scholarly journals Multipreconditioned GMRES for simulating stochastic automata networks

2018 ◽  
Vol 16 (1) ◽  
pp. 986-998
Author(s):  
Chun Wen ◽  
Ting-Zhu Huang ◽  
Xian-Ming Gu ◽  
Zhao-Li Shen ◽  
Hong-Fan Zhang ◽  
...  
Keyword(s):  
Steady State ◽  
Probability Distribution ◽  
Linear Systems ◽  
Iterative Methods ◽  
Communication Systems ◽  
Queueing Systems ◽  
Steady State Probability ◽  
Stochastic Automata ◽  
Automata Networks ◽  
Generator Matrices

AbstractStochastic Automata Networks (SANs) have a large amount of applications in modelling queueing systems and communication systems. To find the steady state probability distribution of the SANs, it often needs to solve linear systems which involve their generator matrices. However, some classical iterative methods such as the Jacobi and the Gauss-Seidel are inefficient due to the huge size of the generator matrices. In this paper, the multipreconditioned GMRES (MPGMRES) is considered by using two or more preconditioners simultaneously. Meanwhile, a selective version of the MPGMRES is presented to overcome the rapid increase of the storage requirements and make it practical. Numerical results on two models of SANs are reported to illustrate the effectiveness of these proposed methods.

The effect of weak Brownian rotations on particles in shear flow

1971 ◽  
Vol 46 (4) ◽  
pp. 685-703 ◽  
Author(s):  
L. G. Leal ◽  
E. J. Hinch
Keyword(s):  
Reynolds Number ◽  
Steady State ◽  
Probability Distribution ◽  
Shear Flow ◽  
Equilibrium Distribution ◽  
Steady State Probability ◽  
Bulk Properties ◽  
Closed Orbits ◽  
Basic Equations

Axisymmetric particles in zero Reynolds number shear flow execute closed orbits. In this paper we consider the role of small Brownian couples in establishing a steady-state probability distribution for a particle being on any particular orbit. After presenting the basic equations, we derive an expression for the equilibrium distribution. This result is then used to calculate some bulk properties for a suspension of such particles, and these predicted properties are compared with available experimental observation.

scholarly journals A mechanistic model for the negative binomial distribution of single-cell mRNA counts

2019 ◽  
Author(s):  
Lisa Amrhein ◽  
Kumar Harsha ◽  
Christiane Fuchs
Keyword(s):  
Steady State ◽  
Probability Distribution ◽  
Single Cell ◽  
Negative Binomial Distribution ◽  
Binomial Distribution ◽  
Negative Binomial ◽  
Probability Distributions ◽  
Mechanistic Model ◽  
Steady State Probability ◽  
Degradation Models

SummarySeveral tools analyze the outcome of single-cell RNA-seq experiments, and they often assume a probability distribution for the observed sequencing counts. It is an open question of which is the most appropriate discrete distribution, not only in terms of model estimation, but also regarding interpretability, complexity and biological plausibility of inherent assumptions. To address the question of interpretability, we investigate mechanistic transcription and degradation models underlying commonly used discrete probability distributions. Known bottom-up approaches infer steady-state probability distributions such as Poisson or Poisson-beta distributions from different underlying transcription-degradation models. By turning this procedure upside down, we show how to infer a corresponding biological model from a given probability distribution, here the negative binomial distribution. Realistic mechanistic models underlying this distributional assumption are unknown so far. Our results indicate that the negative binomial distribution arises as steady-state distribution from a mechanistic model that produces mRNA molecules in bursts. We empirically show that it provides a convenient trade-off between computational complexity and biological simplicity.Graphical Abstract

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