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Origin of Life: Emergence, Self-organization and Evolution
A system-centered perspective on the origin and evolution of Life on Earth
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On stochastic simulation of minimal cell models

On stochastic simulation of minimal cell models | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

If stochastic simulation of minimal cell models intrigues you, see may be interested in:

 

Carletti T, Filisetti A.

The stochastic evolution of a protocell: the gillespie algorithm in a dynamically varying volume.
Comput Math Methods Med. 2012;2012:423627.

 

Lazzerini-Ospri L, Stano P, Luisi P, Marangoni R.

Characterization of the emergent properties of a synthetic quasi-cellular system.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S9.

 

Zachar I, Fedor A, Szathmáry E.

Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

PLoS One. 2011;6(7):e21380. Epub 2011 Jul 19.

 

Van Segbroeck S, Nowé A, Lenaerts T.

Stochastic simulation of the chemoton.

Artif Life. 2009 Spring;15(2):213-26.

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Noise, Stochasticity and Evolvability

Noise, Stochasticity and Evolvability | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Kuwahara and Soyer report about stochastic fluctuations in gene regulation that can lead to increased evolvability of biological systems by pushing "system parameters toward a nonlinear regime where phenotypic diversity is increased and small changes in genotype cause large changes in expression level".

These findings strongly suggest that stochasticity and noise are used by biosystems to increase plasticity and access new phenotypes.

 

Source:

Hiroyuki Kuwahara & Orkun S Soyer. Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology 8:564

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Stochastic simulations of minimal cells: the Ribocell model

Stochastic simulations of minimal cells: the Ribocell model | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models to shed new light on the origin of life and the basic feature of living system as well. In this paper, Mavelli and Mirazo develop a comprehensive platform called ENVIRONMENT suitable for studying the stochastic time evolution of reacting lipid compartments. The software will allow the investigation of random fluctuations and stochastic events tha may lead an open system towards unexpected time evolutions.

 

Source:

Mavelli F.

Stochastic simulations of minimal cells: the Ribocell model.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S10.

 

Mavelli F, Ruiz-Mirazo K.

ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments.

Phys Biol. 2010 Aug 11;7(3):036002.

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