Related papers: A protrusion can "eclipse" looping of a long self-…
We define a new variant of exclusion processes in discrete time that has jump probabilities that depend on the last jump performed. In a particular limit for the jump probabilities and in suitable scaling limits for space and time, we…
This paper discusses the elastic behavior of a single polyelectrolyte chain. A simple scaling analysis as in self avoiding walk chains are not possible, because three interplaying relevant length scales are involved, i.e., the Debye…
Likelihood-free methods, such as approximate Bayesian computation, are powerful tools for practical inference problems with intractable likelihood functions. Markov chain Monte Carlo and sequential Monte Carlo variants of approximate…
Dynamic Programming (DP) suffers from the well-known ``curse of dimensionality'', further exacerbated by the need to compute expectations over process noise in stochastic models. This paper presents a Monte Carlo-based sampling approach for…
We study the distribution of the area and perimeter of the convex hull of the "true" self-avoiding random walk in a plane. Using a Markov chain Monte Carlo sampling method, we obtain the distributions also in their far tails, down to…
We revisit the so-called sampling and discarding approach used to quantify the probability of constraint violation of a solution to convex scenario programs when some of the original samples are allowed to be discarded. Motivated by two…
We consider nearest neighbour spatial random permutations on $\mathbb{Z}^d$. In this case, the energy of the system is proportional the sum of all cycle lengths, and the system can be interpreted as an ensemble of edge-weighted, mutually…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
In this paper we investigate the problem of a long self-avoiding polymer chain immersed in a random medium. We find that in the limit of a very long chain and when the self-avoiding interaction is weak, the conformation of the chain…
We develop a biased Monte Carlo algorithm to measure probabilities of rare events in cluster-cluster aggregation for arbitrary collision kernels. Given a trajectory with a fixed number of collisions, the algorithm modifies both the waiting…
An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates "almost surely". Proving that can be hard, and this paper presents a new method for doing so; it…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Approximating the stationary probability of a state in a Markov chain through Markov chain Monte Carlo techniques is, in general, inefficient. Standard random walk approaches require $\tilde{O}(\tau/\pi(v))$ operations to approximate the…
We consider local Markov chain Monte-Carlo algorithms for sampling from the weighted distribution of independent sets with activity $\l$, where the weight of an independent set $I$ is $\l^{|I|}$. A recent result has established that Gibbs…
We discuss non-reversible Markov-chain Monte Carlo algorithms that, for particle systems, rigorously sample the positional Boltzmann distribution and that have faster than physical dynamics. These algorithms all feature a non-thermal…
We discuss the probability of random knotting for a model of self-avoiding polygons whose segments are given by cylinders of unit length with radius $r$. We show numerically that the characteristic length of random knotting is roughly…
Using Monte-Carlo simulations, we determine the scaling form for the probability distribution of the shortest path, $\ell$, between two lines in a 3-dimensional percolation system at criticality; the two lines can have arbitrary positions,…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…