In the last decade, the improvements of wet-lab techniques is making available novel experimental data about biochemical reactions occurring in single living cells. This information provides evidences that random events arising at the molecular level play important roles in determining the overall behaviour of biological organisms [2, 10]. As a consequence, new interest is rising towards stocha...

Biochemical reactions are often modelled as discrete-state continuoustime stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynamics. We propose a methodology for building stochastic simulation algorithms which model accurately non-Markovian processes in some specific situations. Our methodology is based on and implem...

Cell motility is important for many physiological processes. The biochemical reactions underlying motility have been well-characterized. Mathematical models, using these biochemical reactions, and focusing on different types of spreading behavior have been constructed and analyzed. We built on these previous models to develop a three-dimensional stochastic model of isotropic spreading of mammal...

Enzyme catalysis has been studied as a supportive process in biochemical reactions since the 1800s. The conventional paradigm states that a catalyst accelerates a chemical reaction without affecting its equilibrium) outcome. This notion was formed by decades of analysis of biochemical catalysis under the conditions defined by Henri in 1903, which stipulate that enzyme, substrate and the enzyme-...

Central to a coherent understanding of cellular biology is a faithful representation of biochemical processes as it pertains to its molecular participants. Current representations underspecify our knowledge because they fail to indicate the roles of the molecular components during relevant processes. Here, we describe a knowledge representation using OWL2 that overcomes previous limitations in ...

We describe a novel biochemical sensing method and its potential new biosensing applications. A light-sensitive complementary metal oxide semiconductor (CMOS) chip prepared through a standard 0.5m CMOS process was developed for measuring biochemical reactions. A light producing enzymatic reaction catalyzed by horseradish peroxidase (HRP) was designed as a platform reaction to determine the conc...

We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In order to obtain reduced models we solve the problem of tropical equilibration that is a system of equations in max-plus algebra. In the case of networks with non...