Physically embedded minimal self-replicating structures: studies by simulation

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Title: Physically embedded minimal self-replicating structures: studies by simulation
Authors: Fellermann, Harold
Thesis advisor: Prof. Dr. Horst Malchow
Thesis referee: Dr. Steen Rasmussen
Dr. Norman Packard
Abstract: We present simulation results of a minimal life-like, artificial, molecular aggregate (i.e. protocell) that has been proposed by Steen Rasussen and coworkers and is currently pursued both experimentally and computationally in interdisciplinary international research projects. We develop a space-time continuous physically motivated simulation framework based on the method of dissipative particle dynamics (DPD) which we incrementally extend (most notably by chemical reactions) to cope with the needs of our model. The applicability of the method over the entire length scale of interest is reintroduced, by rejecting a concern that DPD introduces a freezing artifact for any model above the atomistic scale. This is achieved by deriving an alternative scaling procedure for interaction parameters in the model. We perform system-level simulations of the design which attempt to account for theoretical, and experimental knowledge, as well as results from other computational models. This allows us to address key issues of the replicating subsystems container, genome, and metabolism both individually and in mutual coupling. We analyze each step in the life-cycle of the molecular aggregate, and a finnal integrated simulation of the entire life-cycle is prepared. Our simulations confirm most assumptions of the theoretical designs, but also exhibit unanticipated system-level dynamics. These findings are used to revise the original design of the Los Alamos minimal protocell over the course of the analysis. The results support the hypothesis that self-replication and probably other life-like features can be achieved in systems of formerly unanticipated simplicity if these systems exploit physicochemical principles that are immanent to their physical scale.
URL: https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2009082819
Subject Keywords: self-replication; minimal life; artificial life; computer simulation; dissipative particle dynamics
Issue Date: 26-Aug-2009
Type of publication: Dissertation oder Habilitation [doctoralThesis]
Appears in Collections:FB06 - E-Dissertationen

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