MOTIVATION Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses. RESULTS Here we present a flexible and widely applicable noise decompo...

This paper addresses the translation of Systems Biology MarkUp Language (SBML) Level 2 models of network of biochemical reactions to the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by ...

We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of...

Copyright # 20 ABSTRACT: This review focuses on how the mechanistic approach of physical organic chemistry can be used to elucidate the mechanisms behind complex biochemical networks. The dynamics of biochemical reaction networks is difficult to describe by considering their individual reactions, just as the dynamics of organic reactions is difficult to describe by considering individual electr...

Diethylcarbamazine (DEC) treatment for lymphatic filariasis can be accompanied by adverse drug reactions. Severe adverse reactions are usually uncommon but once happen, they could be acute and sometimes life-threatening. We report here a case of 15-year-old patient who was treated with DEC and developed severe adverse reactions including fever, headache, dizziness, chest pain, sore throat, coug...

MOTIVATION Many biochemical networks involve reactions localized on the cell membrane. This can give rise to spatial gradients of the concentration of cytosolic species. Moreover, the number of membrane molecules can be small and stochastic effects can become relevant. Pathways usually consist of a complex interaction network and are characterized by a large set of parameters. The inclusion of ...

A total of 165 strains of Streptococcus sanguis and Str mitior were selected on the basis of their biochemical reactions using established identification procedures. These strains were also classified using API Database and were then screened against five candidate grouping sera. Biochemical tests and serological identification were in general complementary, but no regular associations between ...

This paper proposes a minimal model of a biochemical reaction pathway involving coupled negative and positive feedback mechanisms that are common in cellular processes. The analytical and numerical studies show that this pathway is capable of eliciting a large variety of functional dynamics at different parameter values. Keywords— Biochemical reactions, Feedback, Hopf bifurcation, perioddoublin...

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

We present a method to simulate biochemical networks described by the graphical notation of Molecular Interaction Maps within stochastic Concurrent Constraint Programming. Such maps are compact, as they represent implicitly a wide set of reactions, and therefore not easy to simulate with standard tools. The encoding we propose is capable to stochastically simulate these maps implicitly, without...