The interactions among the components of a biological system can be given a logical representation that is useful for reasoning about them. One of the relevant problems that may be raised in this context is finding what would explain a given behaviour of some component; in other terms, generating hypotheses that, when added to the logical theory modeling the system, imply that behaviour. Tempor...

Vision begins when photons are captured by rhodopsin molecules in photoreceptor cells in the back of the retina. Activation of rhodopsin instigates a cascade of biochemical reactions, which eventually results in reduction of the steady (dark) current across the photoreceptor plasma membrane. This is the photoreceptor response, the signal that propagates to the brain enabling vision. Employing a...

MOTIVATION We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. RESULTS In the regime where the number of molecules is small an...

MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/. This article presents the release of Version 3 of MACiE, which not only extends the dataset to 335 entries, covering 182 of the EC sub-subclasses with a crystal structure available (~90%), but also ...

Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions, which naturally arise due to the very small numbers of genes, RNA, or protein molecules in single cells. Modern measurements of single biomolecules have create...

A cellular system is composed of a considerable number of elements including genes, proteins or enzymes, and metabolites. They are dynamically connected and interdependent to construct a network diagram, which is referred to as a metabolic pathway. The significance of a systems approach has been recognized for understanding the activities of living organisms (Eisenberg et al., 2000; Kanehisa, 2...

We propose a modeling and analysis method for biochemical reactions based on finite state automata. This is a completely different approach compared to traditional modeling of reactions by differential equations. Our method aims to explore the algebraic structure behind chemical reactions using automatically generated coordinate systems. In this paper we briefly summarize the underlying mathema...

We study stochastic dynamics of two competing complexation reactions (i) A + B↔AB and (ii) A + C↔AC. Such reactions are common in biology where different reactants compete for common resources--examples range from binding enzyme kinetics to gene expression. On the other hand, stochasticity is inherent in biological systems due to small copy numbers. We investigate the complex interplay between ...

One gene, one enzyme. What a simple concept, how obvious! This fundamental relationship between gene and gene product, hinted at by several previous investigators, did not become firmly established until George W. Beadle and Edward L. Tatum performed their pioneering analyses with Neurospora crassa. Prior to their proposing the one-gene–oneenzyme hypothesis, in the early 1940s, there was little...