Related papers: Simulating structural transitions by direct transi…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Using state-of-the-art rare-event sampling simulations, we precisely characterize the nucleation of liquid droplets from a supersaturated Lennard-Jones gas and uncover a key physical feature: critical clusters nucleate with a density that…
The most interesting step of condensation is the cluster formation up to the critical size. In a closed system, this is an instationary process, as the vapour is depleted by the emerging liquid phase. This imposes a limitation on direct…
Pressure-induced phase transitions of spin-crossover materials were simulated by a Monte Carlo simulation in the constant pressure ensemble for the first time. Here, as the origin of the cooperative interaction, we adopt elastic interaction…
A Monte Carlo method to sample the classical configurational canonical ensemble is introduced. In contrast to the Metropolis algorithm, where trial moves can be rejected, in this approach collisions take place. The implementation is…
We study sums of directed paths on a hierarchical lattice where each bond has either a positive or negative sign with a probability $p$. Such path sums $J$ have been used to model interference effects by hopping electrons in the strongly…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
We demonstrate the feasibility of performing sufficient configurational sampling of disordered oxides directly from first principles without resorting to the use of fitted models such as cluster expansion. This is achieved by harnessing the…
This Perspective describes current computational efforts in the field of simulating photodynamics of transition metal complexes. We present the typical workflows and feature the strengths and limitations of the different contemporary…
We study approximations of evolving probability measures by an interacting particle system. The particle system dynamics is a combination of independent Markov chain moves and importance sampling/resampling steps. Under global regularity…
We investigate the self-assembly (crystallisation) of particles with hard cores and isotropic, square-well interactions, using a Monte Carlo scheme to simulate overdamped Langevin dynamics. We measure correlation and response functions…
Diffusion is often accompanied by a reaction or sorption which can induce temperature inhomogeneities. Monte Carlo simulations of Lennard-Jones atoms in zeolite NaCaA are reported with a hot zone presumed to be created by a reaction. Our…
Rare events are ubiquitous in many different fields, yet they are notoriously difficult to simulate because few, if any, events are observed in a conventiona l simulation run. Over the past several decades, specialised simulation methods…
The procedures of validating simulation of particle physics events at the LHC are summarized. Because of the strongly fluctuating particle content of LHC events and detector interactions, particle based Monte Carlo methods are an…
Monte Carlo computer simulations of a quasi two dimensional (2D) dipolar fluid at low and intermediate densities indicate that the structure of the fluid is well described by an ideal mixture of self-assembling clusters. A detailed analysis…
Stellar evolution is driven by the changing composition of a star from nuclear reactions. At the late stages of evolution and during explosive events, the timescale can be short and drive strong hydrodynamic flows, making simulations of…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
Recently-proposed particle MCMC methods provide a flexible way of performing Bayesian inference for parameters governing stochastic kinetic models defined as Markov (jump) processes (MJPs). Each iteration of the scheme requires an estimate…
A spherical model of skeleton with junctions is investigated by Monte Carlo simulations. The model is governed by one-dimensional bending energy. The results indicate that the model undergoes a first-order transition separating the smooth…