-cell variation resulting from this stochasticity has been implicated in survival strategies for bacterial populations. However, it …