Topic
Gard model
About: Gard model is a research topic. Over the lifetime, 10 publications have been published within this topic receiving 115 citations.
Papers
TL;DR: The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire, and is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings.
Abstract: The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model—the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.
42 citations
TL;DR: The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes, and is tested with computer simulations of a simple case of monovalent monomers, whereby more complex molecules are formed internally, in a manner resembling biosynthetic metabolism.
Abstract: The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.
30 citations
TL;DR: It is found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed and the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules.
25 citations
30 Dec 1999
TL;DR: It is shown that catalytic closure can sustain self replication up to a critical dilution rate, related to the extent of mutual catalysis, and the capacity for self replication in a mutually catalytic set is shown to be a graded property, quantitated by a critical parameter (lambda) ci.
Abstract: The Graded Autocatalysis Replication Domain (GARD) model described here depicts an early primordial scenario, prior to the emergence of biopolymers, such as RNA or proteins. The model describes, with the help of statistical chemistry computer simulations, a collection of organic molecular species capable of rudimentary selection and evolution. The GARD model provides a rigorous kinetic analysis of simple sets of chemicals that manifest mutual catalysis. It is shown that catalytic closure can sustain self replication up to a critical dilution rate, related to the extent of mutual catalysis. The capacity for self replication in a mutually catalytic set is shown to be a graded property, quantitated by a critical parameter (lambda) ci. GARD could be a simple model for a primordial scenario, in which replication and catalysis are performed by the same set of molecules.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
2 citations
1 Jan 2005
TL;DR: The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes, and is tested with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosyn- thetic metabolism.
Abstract: The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assem- bly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosyn- thetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.
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Performance Metrics
| Year | Papers |
|---|---|
| 2019 | 1 |
| 2018 | 1 |
| 2015 | 1 |
| 2014 | 1 |
| 2012 | 1 |
| 2007 | 1 |