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Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
The paper develops methods to construct a one-stage optimal design of dilution experiments under the total available volume constraint typical for bio-medical applications. We consider various design criteria based on the Fisher information…
We investigate, using numerical simulations, the conformations of isolated active ring polymers. We find that the their behaviour depends crucially on their size: short rings ($N \lesssim$ 100) are swelled whereas longer rings ($N \gtrsim$…
We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an…
By molecular dynamics simulations and free energy calculations based on Monte Carlo method, the detailed balance between Pt cluster isomers was investigated. For clusters of n<=50, stationary equilibrium is achieved in 100 ns in the…
We consider the problem of undirected polymers (tied at the endpoints) in random environment, also known as the unoriented first passage percolation on the hypercube, in the limit of large dimensions. By means of the multiscale refinement…
A system formed by a crowded environment of catalytic obstacles and complex oscillatory chemical reactions is inquired. The obstacles are static spheres of equal radius, which are placed in a random way. The chemical reactions are carried…
Chemical, physical and ecological systems passing through a saddle-node bifurcation will, momentarily, find themselves balanced at a semi-stable steady state. If perturbed by noise, such systems will escape from the zero-steady state, with…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
We study an optimal stopping problem under non-exponential discounting, where the state process is a multi-dimensional continuous strong Markov process. The discount function is taken to be log sub-additive, capturing decreasing impatience…
Entropy production in stochastic mechanical systems is examined here with strict bounds on its rate. Stochastic mechanical systems include pure diffusions in Euclidean space or on Lie groups, as well as systems evolving on phase space for…
During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures…
When working with quantum states, analysis of the final quantum state generated through probabilistic measurements is essential. This analysis is typically conducted by constructing the density matrix from either partial or full tomography…
We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
We study an energy relaxation process after many degrees of freedom are excited in a Hamiltonian system with a large number of degrees of freedom. Bottlenecks of relaxation, where relaxations of the excited elements are drastically slowed…
In this paper we consider the coalescence dynamics of a tagged particle moving in a random distribution of particles with volumes independently distributed according to a probability distribution (CTP model). We provide a rigorous…
In quantum statistical mechanics, it is of fundamental interest to understand how close the bipartite entanglement entropy of eigenstates of quantum chaotic Hamiltonians is to maximal. For random pure states in the Hilbert space, the…
For continuous-space diffusion processes, there is a strong connection between conservative forces and entropy production. For a given time evolution of the system's state, the entropy production is minimized when the system is driven by a…
We analyze a macroscopic model with a maximal density constraint which describes short range repulsion in biological systems. This system aims at modeling finite-size particles which cannot overlap and repel each other when they are too…