Journal of Systems Chemistry
1759-2208
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Serial transfer can aid the evolution of autocatalytic setsAbstract
Background
The concept of an autocatalytic set of molecules has been posited theoretically and demonstrated empirically with catalytic RNA molecules. For this concept to have significance in a realistic origins-of-life scenario, it will be important to demonstrate the evolvability of suc... ...
- 2014
Systems chemistry: using thermodynamically controlled networks to assess molecular similarityAbstract
Background
The assessment of molecular similarity is a key step in the drug discovery process that has thus far relied almost exclusively on computational approaches. We now report an experimental method for similarity assessment based on dynamic combinatorial chemistry.
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Tập 4 Số 1 - 2013
Synthesis of information-carrying polymers of mixed sequences from double stranded short deoxynucleotides
Tập 1 - Trang 1-16 - 2010
The "RNA World" hypothesis suggests that an early form of life on Earth was based on nucleic acid strands able to store genetic information and catalyze a wide range of reactions including those which lead to self-replication. For this hypothesis to be true there must exist an efficient process for creating RNA or RNA-like polymers of mixed sequences from short precursors, where these polymers hav......
Unravelling a fulvene based Replicator: Experiment and Theory in Interplay
Tập 1 - Trang 1-6 - 2010
A self-replicating system based on a cycloaddition of a fulvene derivative and a maleinimide is investigated using a two-pronged approach combining NMR spectroscopy with computer simulations. In the course of the reaction, two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, a network emerges in which one diastereomer takes over the resource......
The eightfold path to non-enzymatic RNA replication
Tập 3 - Trang 1-14 - 2012
The first RNA World models were based on the concept of an RNA replicase - a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. At first glance the alternative, in which RNA replication is driven purely by chemical an......
Toward a general theory of evolution: Extending Darwinian theory to inanimate matter
Tập 2 - Trang 1-14 - 2011
Though Darwinian theory dramatically revolutionized biological understanding, its strictly biological focus has resulted in a widening conceptual gulf between the biological and physical sciences. In this paper we strive to extend and reformulate Darwinian theory in physicochemical terms so it can accommodate both animate and inanimate systems, thereby helping to bridge this scientific divide. The......
Evolution of metabolic networks: a computational frame-work
Tập 1 - Trang 1-14 - 2010
The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis of extant genomes. Alternatively, the principles of metaboli......
Inferring chemical reaction patterns using rule composition in graph grammars
- 2013
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactio......