Fig. 1. Example Biochemical processes in organisms are considered as very large networks consisting of reactants, products and enzymes with interconnections representing reactions and regulation. Examples are given by the well known Boehringer poster [4] and the Biochemical Pathways atlas [5]. These networks are very complex and grow fast by the steady progress of knowledge in life sciences. Bi...

Professor Robert A. Alberty has created a legacy of excellence both in scientific research and in university education and administration. His career spans 67 years, during which time he has made many critical and seminal contributions in the areas of thermodynamics and kineticssthe vast majority of it dealing with biochemical reactions. The complexity of biochemical substances is largely attri...

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specifi...

The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for...

This article is concerned with the general question of how to represent biological knowledge in computers such that it may be used in multiple problem solving tasks. In particular, I present a model of a bacterial gene regulation system that is used by a program that simulates gene regulation experiments , and by a second program that formulates hypotheses to account for errors in predicted exp...

Mathematical modeling can provide unique insights and predictions about a signaling pathway. Parameter variations allow identification of key reactions that govern signaling features such as the response time that may have a direct impact on the functional outcome. The effect of varying one parameter, however, may depend on values of another. To address the issue, we performed multi-parameter v...

To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs integrated with a 30 mm long flow-cell of 109 μm optical path length constructed from two parallel sheets...

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneou...

Sensitivity Analysis (SA) provides techniques which can be used to identify the parameters which have the greatest influence on the results obtained from a model. Classical SA methods apply to deterministic simulations of ODE models. We extend these to stochastic simulations and consider the analysis of models with bifurcation points and bistable behaviour. We consider local, global and screeni...