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Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel
Author to whom correspondence should be addressed.
Received: 16 April 2019 / Revised: 6 May 2019 / Accepted: 8 May 2019 / Published: 10 May 2019
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding. View Full-Text
Keywords: systems chemistry; systems protobiology; molecular dynamics; gard; lipid world; micelle; origin of life systems chemistry; systems protobiology; molecular dynamics; gard; lipid world; micelle; origin of life

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Kahana, A.; Lancet, D. Protobiotic Systems Chemistry Analyzed by Molecular Dynamics. Life 2019, 9, 38.

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