Cellular processes are subject to vast amounts of random variation, which can cause isogenic cells to respond differently, despite identical environmental conditions. Recent experimental techniques make it possible to measure this variation in gene expression, protein abundance, and cellular behavior. Combined with computational modeling, these techniques enable us to uncover the causes and eff...

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 ...

The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jump...

The sensitivity and reproducibility of the radioenzymatic adenylylating assay for spectinomycin were improved by modifications of the assay procedure and by partial purification of the enzyme. The presence of Bacillus subtilis ribosomes or S-150 fraction in the enzymatic reaction mixture interfered with the ability to measure spectinomycin by this method.

One of the most challenging tasks in systems biology is parameter identification from experimental data. In particular, if the available data are noisy, the resulting parameter uncertainty can be huge and should be quantified. In this work, a set-based approach for parameter identification in discrete time models of biochemical reaction networks from time series data is developed. The basic ide...

The "RNA world" hypothesis proposes that early in the evolution of life, RNA was responsible both for the storage and transfer of genetic information and for the catalysis of biochemical reactions. One of the problems of the hypothesis is that RNA is known to be temperature sensitive. Nevertheless, different types of sequences with a thermostable phenotype may exist. In order to test this possi...

We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the system can also "learn" by association, to later respond to the second input if it is initially applied in combination with the triggering input as the "tra...

How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal models of stochastic chemical reactions commonly found in cell signaling and gene regulatory systems. Employing exact solutions and semi-analytical methods ...

Two different approaches were used to study the kinetics of the enzymatic reaction under heterogeneous conditions to interpret the unusual nonlinear pharmacokinetics of mibefradil. Firstly, a detailed model based on the kinetic differential equations is proposed to study the enzymatic reaction under spatial constraints and in vivo conditions. Secondly, Monte Carlo simulations of the enzyme reac...

Experimental and theoretical studies have suggested that bifunctional enzymes catalyzing opposing modification and demodification reactions can confer steady-state concentration robustness to their substrates. However, the types of robustness and the biochemical basis for them have remained elusive. Here we report a systematic study of the most general biochemical reaction network for a bifunct...