Related papers: Optimal size for emergence of self-replicating pol…
Emergence, optimization and stability of a motor-like motion in a fluctuating environment are analyzed. The emergence of motion is shown to be a general phenomenon. A motor converges to the state with the minimum of effective temperature…
Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise…
We study an autocatalytic system consisting of several interacting chemical species. We observe a strong dependence of the concentrations of the chemicals on the size of the system. This dependence is caused by the discrete nature of the…
Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates.…
We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X, X+X -> A+X, X -> B provided that the distribution of reacting particles in the system volume is uniform, i.e. the point model of reaction…
In this paper, we consider the stochastic optimal control problem for the interacting particle system. We obtain the stochastic maximum principle of the optimal control system by introducing a generalized backward stochastic differential…
This work is devoted to the investigation of the most probable transition time between metastable states for stochastic dynamical systems. Such a system is modeled by a stochastic differential equation with non-vanishing Brownian noise, and…
In this paper a stochastic reaction diffusion system is considered, which models the spread of a finite population reacting with a non-renewable resource in the presence of individual based noise. A two-parameter phase diagram is…
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Large and complex molecules are building blocks for life. We compute probabilities for their formation from an average non-equilibrium model. As the distance from thermodynamic equilibrium is increased in this model, so too are the chances…
This paper describes a 2D particle system in which autopoietic vesicles that are able to grow, repair, and reproduce can emerge from an initial random distribution of individual components. The reproduction process also exhibits inheritance…
We study reversible polymerization of rings. In this stochastic process, two monomers bond and as a consequence, two disjoint rings may merge into a compound ring, or, a single ring may split into two fragment rings. This…
A system of impulsive differential equations with state-dependent impulses is used to model the growth of a single population on two limiting essential resources in a self-cycling fermentor. Potential applications include water purification…
We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law…
A binary fluid mixture in contact with lateral particle reservoirs is considered. By imposing different particle concentrations in these reservoirs, the system can be maintained under controlled non-equilibrium conditions. Previous…
Recent numerical work by Bardarson et. al. [Phys. Rev. Lett. 109, 017202 (2012)] revealed a slow, logarithmic in time, growth of entanglement entropy for initial product states in a putative many-body localized phase. We show that this…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
We study minimal time strategies for the treatment of pollution of large volumes, such as lakes or natural reservoirs, with the help of an autonomous bioreactor. The control consists in feeding the bioreactor from the resource, the clean…