Recent interest in modeling biochemical networks raises questions about the relationship between often complex mathematical models and familiar arithmetic concepts from classical enzymology, and also about connections between modeling and experimental data. This review addresses both topics by familiarizing readers with key concepts (and terminology) in the construction, validation, and applica...

We propose a numerical technique for parameter inference in Markov models of biological processes. Based on time-series data of a process we estimate the kinetic rate constants by maximizing the likelihood of the data. The computation of the likelihood relies on a dynamic abstraction of the discrete state space of the Markov model which successfully mitigates the problem of state space largenes...

Natural computing is concerned with human-designed computing inspired by nature as well as with computations taking place in nature, i.e., it investigates phenomena taking place in nature in terms of information processing. Well-known examples of the first strand of research are evolutionary computing, neural computation, cellular automata, swarm intelligence, molecular computing, quantum compu...

Equilibrium compositions of solutions of biochemical species can be calculated by use of general equilibrium computer programs that minimize the Gibbs energy. The standard Gibbs energies of formation and standard enthalpies of formation of the species in a biochemical system can be calculated by Gaussian reduction of the augmented transpose of the stoichiometric number matrix for the system. Th...

Yersinia enterocolitica was isolated from human mesenteric lymph nodes. Its morphological characteristics and biochemical and serological reactions are described.

Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used t...

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on sp...

In Nature, protons (H(+)) can mediate metabolic process through enzymatic reactions. Examples include glucose oxidation with glucose dehydrogenase to regulate blood glucose level, alcohol dissolution into carboxylic acid through alcohol dehydrogenase, and voltage-regulated H(+) channels activating bioluminescence in firefly and jellyfish. Artificial devices that control H(+) currents and H(+) c...

T he scientific literature is replete with studies of the influence of weak magnetic fields on biological systems. Often motivated by alleged health hazards of the stray electromagnetic fields that accompany the distribution and use of electrical power, the majority of these articles report definite effects. However, in the relatively few cases in which independent replication has been attempte...

All biochemical reactions involve recognition, binding and the formation of noncovalent complexes. Since the characterization of binding events is central to understanding any physiological process at the molecular level, biochemical and biomedical research requires methodologies for precisely analyzing binding reactions. Isothermal titration calorimetry (ITC) is rapidly becoming the method of ...