Related papers: Tracking Cluster Continuity and Dynamics in Time-S…
The last decades have not only been characterized by an explosive growth of data, but also an increasing appreciation of data as a valuable resource. Their value comes with the ability to extract meaningful patterns that are of economic,…
Spatial-temporal data, that is information about objects that exist at a particular location and time period, are rich in value and, as a consequence, the target of so many initiative efforts. Clustering approaches aim at grouping…
We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the…
Critical phase transitions have proven to be a powerful concept to capture the phenomenology of many systems, including deeply non-equilibrium ones like living systems. The study of these phase transitions has overwhelmingly relied on…
In several environmental applications data are functions of time, essentially con- tinuous, observed and recorded discretely, and spatially correlated. Most of the methods for analyzing such data are extensions of spatial statistical tools…
Spatiotemporal data is increasingly available due to emerging sensor and data acquisition technologies that track moving objects. Spatiotemporal clustering addresses the need to efficiently discover patterns and trends in moving object…
Temporal data, obtained in the setting where it is only possible to observe one time point per experiment, is widely used in different research fields, yet remains insufficiently addressed from the statistical point of view. Such data often…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
A given set of data-points in some feature space may be associated with a Schrodinger equation whose potential is determined by the data. This is known to lead to good clustering solutions. Here we extend this approach into a full-fledged…
We here discuss the results of 3d MonteCarlo simulations of a minimal lattice model for gelling systems. We focus on the dynamics, investigated by means of the time autocorrelation function of the density fluctuations and the particle mean…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model…
The analysis of the spatial distribution and kinematics of galaxies in clusters allows one to determine the cluster internal dynamics. In this paper, I review the state of the art of this topic. In particular, I summarize what we have…
Molecular dynamics simulations are used to study the local dynamics of counterion-charged polymer association at charge densities above and below the counterion condensation threshold. Surprisingly, the counterions form weakly-interacting…
The evolution of many dynamical systems that describe relationships or interactions between objects can be effectively modeled by temporal networks, which are typically represented as a sequence of static network snapshots. In this paper,…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
Deterministic simulations of the rate equations governing cluster dynamics in materials are limited by the number of equations to integrate. Stochastic simulations are limited by the high frequency of certain events. We propose a coupling…