Stochastic delay differential equations for genetic regulatory networks

Time delay is an important aspect in the modelling of genetic regulation due to slow biochemical reactions such as gene transcription and translation, and protein diffusion between the cytosol and nucleus. In this paper we introduce a general mathematical formalism via stochastic delay differential equations for describing time delays in genetic regulatory networks. Based on recent developments with the delay stochastic simulation algorithm, the delay chemical masterequation and the delay reaction rate equation are developed for describing biological reactions with time delay, which leads to stochastic delay differential equations derived from the Langevin approach. Two simple genetic regulatory networks are used to study the impact of' intrinsic noise on the system dynamics where there are delays. (c) 2006 Elsevier B.V. All rights reserved.

Student Difficulties with units in differential equations in modelling contexts

First-year undergraduate engineering students' understanding of the units of factors and terms in first-order ordinary differential equations used in modelling contexts was investigated using diagnostic quiz questions. Few students appeared to realize that the units of each term in such equations must be the same, or if they did, nevertheless failed to apply that knowledge when needed. In addition, few students were able to determine the units of a proportionality factor in a simple equation. These results indicate that lecturers of modelling courses cannot take this foundational knowledge for granted and should explicitly include it in instruction.

Gaussian process approximations of stochastic differential equations

Stochastic differential equations arise naturally in a range of contexts, from financial to environmental modeling. Current solution methods are limited in their representation of the posterior process in the presence of data. In this work, we present a novel Gaussian process approximation to the posterior measure over paths for a general class of stochastic differential equations in the presence of observations. The method is applied to two simple problems: the Ornstein-Uhlenbeck process, of which the exact solution is known and can be compared to, and the double-well system, for which standard approaches such as the ensemble Kalman smoother fail to provide a satisfactory result. Experiments show that our variational approximation is viable and that the results are very promising as the variational approximate solution outperforms standard Gaussian process regression for non-Gaussian Markov processes.

Some aspects of the solution of non-linear differential equations

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Solving Differential Equations by Parallel Laplace Method with Assured Accuracy

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

Differential Equations in Abstract Cones

We extend the method of quasilinearization to differential equations in abstract normal cones. Under some assumptions, corresponding monotone iterations converge to the unique solution of our problem and this convergence is superlinear or semi–superlinear

Integral Manifolds and Bounded Solutions of Singularly Perturbed Systems of Impulsive Differential Equations

Sufficient conditions for the existence of bounded solutions of singularly perturbed impulsive differential equations are obtained. For this purpose integral manifolds are used.

Extremal Solutions for a Class of Functional Differential Equations

We study, in Carathéodory assumptions, existence, continuation and continuous dependence of extremal solutions for an abstract and rather general class of hereditary differential equations. By some examples we prove that, unlike the nonfunctional case, solved Cauchy problems for hereditary differential equations may not have local extremal solutions.

Oscillation Theorems for Second Order Sublinear Ordinary Differential Equations

Oscillation criteria are given for the second order sublinear non-autonomous differential equation. (r(t) (x)x′(t))′ + q(t)g(x(t)) = (t). These criteria extends and improves earlier oscillation criteria of Kamenev, Kura, Philos and Wong. Oscillation criteria are also given for second order sublinear damped non-autonomous differential equations.

Application of Lyapunov's Direct Method to the Existence of Integral Manifolds of Impulsive Differential Equations

The present paper investigates the existence of integral manifolds for impulsive differential equations with variable perturbations. By means of piecewise continuous functions which are generalizations of the classical Lyapunov’s functions, sufficient conditions for the existence of integral manifolds of such equations are found.