Related papers: An introduction to stochastic self-assembly: theor…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
We introduce a sequential model for the deposition and aggregation of particles in the submonolayer regime. Once a particle has been randomly deposited on the substrate, it sticks to the closest atom or island within a distance \ell,…
In this tutorial, three examples of stochastic systems are considered: A strongly-damped oscillator, a weakly-damped oscillator and an undamped oscillator (integrator) driven by noise. The evolution of these systems is characterized by the…
A kinetic Ising model is analyzed where spin variables correspond to lattice cells with mobile or immobile particles. Introducing additional restrictions for the flip processes according to the n-spin facilitated kinetic Ising model and…
In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational…
We review the recent literature on the simulation of the structure and deformation of amorphous glasses, including oxide and metallic glasses. We consider simulations at different length and time scales. At the nanometer scale, we review…
Time-dependent correlation functions of (unstable) particles undergoing biased or unbiased diffusion, coagulation and annihilation are calculated. This is achieved by similarity transformations between different stochastic models and…
We study scaling properties of stochastic aggregation processes in one dimension. Numerical simulations for both diffusive and ballistic transport show that the mass distribution is characterized by two independent nontrivial exponents…
This paper is about partitioning in parallel and distributed simulation. That means decomposing the simulation model into a numberof components and to properly allocate them on the execution units. An adaptive solution based on…
Stochastic Spatio-Temporal processes are prevalent across domains ranging from modeling of plasma to the turbulence in fluids to the wave function of quantum systems. This letter studies a measure-theoretic description of such systems by…
We investigate a suggested path to self-organized criticality. Originally, this path was devised to "generate criticality" in systems displaying an absorbing-state phase transition, but closer examination of the mechanism reveals that it…
Models of active nematics in biological systems normally require complexity arising from the hydrodynamics involved at the microscopic level as well as the viscoelastic nature of the system. Here we show that a minimal, space-independent,…
The random current representation of the Ising model, along with a related path expansion, has been a source of insight on the stochastic geometric underpinning of the ferromagnetic model's phase structure and critical behavior in different…
Macroscopic dynamical descriptions of complex physical systems are crucial for understanding and controlling material behavior. With the growing availability of data and compute, machine learning has become a promising alternative to…
We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using…
Machine learning has become a central technique for modeling in science and engineering, either complementing or as surrogates to physics-based models. Significant efforts have recently been devoted to models capable of predicting field…
In this paper we will investigate dynamic stability of percolation for the stochastic Ising model and the contact process. We also introduce the notion of downward and upward $\epsilon$-movability which will be a key tool for our analysis.
A spatial stochastic model is developed which describes the 3D nanomorphology of composite materials, being blends of two different (organic and inorganic) solid phases. Such materials are used, for example, in photoactive layers of hybrid…
We present a brief review on the Impulse Approximation method to study processes of scattering off composite particles. We first construct the model in a non-relativistic fashion that enables us to extend the model to a covariant Impulse…
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…