نتایج جستجو برای: gillespie algorithm
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Biological processes involving the random interaction of d species with integer particle numbers are often modeled by a Markov jump process on N0. Realizations of this process can, in principle, be generated with the classical stochastic simulation algorithm proposed in [19], but for very reactive systems this method is usually inefficient. Hybrid models based on piecewise deterministic process...
A novel method is presented to compute the exit time for the stochastic simulation algorithm. The method is based on the addition of a series of random variables and is derived using the convolution theorem. The final distribution is derived and approximated in the frequency domain. The distribution for the final time is transformed back to the real domain and can be sampled from in a simulatio...
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind of differential equations in which the derivative of the unknown function at a certain time is given in terms of the values of the function at previous time...
We develop a stochastic model to study the specific response of the immune system. The model is based on the dynamical interaction between Regulatory and Effector CD4+ T cells in the presence of Antigen Presenting Cells inside a lymphatic node. At a mean field level the model predicts the existence of different regimes where active, tolerant, or cyclic immune responses are possible. To study th...
Gillespie (1986a) suggests a model of molecular evolution by natural selection. He has chosen this model to fit some statistical aspects of the sequence data that he examined. In the present letter I show that there may be more “wobble” in sequence data than the reader might suspect. The data for each protein sequence are taken to come from a star phylogeny and inference is for N,(t), the numbe...
We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay). Array-based comparative genomic ...
Discrete stochastic models in continuous time are the simplest way to turn survival analysis of an ecological system into a simulation of that system. They build models most faithful to a picture of individuals making choices which affect each other. This article describes how rules for individual behavior can construct a simulation of a population. It argues that, within the context of discret...
Brent Gillespie, Mark Cutkosky ABSTRACT The simulation of virtual environments which are multi-degreeof-freedom presents unique challenges to the designer of control software for haptic display devices. Once the successfully rendered stiffness, damping, and mass elements are interconnected to form multibody systems, a host of controller implementation choices arise. For one, the control law mus...
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