Related papers: Work distribution in manipulated single biomolecul…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
Population Monte Carlo has been introduced as a sequential importance sampling technique to overcome poor fit of the importance function. In this paper, we compare the performances of the original Population Monte Carlo algorithm with a…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
We study proliferation of an action in binary action network coordination games that are generalized to include global effects. This captures important aspects of proliferation of a particular action or narrative in online social networks,…
We compute the distribution of the work done in stretching a Gaussian polymer, made of N monomers, at a finite rate. For a one-dimensional polymer undergoing Rouse dynamics, the work distribution is a Gaussian and we explicitly compute the…
The interplay between Coulomb friction and random excitations is studied experimentally by means of a rotating probe in contact with a stationary granular gas. The granular material is independently fluidized by a vertical shaker, acting as…
We propose a macroscopic realization of planar Brownian motion by vertically vibrated disks. We perform a systematic statistical analysis of many random trajectories of individual disks. The distribution of increments is shown to be almost…
Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here we consider the…
During the morphogenesis of tissues and tumors, cells often interact with neighbors with different mechanical properties, but the understanding of its role is lacking. We use active Brownian Dynamics simulations to study a model co-culture…
Dynamic density functionals (DDFs) are popular tools for studying the dynamical evolution of inhomogeneous polymer systems. Here, we present a systematic evaluation of a set of diffusive DDF theories by comparing their predictions with data…
Bubble-nucleation processes of a Lennard-Jones liquid are studied by molecular dynamics simulations. Waiting time, which is the lifetime of a superheated liquid, is determined for several system sizes, and the apparent finite-size effect of…
Multitype branching processes (MTBP) model branching structures, where the nodes of the resulting tree are objects of different types. One field of application of such models in biology is in studies of cell proliferation. A sampling scheme…
A study of time homogeneous, real valued Markov processes with a special property and a non-atomic initial distribution is provided. The new notion of a function of evolution of distribution which determines the dependency between one…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in…
Computing systems interacting with real-world processes must safely and reliably process uncertain data. The Monte Carlo method is a popular approach for computing with such uncertain values. This article introduces a framework for…
The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and…
We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known.…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
In the idealized Morgan model of crossover, we study the probability distributions of shared DNA (identical by descent) between individuals having a wide range of relationships (not just lineal descendants), especially cases for which…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…