Based on a master equation formalism for mesoscopic, unimolecular biochemical reactions, we show the periodic oscillation arising from severe nonequilibrium pumping is intimately related to the periodic motion in recently studied stochastic resonance (SR). The white noise in SR is naturally identified with the temperature in the biochemical reactions; the drift in the SR is associated with the ...

This paper demonstrates the equivalence between simple feedback loops and the biochemical enzyme reactions in confined media that obey Michaelis-Menten kinetics. Single and cascaded reactions are modeled, and general principles to achieve enzyme transfer functions are set out. Reaction rate and concentration difference are identified as the through and across variables of biochemical networks, ...

We present an expression for the power spectrum of the output signal of a biochemical network, which reveals that the reactions that allow a network to detect biochemical signals, induce correlations between the extrinsic noise of the input signals and the intrinsic noise of the reactions that form the network. We show that anticorrelations between the extrinsic and intrinsic noise enhance the ...

SABIO-RK (http://sabio.villa-bosch.de/SABIORK), a database system we have developed to provide experimental data, offers information about biochemical reactions and their corresponding kinetics [1]. The database is populated by merging information about reactions and pathways mainly derived from public databases with the corresponding kinetic data manually extracted from literature. The integra...

This paper presents a stochastic model, a theoretical multi-variate probability function describing concentrations of reactants in a closed biochemical system at equilibrium. The theory applies to the complete range of biochemical systems from single enzyme reactions to combinations of reactions to complete pathways. Prior to examining the general system, probability functions are derived for t...

We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current method, unlike some of the graphical approaches proposed in the literature, uses the values of the experimental measurements only relative to the geometry of th...

Signaling as an overall cellular process is a prerequisite for the life of normal and cancer cells and is regulated by a multiplicity of mechanisms including "cross-talks" among pathways. Cross-talk is often critical in determining the decision of a cell to go toward a specific biological direction, such as proliferation, apoptosis, or differentiation. Both signaling pathways and cross-talk amo...

There is an evolutionary advantage in having multiple components with overlapping functionality (i.e degeneracy) in organisms. While theoretical considerations of degeneracy have been well established in neural networks using information theory, the same concepts have not been developed for differential systems, which form the basis of many biochemical reaction network descriptions in systems b...

Acyl chain remodeling in lipids is a critical biochemical process that plays a central role in disease. However, remodeling remains poorly understood, despite massive increases in lipidomic data. In this work, we determine the dynamic network of ethanolamine glycerophospholipid (PE) remodeling, using data from pulse-chase experiments and a novel bioinformatic network inference approach. The mod...