Related papers: Automated analysis of continuum fields from atomis…

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…

Correlated random fields are a common way to model dependence struc- tures in high-dimensional data, especially for data collected in imaging. One important parameter characterizing the degree of dependence is the asymp- totic variance…

We discuss how simulations of mechanical properties of materials require descriptions at many different length scales --- from the nanoscale where an atomic description is appropriate, through a mesoscale where dislocation based…

Recently it has been reported that biased range-measurements among neighboring agents in the gradient distance-based formation control can lead to predictable collective motion. In this paper we take advantage of this effect and by…

The kinetics of dislocations is studied with computer simulation at loadings of different intensity. It is established that the dislocations have a few different structural states. The dislocations "with the micropore" play important role…

Employing a recently developed method that is numerically accurate within a model space simulating the real-time dynamics of few-body systems interacting with macroscopic environmental quantum fields, we analyze the full dynamics of an…

Atomistic deformation simulations in the nominally elastic regime are performed for a model binary glass with strain rates as low as $10^{4}$/sec (corresponding to 0.01 shear strain per 1$\mu$sec). A robust elasticity is revealed that…

Graphical models are a key class of probabilistic models for studying the conditional independence structure of a set of random variables. Circular variables are special variables, characterized by periodicity, arising in several contexts…

Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…

Accurate knowledge of the atomistic transition pathways in materials and material surfaces is crucial for many material science problems. However, conventional simulation techniques used to find these transitions are extremely…

We propose an approach for exploiting machine learning to approximate electronic fields in crystalline solids subjected to deformation. Strain engineering is emerging as a widely used method for tuning the properties of materials, and this…

The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…

Many engineering systems are subject to spatially distributed uncertainty, i.e. uncertainty that can be modeled as a random field. Altering the mean or covariance of this uncertainty will in general change the statistical distribution of…

We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…

In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the problem into different…

Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex…

Molecular dynamics simulations were used to quantify mechanically-induced structural evolution in nanocrystalline Al with an average grain size of 5 nm. A polycrystalline sample was cyclically strained at different temperatures, while a…

Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…

We present a statistical framework to compare spectral-line data cubes of molecular clouds and use the framework to perform an analysis of various statistical tools developed from methods proposed in the literature. We test whether our…

Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…