Related papers: Optimal size for emergence of self-replicating pol…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
In many real life applications, a continuous culture bioreactor may cease to function properly due to bioclogging which is typically caused by the microbial overgrowth. This is a problem that has been largely overlooked in the chemostat…
Research on the birth and evolution of life are reviewed with reference to the maximum entropy production principle (MEPP). It has been shown that this principle is essential for consistent understanding of the birth and evolution of life.…
The fuel-driven process of replication in living systems generates distributions of copied entities with varying degrees of copying accuracy. Here we introduce a thermodynamically consistent ensemble for investigating universal population…
The investigation of optimal processes has a long history in the field of thermodynamics. It is well known that finite-time processes that minimize dissipation often exhibit discontinuities. We use a combination of numerical and analytical…
Vibrating systems can respond to an infinite number of initial conditions and the overall dynamics of the system can be strongly affected by them. Therefore, it is of practical importance to have methods by which we can determine the…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
Implicit in the RNA world hypothesis is that prebiotic RNA synthesis, despite occurring in an environment without biochemical catalysts, produced the long RNA polymers which are essential to the formation of life. In order to investigate…
We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…
A dynamical system entrains to a periodic input if its state converges globally to an attractor with the same period. In particular, for a constant input the state converges to a unique equilibrium point for any initial condition. We…
The new method of the mean-field approximation is extended. An approach which enables to estimate some parameters of the transition from the isotropic state of hard sticks to the nematic ordering phase is suggested. An technique of the…
We argue that one can associate a pseudo-time with sequences of configurations generated in the course of classical Monte Carlo simulations for a single-minimum bound state, if the sampling is optimal. Hereby the sampling rates can be,…
Directed transport is a characteristic feature of numerous biological systems in response to signals such as nutrient and chemical gradients. These signals often depend on time owing to the high complexity of interactions in these systems.…
We solve numerically a kinetic model of chiral polymerization in systems closed to matter and energy flow, paying special emphasis to its ability to amplify the small initial enantiomeric excesses due to the internal and unavoidable…
We study time evolution of a subsystem's density matrix under unitary evolution, generated by a sufficiently complex, say quantum chaotic, Hamiltonian, modeled by a random matrix. We exactly calculate all coherences, purity and…
The observed single-handedness of biological amino acids and sugars has long been attributed to autocatalysis. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross inhibition of the two chiral…