We describe a novel application of a stochastic name-passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant of the stochastic π-calculus, yielding a model which is mathematically well-defined and biologically faithful. We adapt the operational semantics of the calculus to account for both the time and probability of bio...

An increasing number of researchers is trying to define models of biochemical pathways via theoretical and technological tools, allowing biologists to simulate reactions before doing them in vitro. The advantages are obvious: a computation normally requires less time then a real experiment, simulation of reactions is cheaper than doing them effectively, and so on. The problem is to find a forma...

In biochemical networks, identifying key proteins and protein-protein reactions that regulate fluctuation-driven transitions leading to pathological cellular function is an important challenge. Using large deviation theory, we develop a semianalytical method to determine how changes in protein expression and rate parameters of protein-protein reactions influence the rate of such transitions. Ou...

Proton pump inhibitors (PPIs) are widely prescribed drugs in daily practice. Allergic reactions, even small number of anaphylactic reactions to PPIs have been reported. Omeprazole, lansoprazole, pantoprazole, rapeprazol and esomeprazole are classified in the same group. Despite the similarity of biochemical structures among these drugs, presence of cross-reactivity between PPIs is controversial...

A goal of systems biology is to build a concrete biochemical network map, which provides an important instruction to trace the pathways of interest or to understand the mechanism of a biological system. In the postgenomic era, not only the concrete biochemical maps, but also postgenomic maps (mRNA coexpression and protein-protein interaction networks) have been extensively produced. In the bioc...

Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signaling networks. However, the biochemical reactions making up these networks are intrinsically noisy, which limits the reliability of intracellular signaling. Here we use information theory to characterize the reliability of transmission of time-varying ...

3.1 Kinetic models and their dynamic behaviour in a nutshell Examples: Metabolic network; transport reactions; signaling system; gene expression Stoichiometric coefficients nir Stoichiometric coefficients denote the proportions, with which the molecules of substrates and products enter the biochemical reactions. One can summarise the stoichiometric coefficients in a matrix N. The rows refer to ...

A hypothesis is presented that electronic and vibrational resonant energy states are important in biochemical reactions due to their coupling to hydrogen transfer reactions. The hypothesis is based upon (1) the involvement of hydrogen in most biochemical reactions, (2) the unique abiity of hydrogen to act as an energy trap for resonant energy and (3) demonstrations of the coupling of resonant e...

The present study aimed to detect Staphylococcus aureus (S. aureus) among other coagulase positive staphylococci from animal origin by using conventional methods (biochemical tests and latex agglutination) and a molecular method, based on the nuc gene, as the gold standard and to assess the usefulness of these methods. For this purpose, total of 344 staphylococcal isolates were collected and an...

Chemical genomics is the next stage of post-genomic analysis. Drugs, environmental substances and various chemical compounds contribute to the fluctuation of bio-systems. Therefore, chemical genomic analysis would require the investigation of relationships between genomes and their extracellular environments. These relationships between bio-systems and environments include complicated biochemic...