Previously we reported [A. Wynveen, Phys. Rev. E 89, 022725 (2014)PLEEE81539-375510.1103/PhysRevE.89.022725] that requiring that the systems regarded as lifelike be out of chemical equilibrium in a model of abstracted polymers undergoing ligation and scission first introduced by Kauffman [S. A. Kauffman, The Origins of Order (Oxford University Press, New York, 1993), Chap. 7] implied that lifelike systems were most probable when the reaction network was sparse. The model was entirely statistical and took no account of the bond energies or other energetic constraints. Here we report results of an extension of the model to include effects of a finite bonding energy in the model. We studied two conditions: (1) A food set is continuously replenished and the total polymer population is constrained but the system is otherwise isolated and (2) in addition to the constraints in (1) the system is in contact with a finite-temperature heat bath. In each case, detailed balance in the dynamics is guaranteed during the computations by continuous recomputation of a temperature [in case (1)] and of the chemical potential (in both cases) toward which the system is driven by the dynamics. In the isolated case, the probability of reaching a metastable nonequilibrium state in this model depends significantly on the composition of the food set, and the nonequilibrium states satisfying lifelike condition turn out to be at energies and particle numbers consistent with an equilibrium state at high negative temperature. As a function of the sparseness of the reaction network, the lifelike probability is nonmonotonic, as in our previous model, but the maximum probability occurs when the network is less sparse. In the case of contact with a thermal bath at a positive ambient temperature, we identify two types of metastable nonequilibrium states, termed locally and thermally alive, and locally dead and thermally alive, and evaluate their likelihood of appearance, finding maxima at an optimal temperature and an optimal degree of sparseness in the network. We use a Euclidean metric in the space of polymer populations to distinguish these states from one another and from fully equilibrated states. The metric can be used to characterize the degree and type of chemical equilibrium in observed systems, as we illustrate for the proteome of the ribosome.
Bibliographical noteFunding Information:
This work was supported by the United States National Aeronautics and Space Administration (NASA) through Grant No. NNX14AQ05G and used the computational resources of the Minnesota Supercomputing Institute, the Open Science Grid, the University of Minnesota School of Physics and Astronomy Condor cluster, and the NASA Advanced Supercomputing division Pleiades supercomputer. We thank A. Wynveen for many helpful discussions and for reading and helpfully commenting on a preliminary version of the manuscript. We thank Professor Niels Fischer for assistance in locating the data on the ribosome which was used to produce Fig. 10 .
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