Related papers: Tracking Cluster Continuity and Dynamics in Time-S…
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…
We present molecular dynamics (MD) simulations results for dense fluids of ultrasoft, fully-penetrable particles. These are a binary mixture and a polydisperse system of particles interacting via the generalized exponential model, which is…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
We describe a novel method of tracking the rotational motion of clusters of colloidal particles. Our method utilizes rigid body transfor- mations to determine the rotations of a cluster and extends conventional proven particle tracking…
In this article, a novel cluster analysis algorithm was employed in the study of polymer coil to globule transition via single chain Monte Carlo simulations. The algorithm, which has been recently applied in Molecular Dynamics simulations…
We propose a new method for clustering multivariate time-series data based on Dynamic Linear Models. Whereas usual time-series clustering methods obtain static membership parameters, our proposal allows each time-series to dynamically…
We present a novel probabilistic clustering model for objects that are represented via pairwise distances and observed at different time points. The proposed method utilizes the information given by adjacent time points to find the…
We examine entanglements using monomer contacts between pairs of chains in a Brownian-dynamics simulation of a polymer melt. A map of contact positions with respect to the contacting monomer numbers (i,j) shows clustering in small regions…
Granular simulations are used to probe the particle scale dynamics at short, intermediate, and long time scales for gravity driven, dense granular flows down an inclined plane. On approach to the angle of repose, where motion ceases, the…
Numerical simulations of clusters of galaxies provide a unique way to follow the dynamics of these systems. The models reveal many characteristics of the merging process of subclusters: shock structure and strength, temperature distribution…
Using molecular dynamics simulation, we investigate the slow dynamics of a supercooled binary mixture of soft particles interacting with a generalized Hertzian potential. At low density, it displays typical slow dynamics near its glass…
Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures. These, however, by virtue of aggregation, hide structural…
This paper proposes an early detection method for cluster structural changes. Cluster structure refers to discrete structural characteristics, such as the number of clusters, when data are represented using finite mixture models, such as…
A theoretical and numerically study of dynamical properties in the sol-gel transition is presented. In particular, the complex phenomenology observed experimentally and numerically in gelling systems is reproduced in the framework of…
The spatial correlations of entangled polymer dynamics are examined by molecular dynamics simulations and neutron spin-echo spectroscopy. Due to the soft nature of topological constraints, the initial spatial decays of intermediate…
We present an efficient method to perform overdamped Brownian dynamics simulations in external force fields and for particle interactions that include a hardcore part. The method applies to particle motion in one dimension, where it is…
Spatial self-similarity is a hallmark of critical phenomena. We investigate the dynamic process of percolation, in which bonds are incrementally inserted to an empty lattice until fully occupied, and track the gaps describing the changes in…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
We present a new algorithm for clustering longitudinal data. Data of this type can be conceptualized as consisting of individuals and, for each such individual, observations of a time-dependent variable made at various times. Generically,…
Globular clusters are stellar dynamical systems which evolve on stellar evolutionary and both internal and external dynamical timescales. Quantitative comparison of cluster properties with realistic evolutionary dynamical models is becoming…