Engineering biochemical reactions for computational purposes is a common pursue in synthetic biology [1]. In such design tasks, molecular species have to be carefully engineered to ensure modularity and orthogonality [3, 7], and are scarce resources. Minimizing the number of involved molecular species is crucial to accomplish a complex computation within a confined biochemical environment. This...

We introduce, analyze, and implement a new method for parameter identification for system of ordinary differential equations that are used to model sets of biochemical reactions. Our method relies on the integral formulation of the ODE system and a method of linear least squares applied to the integral equations. Certain variants of this method are also introduced in this paper.

Suppose one is given a (incomplete) specification of a set of interacting reactions. We would use this set of formulas as the background theory T . Suppose additionally, that a number of observations are made referring to reactions known to have occurred, or compounds known to be available for participation in a reaction, etc. Let α denote the formula representing these observations. Generally,...

To comprehend dynamic behaviors of biological systems, many models have been proposed. These models need literatures data to represent detailed and accurate dynamics. However, those data are sufficient only in few cases. To solve this problem, many techniques have been developed, including Genetic Algorithm (GA). Those methods require defining equations before predicting biological systems. To ...

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and meas...

Plants react biochemically to ozone in three phases: with constitutive chemicals in the apoplastic fluid and cell membranes; by forming messenger molecules by the affected constitutive materials (ethylene); and by responding to the messenger molecules with pathogenic RNAs and proteins. For instance, plant reactions with ozone result in constitutive molecules such as the ozonolysis of ethylene i...

We develop theory for the dynamics and fluctuations in some cyclic and linear biochemical reactions. We use the approach of maximum caliber, which computes the ensemble of paths taken by the system, given a few experimental observables. This approach may be useful for interpreting single-molecule or few-particle experiments on molecular motors, enzyme reactions, ion-channels, and phosphorylatio...

unsuitable as colloidal infusion solutions, for which reason they are depolymerized by acid hydrolysis to products of suitable molecular size (average molecular weight 7500). This book constitutes a review of the history of the development of dextran to its present place, and a review of most of the literature available on the subject. The author, Anders Gr6nwall, is Professor of Clinical Chemi...

After an injury occurs, mechanical/biochemical loads on muscles influence the composition and structure of recovering muscles; this effect likely occurs in other tissues, cells and biological molecules as well owing to the similarity, interassociation and interaction among biochemical reactions and molecules. The 'damage and reconstruction' model provides an explanation for how an ideal cytoarc...

Enzymes so called (Enz’-a-ai-am) are biologically active protein molecules responsible of biochemical reactions in the bacteria, cells and organs. Enzymes regulate the rates of biochemical reactions to maintain the metabolism to keep active physiological actions in the body. High enzyme activities or high rates of reactions cause higher product formation or deposits to initiate disease. Drugs a...