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The Markov chain Monte Carlo method is a versatile tool in statistical physics to evaluate multi-dimensional integrals numerically. For the method to work effectively, we must consider the following key issues: the choice of ensemble, the…
We investigate the catalytic reactions model used in cell modeling. The reaction kinetic is defined through the energies of different species of molecules following random independent distribution. The related statistical physics model has…
A new acceleration algorithm to address the problem of multiple time scales in variational Monte Carlo simulations is presented. After a first attempted move has been rejected, the delayed rejection algorithm attempts a second move with a…
It is well known that the consensus problem cannot be solved deterministically in an asynchronous environment, but that randomized solutions are possible. We propose a new model, called noisy scheduling, in which an adversarial schedule is…
We show that strategy independent adaptations of random interaction networks can induce powerful mechanisms, ranging from the Red Queen to group selection, that promote cooperation in evolutionary social dilemmas. These two mechanisms…
In quantum game theory, one of the most intriguing and important questions is, "Is it possible to get quantum advantages without any modification of the classical game?" The answer to this question so far has largely been negative. So far,…
Within systems biology there is an increasing interest in the stochastic behavior of genetic and biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous…
We consider a deterministic game with alternate moves and complete information, of which the issue is always the victory of one of the two opponents. We assume that this game is the realization of a random model enjoying some independence…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
We propose a Constraint Molecular Dynamics model for Fermionic system. In this approach the equations of motion of wave packets for the nuclear many-body problem are solved by imposing that the one-body occupation probability…
Many biological and artificial transport channels function without direct input of metabolic energy during a transport event and without structural rearrangements involving transitions from a 'closed' to an 'open' state. Nevertheless, such…
The Iterated Prisoner's Dilemma has guided research on social dilemmas for decades. However, it distinguishes between only two atomic actions: cooperate and defect. In real-world prisoner's dilemmas, these choices are temporally extended…
In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a…
Splitting probabilities quantify the likelihood of a given outcome out of competitive events. This key observable of random walk theory, historically introduced as the gambler's ruin problem, is well understood for memoryless (Markovian)…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however,…
Reaction rates of chemical reactions under nonequilibrium conditions can be determined through the construction of the normally hyperbolic invariant manifold (NHIM) [and moving dividing surface (DS)] associated with the transition state…
The active-space quantum chemical methods could provide very accurate description of strongly correlated electronic systems, which is of tremendous value for natural sciences. The proper choice of the active space is crucial, but a…