Methodologies in the Use of Computational Models for Theoretical Biology 1.1 Exploring Experimental Hypotheses
This paper is a brief discussion of the methodological issues I have considered and approaches I have taken in the course of my research, and it is my hope that these methodologies may prove useful to the reader.
Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution
- BiologyPloS one
This paper confirms that the coexistence of parasite RNAs and replicases is possible in a spatially extended system, and shows that the presence of trade-off that takes into the account an RNA folding process could still pose a serious obstacle to the evolution of replication.
Spatial dynamics of synthetic microbial mutualists and their parasites
- Environmental SciencePLoS Comput. Biol.
It is shown that improved environments can slow down mutualistic range expansions as a result of genetic drift effects preceding local resource depletion, and that a parasitic strain is excluded from the population during range expansions (which acknowledges a classical prediction).
Understanding Life: A Bioinformatics Perspective
- BiologyEuropean Review
It seems likely that linking efforts and knowledge from the various fields of science into a holistic bioinformatics perspective offers the opportunity to come one step closer to a solution to the question of the origin of life, which is one of the greatest mysteries of humankind.
- BiologyPLoS Comput. Biol.
The most important properties of hypercycles are autocatalytic growth competition between cycles, once-for-ever selective behaviour, utilization of small selective advantage, rapid evolvability, increased information capacity, and selection against parasitic branches.
Définition du vivant et émergence de la vie : entre rupture et continuité, saisir l'originalité du vivant
Comment caracteriser le vivant dans le cadre scientifique tel qu'il se pratique et partant, identifier les contraintes et limites epistemiques qui rendent si delicate la theorisation d'un systeme…
Hierarchical Heterogenity Of Populations: Modeling By The Open Eigen Hypercycle
The case of a biological population, which consists of several sub-populations (different kinds of the population ”social” groups: families, bevies, etc.), has been considered, and a model of ”open the Eigen hypercycle” has been proposed, which shows dependence of a complexity of population “social structure” from the size of its niche.
The Behavior-Based Hypercycle: From Parasitic Reaction to Symbiotic Behavior
It is demonstrated for the first time that a parasitic sidereaction on the metabolic level can lead to self-motility on the behavioral level of the chemical system as a whole, thus constituting a symbiotic, behavior-based hypercycle.
SHOWING 1-9 OF 9 REFERENCES
Two-dimensional spectrophotometry of spiral wave propagation in the Belousov—Zhabotinskii reaction. I. experiments and digital data representation
A cellular automation model of excitable media including curvature and dispersion.
The revised model shows curvature and dispersion effects comparable to those of continuous models, it predicts rotating spiral wave solutions in quantitative accord with the theory of continuous excitable media, and it is parameterized so that the spatial step size of the automation can be adjusted for finer resolution of traveling waves.
Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet.
- Environmental ScienceJournal of theoretical biology
Hypercycles and the origin of life
The central problem discussed in a series of papers by Manfred Eigen and Peter Schuster proposing the ‘hypercycle’ as a necessary intermediate stage is that one cannot have accurate replication without a length of RNA, say, 2000 or more base pairs, and one cannotHave that much RNA without accurate replication.
Spatial structure and chaos in insect population dynamics
- Environmental ScienceNature
MOST environments are spatially subdivided, or patchy, and there has been much interest in the relationship between the dynamics of populations at the local and regional (metapopulation) scales1.…