Related papers: Stochastic Lag Time in Nucleated Linear Self-Assem…

In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…

Autonomous oscillations in biological systems may have a biochemical origin or result from an interplay between force-generating and visco-elastic elements. In molecular motor assemblies the force-generating elements are molecular engines…

Many unicellular organisms allocate their key proteins asymmetrically between the mother and daughter cells, especially in a stressed environment. A recent theoretical model is able to predict when the asymmetry in segregation of key…

Inspired by motile cells in tissue formation, we find that active systems of self-aligning adhesive particles undergo ballistic aggregation through a flocking transition. This kinetic regime emerges when the cluster persistence length grows…

Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…

We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler,…

The effectiveness of stochastic algorithms based on Monte Carlo dynamics in solving hard optimization problems is mostly unknown. Beyond the basic statement that at a dynamical phase transition the ergodicity breaks and a Monte Carlo…

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…

Discrepancies play an important role in the study of uniformity properties of point sets. Their probability distributions are a help in the analysis of the efficiency of the Quasi Monte Carlo method of numerical integration, which uses…

We investigate the work fluctuations in an overdamped non-equilibrium process that is stopped at a stochastic time. The latter is characterized by a first passage event that marks the completion of the non-equilibrium process. In…

In order to study linker-mediated aggregation of colloidal particles with limited valence, we combine kinetic Monte Carlo simulations and an approximate theory based on the Smoluchowski equations. We found that aggregation depends strongly…

We overview a series of recent works devoted to variance reduction techniques for numerical stochastic homogenization. Numerical homogenization requires solving a set of problems at the micro scale, the so-called corrector problems. In a…

In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub - steps…

A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness…

Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize…

In stochastic processes with absorbing states, the quasi-stationary distribution provides valuable insights into the long-term behaviour prior to absorption. In this work, we revisit two well-established numerical methods for its…

Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…

The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…

Ladder polymers, known for their rigid, ladder-like structures, exhibit exceptional thermal stability and mechanical strength, positioning them as candidates for advanced applications. However, accurately determining their structure from…