Using the G-Scheme, we have developed a specific procedure to generate simplified mechanisms for chemical kinetics processes, to analyze them in order to understand the role of the most important reactions, and to identify the most important reactions paths of the processes. The procedure is based on participation indices specifically created for a GScheme generated database. The effectiveness ...

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 ...

Interest in chemical computation has followed four different paths. It is one of the natural extensions of discussions about information and thermodynamics, which go back to Maxwell demon arguments and Szilard’s work [1–5]. It is also a rather natural extension to the application of dynamical systems theory to chemical reactions [6–8], in particular logic networks stemming from bistable reactio...

We consider nondeterministic and probabilistic termination problems in a process algebra that is equivalent to basic chemistry. We show that the existence of a terminating computation is decidable, but that termination with any probability strictly greater than zero is undecidable. Moreover, we show that the fairness intrinsic in stochastic computations implies that termination of all computati...

Tadalafil is PDE5 inhibitor that has recently been approved for the treatment of ED. The mechanism of action of tadalafil is similar to sildenafil and vardenafil through the inhibition of PDE. In both chemical structure and PDE subtype selectivity profile, tadalafil differs markedly from sildenafil and vardenafil. Compared with sildenafil and vardenafil, tadalafil exhibits a prolonged plasma re...

Self-healing polymers, based on microencapsulated dicyclopentadiene and Grubbs' catalyst embedded in the polymer matrix, are capable of responding to propagating fatigue cracks by autonomic processes that lead to higher endurance limits and life extension, or even the complete arrest of the crack growth. The amount of fatigue-life extension depends on the relative magnitude of the mechanical ki...

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type o...

Models involving stochastic differential equations (SDEs) play a prominent role in a wide range of applications where systems are not at the thermodynamic limit, for example, biological population dynamics. Therefore there is a need for numerical schemes that are capable of accurately and efficiently integrating systems of SDEs. In this work we introduce a variable size step algorithm and apply...

Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequ...

Many processes in cell biology encode and process information and enact responses by modulating the concentrations of biological molecules. Such modulations serve functions ranging from encoding and transmitting information about external stimuli to regulating internal metabolic states. To understand how such processes operate requires gaining insights into the basic mechanisms by which biochem...