Related papers: Stochastic Lag Time in Nucleated Linear Self-Assem…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
We study the feature-scaled version of the Monte Carlo algorithm with linear function approximation. This algorithm converges to a scale-invariant solution, which is not unduly affected by states having feature vectors with large norms. The…
In this paper we investigate how the complexity of chaotic phase spaces affect the efficiency of importance sampling Monte Carlo simulations. We focus on a flat-histogram simulation of the distribution of finite-time Lyapunov exponent in a…
Nobel metals that are deposited on a polymer surface exhibit surface diffusion and diffusion into the bulk. At the same time the metal atoms tend to form clusters because their cohesive energy is about two orders of magnitude higher than…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
Large deviations for additive path functionals of stochastic dynamics and related numerical approaches have attracted significant recent research interest. We focus on the question of convergence properties for cloning algorithms in…
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed…
In contrast to extensively studied defects in traditional materials, we report here for the first time a systematic investigation of the formation mechanism of intrinsic defects in self-assembled peptide nanostructures. The Monte Carlo…
Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…
The self-assembly of anisotropic building blocks into complex spatial architectures is an important design strategy in material science but the mechanisms by which the anisotropic interactions influence the early-stage growth and formation…
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
The step-growth polymerisation of a mixture of arbitrary-functional monomers is viewed as a time-continuos random graph process with degree bounds that are not necessarily the same for different vertices. The sequence of degree bounds acts…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
We study the behavior of an assembly of $N$ granular particles contained in two compartments within a simple kinetic approach. The particles belonging to each compartment collide inelastically with each other and are driven by a stochastic…
Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization. At equilibrium, the structure is encoded through specific interactions,…
Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal…
We study the depletion-induced self-assembly of indented colloids. Using state-of-the-art Monte Carlo simulation techniques that treat the depletant particles explicitly, we demonstrate that colloids assemble by a lock-and-key mechanism,…
Atomistic simulations provide valuable insights into the physical processes governing material behavior. However, their applicability is fundamentally constrained by the limited time scales accessible to brute-force simulations. This…