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A Brownian particle moving in a staircase-like potential with feedback control offers a way to implement Maxwell's demon. An experimental demonstration of such a system using sinusoidal periodic potential carried out by Toyabe et al. has…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
In physics we often use very simple models to describe systems with many degrees of freedom, but it is not clear why or how this success can be transferred to the more complex biological context. We consider models for the joint…
Experiments have found that diffusion in metabolically active cells is much faster than in dormant cells, especially for large particles. However, the mechanism of this size-dependent diffusion enhancement in living cells is still unclear.…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
This paper reviews the basic ideas behind a Bayesian unfolding published some years ago and improves their implementation. In particular, uncertainties are now treated at all levels by probability density functions and their propagation is…
Parameter estimation for discretely observed Markov processes is a challenging problem. However, simulation of Markov processes is straightforward using the Gillespie algorithm. We exploit this ease of simulation to develop an effective…
We review briefly the concept of colloidal dispersions, their general properties and some of their most important applications, as well as the basic molecular interactions that give rise to their properties in equilibrium. Similarly, we…
We experimentally investigate the distribution of the non-equilibrium work done by an external force on a mesoscopic system with many coupled degrees of freedom: a colloidal monolayer mechanically driven across a periodic light field. Since…
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of…
We characterise the steady states of a suspension of two-dimensional active brownian particles (ABPs). We calculate the steady-state probability distribution to lowest order in Peclet number. We show that macroscopic quantities can be…
Aim of this note is to analyse branching Brownian motion within the class of models introduced in the recent paper [4] and called chemical diffusion master equations. These models provide a description for the probabilistic evolution of…
We propose an approach to compute the boundary crossing probabilities for a class of diffusion processes which can be expressed as piecewise monotone (not necessarily one-to-one) functionals of a standard Brownian motion. This class…
We propose a bilinear sampling algorithm in Green's function Monte Carlo for expectation values of operators that do not commute with the Hamiltonian and for differences between eigenvalues of different Hamiltonians. The integral…
The unfolding of detector effects is a key aspect of comparing experimental data with theoretical predictions. In recent years, different Machine-Learning methods have been developed to provide novel features, e.g. high dimensionality or a…
We construct a theoretical model for equilibrium distribution of workers across sectors with different labor productivity, assuming that a sector can accommodate a limited number of workers which depends only on its productivity. A general…
The main objective of this paper consists in creating a new class of copulae from various joint distributions occurring in connection with certain Brownian motion processes. We focus our attention on the distributions of univariate Brownian…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
The correspondence between the telegraph random process and transport within a binary stochastic Markovian mixture is established. This equivalence is used to derive the distribution function for the transit length, defined as the distance…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…