Related papers: Simulating flexible polymers in a potential of ran…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
We determine the critical layer thickness for the appearance of misfit dislocations as a function of the misfit between the lattice constants of the substrate and the adsorbate from Kinetic Monte Carlo (KMC) simulations of heteroepitaxial…
We present approximate algorithms for performing smoothing in a class of high-dimensional state-space models via sequential Monte Carlo methods ("particle filters"). In high dimensions, a prohibitively large number of Monte Carlo samples…
We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also…
Robust clustering of high-dimensional data is an important topic because clusters in real datasets are often heavy-tailed and/or asymmetric. Traditional approaches to model-based clustering often fail for high dimensional data, e.g., due to…
Monte Carlo simulations have been performed to analyze the sub-diffusion dynamics of a tagged monomer in self-avoiding polymerized membranes in the flat phase. By decomposing the mean square displacement into the out-of-plane ($\parallel$)…
We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by external fields. The insertion free energy of a single colloid into the polymer layer is qualitatively different for surfaces with an ordered…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…
In this paper I describe the computer simulations that I have performed to critically examine the Lauritzen-Hoffman and the Sadler-Gilmer theories of polymer crystallization. In particular, I have computed the free energy profile for…
We introduce an algorithm based on Generalized Dual Method (GDM) to efficiently study the dynamics of a particle in quasiperiodic environments without the need to use periodic approximations or to save the information of the vertices that…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
We use numerical simulations to study the dynamics of dense assemblies of self-propelled particles in the limit of extremely large, but finite, persistence times. In this limit, the system evolves intermittently between mechanical…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
A mixture of hard squares, dimers and vacancies on a square lattice is known to undergo a transition from a low-density disordered phase to high-density columnar ordered phase. Along the fully packed square-dimer line, the system undergoes…
We describe a general strategy, PERM (Pruned-Enriched Rosenbluth Method), for sampling configurations from a given Gibbs-Boltzmann distribution. The method is not based on the Metropolis concept of establishing a Markov process whose…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
We propose and compare different strategies to construct dynamic density functional theories (DDFTs) for inhomogeneous polymer systems close to equilibrium from microscopic simulation trajectories. We focus on the systematic construction of…
We create mechanically stable (MS) packings of bidisperse disks using an algorithm in which we successively grow or shrink soft repulsive disks followed by energy minimization until the overlaps are vanishingly small. We focus on small…
In this study we present a Microcanonical Monte Carlo investigation of one dimensional self-gravitating toy models. We study the effect of hard-core potentials and compare to those results obtained with softening parameters and also the…
In this paper, we perform molecular dynamics (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from $1.0 \, \mu m$ to $7.0 \, \mu m$. The system was allowed to…