Related papers: GMXPolymer: a generated polymerization algorithm b…
The recently proposed generalized epidemic modeling framework (GEMF) \cite{sahneh2013generalized} lays the groundwork for systematically constructing a broad spectrum of stochastic spreading processes over complex networks. This article…
From understanding the sand on the beach to the foam on your beer, soft sphere simulations have been crucial to the study of the amorphous world around us. However, many of the materials we interact with on a daily basis aren't comprised of…
Graph Neural Networks (GNNs) have achieved strong results in molecular property prediction, but polymers present distinct challenges: labeled datasets are scarce and small (typically in the order of hundreds of polymers) due to the need for…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
We developed an interface program between a program suite for an automated search of chemical reaction pathways, GRRM, and a program package of semiempirical methods, MOPAC. A two-step structural search is proposed as an application of this…
The Generalized Linear Model (GLM) for the Gamma distribution (glmGamma) is widely used in modeling continuous, non-negative and positive-skewed data, such as insurance claims and survival data. However, model selection for GLM depends on…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Determining atomistic structures from characterization data is one of the most common yet intricate problems in materials science. Particularly in amorphous materials, proposing structures that balance realism and agreement with experiments…
This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…
The mathematical software system polymake provides a wide range of functions for convex polytopes, simplicial complexes, and other objects. A large part of this paper is dedicated to a tutorial which exemplifies the usage. Later sections…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our…
Polymers, composed of repeating structural units called monomers, are fundamental materials in daily life and industry. Accurate property prediction for polymers is essential for their design, development, and application. However, existing…
Magnetizations are introduced to the Generalized Random Energy Model (GREM) and numerical simulations on ac susceptibility is made for direct comparison with experiments in glassy materials. Prominent dynamical natures of spin glasses, {\it…
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for…
We simulate a series of model polymer composites, composed of linear polymer strands and spherical, monodisperse filler particles (FP). These molecular dynamics simulations implement a coarse-grained, bead-spring force field and we vary…
The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with…
The gradient scheme framework is based on a small number of properties and encompasses a large number of numerical methods for diffusion models. We recall these properties and develop some new generic tools associated with the gradient…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
The task of atom rearrangement has emerged in the last decade as a fundamental building block for the development of neutral atom-based quantum processors. However, despite many recent efforts to develop algorithms with favorable asymptotic…