Marta Tyran-Kaminska

This monograph has arisen out of a number of attempts spanning almost five decades to understand how one might examine the evolution of densities in systems whose dynamics are described by differential delay equations. Though the authors have no definitive solution to the problem, they offer this contribution in an attempt to define the problem as they see it, and to sketch out several obvious attempts that have been suggested to solve the problem and which seem to have failed. They hope that by being available to the general mathematical community, they will inspire others to consider–and hopefully solve–the problem. Serious attempts have been made by all of the authors over the years and they have made reference to these where appropriate.

This monograph has arisen out of a number of attempts spanning almost five decades to understand how one might examine the evolution of densities in systems whose dynamics are described by differential delay equations. Though the authors have no definitive solution to the problem, they offer this contribution in an attempt to define the problem as they see it, and to sketch out several obvious attempts that have been suggested to solve the problem and which seem to have failed. They hope that by being available to the general mathematical community, they will inspire others to consider–and hopefully solve–the problem. Serious attempts have been made by all of the authors over the years and they have made reference to these where appropriate.

This book presents a concise introduction to piecewise deterministic Markov processes (PDMPs), with particular emphasis on their applications to biological models. Further, it presents examples of biological phenomena, such as gene activity and population growth, where different types of PDMPs appear: continuous time Markov chains, deterministic processes with jumps, processes with switching dynamics, and point processes. Subsequent chapters present the necessary tools from the theory of stochastic processes and semigroups of linear operators, as well as theoretical results concerning the long-time behaviour of stochastic semigroups induced by PDMPs and their applications to biological models. As such, the book offers a valuable resource for mathematicians and biologists alike. The first group will find new biological models that lead to interesting and often new mathematical questions, while the second can observe how to include seemingly disparate biological processesinto a unified mathematical theory, and to arrive at revealing biological conclusions. The target audience primarily comprises of researchers in these two fields, but the book will also benefit graduate students.

This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the presence of noise—either arising from low numbers of molecules involved, or due to noise external to the regulatory process. The third and final part of the notes gives a detailed treatment of three well studied and concrete examples of gene-network dynamics by considering the lactose operon, the tryptophan operon, and the lysis-lysogeny switch. The notes contain an index for easy location of particular topics as well as an extensive bibliography of the current literature. The target audience of these notes are mainly graduates students and young researchers with a solid mathematical background (calculus, ordinary differential equations, and probability theory at a minimum), as well as with basic notions of biochemistry, cell biology, and molecular biology. They are meant to serve as a readable and brief entry point into a field that is currently highly active, and will allow the reader to grasp the current state of research and so prepare them for defining and tackling new research problems.