These notes are shamelessly cribbed from the extremely helpful online notes [2]. Even most of the notation is the same. I wrote them because, like Goethe’s Frenchman, I wanted to translate Gunawardena’s notes into my own language. I also benefitted from conversations with Moe Hirsch and Gheorghe Craciun and from lectures by Gheorghe Craciun and David Anderson. 1. Notation. The positive real num...

Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising programming language for the design of artificial molecular control circuitry. Due to a formal equivalence between CRNs and a model of ...

There is also some overlap with Discussion 67 (1979) on State-Selected Kinetics and Discussion 75 (1983) on Intramolecular Kinetics. However, the present symposium di†ers from all these in two very important ways : (1) condensed-phase reactions are also included, and (2) the discussion is focused exclusively on theory. With these aspects in mind one could include a number of earlier predecessor...

We consider the dynamics of chemical reaction networks under the assumption of mass-action kinetics. We show that there exist reaction networks R for which the reaction rate constants are not uniquely identifiable, even if we are given complete information on the dynamics of concentrations for all chemical species of R. Also, we show that there exist reaction networks R1 6= R2 such that their d...

Mathematical modeling and simulation of biochemical reaction networks facilitates our understanding of metabolic and signaling processes. For closed, well-mixed reaction systems, it is straightforward to derive kinetic equations that govern the concentrations of the reactants and products. The usual way of deriving kinetic equations involves application of the principle of conservation of mass ...

Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical s...

With the advances in measurement technology for molecular biology, predictive mathematical models of cellular processes come in reach. A large fraction of such models addresses the kinetics of interaction between biomolecules such as proteins, transcription factors, genes, and messenger RNA. In contrast to classical chemical kinetics – utilizing the reaction-rate equation – the small volume of ...

Elongation factor Tu (EF-Tu), the protein responsible for delivering aminoacyl-tRNAs (aa-tRNAs) to ribosomal A site during translation, belongs to the group of guanosine-nucleotide (GTP/GDP) binding proteins. Its active 'on'-state corresponds to the GTP-bound form, while the inactive 'off'-state corresponds to the GDP-bound form. In this work we focus on the chemical step, GTP+H(2)O-->GDP+Pi, o...

This paper presents the work carried out on the chemical reaction, mechanism, role of materials, applications and microstructure of fly ash geopolymer cement. Geopolymer is a type of amorphous alumino-silicate cementitious material. Geopolymer can be synthesized by polycondensation reaction of geopolymeric precursor, and alkali polysilicates. Literature demonstrates that the exact geopolymeriza...

Reactive spinning of nanoand microfibers that involves very fast diffusion-limited chemical reaction and ion exchange is very challenging for the major nanofiber formation methods. The two-droplet reactive magnetospinning method introduced here offers a new technique for spinning fibers when the polymer formation or post-polymerization modification is limited by diffusion. This method can be re...