A fundamental issue of evolution of life is the emergence and maintenance of self-referential autocatalytic systems (e.g. living cells). In this paper the problem is analyzed from a computational perspective. It is proposed that such systems have to be infinite autocatalytic systems, which can be considered equivalent to Turing machines. The implication of this is that searching for finite auto...

We model chemical reaction networks as directed hypergraphs that are generated in rule-based manner, using graph grammars as models of given sets of reaction mechanisms. Graphs serve as abstractions of molecules. This provide a level of chemical realism sufficient to ensure conservation of mass, atom type, and charge. Atom maps, for instance, are thus consistently defined within the model. The ...

This paper presents an understanding of how initial molecular weight and initial monomer fraction affect the degradation of bioresorbable polymers in terms of the underlying hydrolysis mechanisms. A mathematical model was used to analyse the effects of initial molecular weight for various hydrolysis mechanisms including noncatalytic random scission, autocatalytic random scission, noncatalytic e...

In the present work, we study autocatalytic pathways which contain reactions that need the use of one of their own productions. These pathways are common in biology; one of the simplest and widely studied autocatalytic pathways is Glycolysis. This pathway produces energy by breaking down Glucose. It is shown that this pathway can be simplified as a network of three biochemical reactions. We fir...

A particular class of ordinary differential equations (ODEs) describing catalyzed, template-induced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting for the correct replication and a mutation term accounting for all miscopying processes. The set of all species is divided into the catalytically active "viable" species and an error tail subsuming...

A particular class of ordinary diierential equations (ODE) describing catalyzed, template-induced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting for the correct replication and a mutation term accounting for all miscopying processes. The set of all species is divided into the catalytically active \viable" species and an error-tail subsuming a...

Protein kinase D1 (PKD1) is a Ser/Thr kinase implicated in a wide variety of cellular responses. PKD1 activation is generally attributed to a PKC-dependent pathway that leads to phosphorylation of the activation loop at Ser(744)/Ser(748). This modification increases catalytic activity, including that toward an autophosphorylation site (Ser(916)) in a postsynaptic density-95/disks large/zonula o...

BACKGROUND A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of st...

A simple computational model for the emergence of autocatalytic sets as described in (Farmer et al., 1986) is reimplemented. Results are found to generally agree with the major theme in the original work: increasing the initial polymer variety in a toy chemical soup scenario increases the likelihood that a complex autocatalytic set will suddenly bootstrap itself into existence. Quantitatively, ...

In this thesis, we study two types of reaction-diffusion systems which have direct applications in understanding wide range of phenomena in chemical reaction, biological pattern formation and theoretical ecology. The first part of this thesis is on propagating traveling waves in a class of reaction-diffusion systems which model isothermal autocatalytic chemical reactions as well as microbial gr...