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The microscopic model in which nodes interacting with each other are statistical systems is introduced. The nodes conditions are connected with a string of distinct microscopic configurations and depend on external parameters (pressure and…
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when…
A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage…
A first order phase transition leading to deconfinement and chiral restoration is a likely possibility for QCD, at least in some region of the temperature-density plane. A signal for a unique transition is that the order parameters for such…
The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully…
Mutation is introduced into autocatalytic reaction networks. Examples of low dimensional dynamical systems --- n = 2, 3 and 4 --- are discussed and complete qualitative analysis is presented. Error thresholds known from simple…
The effect of inclusion of higher-order interactions in the {\it XY} model on critical properties is studied by Monte Carlo simulations. It is found that an increasing number of the higher-order terms in the Hamiltonian modifies the shape…
The error threshold transition in a stochastic (i.e. finite population) version of the quasispecies model of molecular evolution is studied using finite-size scaling. For the single-sharp-peak replication landscape, the deterministic model…
One-dimensional model of a system where first-order phase transition occurs is examined in the present paper. It is shown that basic properties of the phenomenon, such as a well defined temperature of transition, are caused both by…
This work reports deep-learning-unique first-order and second-order phase transitions, whose phenomenology closely follows that in statistical physics. In particular, we prove that the competition between prediction error and model…
Several pathogens use evolvability as a survival strategy against acquired immunity of the host. Despite their high variability in time, some of them exhibit quite low variability within the population at any given time, a somehow…
The scaling theory of critical phenomena has been successfully extended for classical first order transitions even though the correlation length does not diverge in these transitions. In this paper we apply the scaling ideas to quantum…
Recombination is introduced into Eigen's theory of quasispecies evolution. Comparing numerical simulations of the rate equations in the non-recombining and recombining cases show that recombination has a strong effect on the error threshold…
This paper extends Eigen's quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness…
In this conference proceeding, I discuss in detail the deconfinement to quark matter that takes place at large densities and/or temperatures. The first-order phase transition that is assumed to appear beyond a critical point gives rise to…
We study the impact of quantum and thermal fluctuations on properties of quantum phase transitions occurring in systems of itinerant fermions with main focus on the order of these transitions. Our approach is based on a set of flow…
A quasispecies is a set of interrelated genotypes that have reached a situation of equilibrium while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…