Solving the chemical master equation using sliding windows
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Background: In this paper, we present a framework for improving the accuracy of fixed-step methods for Monte Carlo simulation of discrete stochastic chemical kinetics. Stochasticity is ubiquitous in many areas of cell biology, for example in gene regulatio ...
Within systems biology there is an increasing interest in the stochastic behaviour of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). ...
We consider the long time behavior of the semidiscrete scheme for the Perona-Malik equation in one dimension. We prove that approximated solutions converge, in a slow time scale, to solutions of a limit problem. This limit problem evolves piecewise constan ...
Shape Optimization problems governed by partial differential equations result from many applications in computational fluid dynamics; they involve the repetitive evaluation of outputs expressed as functionals of the field variables and usually imply big co ...
B-series are a fundamental tool in practical and theoretical aspects of numerical integrators for ordinary differential equations. A composition law for B-series permits an elegant derivation of order conditions, and a substitution law gives much insight i ...
The numerical analysis of a dynamic constrained optimization problem is presented. It consists of a global minimization problem that is coupled with a system of ordinary differential equations. The activation and the deactivation of inequality constraints ...
Isogeometric analysis (IGA) is a computational methodology recently developed to numerically approximate Partial Differential Equation (PDEs). It is based on the isogeometric paradigm, for which the same basis functions used to represent the geometry are t ...
A new algorithm, called boosted hybrid method, is proposed for the simulation of chemical reaction systems with scale-separation in time and disparity in species population. For such stiff systems, the algorithm can automatically identify scale-separation ...
In this thesis we investigate different ways of approximating the solution of the chemical master equation (CME). The CME is a system of differential equations that models the stochastic transient behaviour of biochemical reaction networks. It does so by d ...
A finite volume method for solving the monodomain and bidomain models for the electrical activity of myocardial tissue is presented. These models consist of a parabolic PDE and a system of a parabolic and an elliptic PDE, respectively, for certain electric ...