Related papers: Collective mode mining from molecular dynamics sim…
Collective motion in animal groups, such as swarms of insects, flocks of birds, and schools of fish, are some of the most visually striking examples of emergent behavior. Empirical analysis of these behaviors in experiment or computational…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
We review various numerical approaches to compute transport coefficients in molecular dynamics. These approaches can be broadly classified into three groups: (i) nonequilibrium methods based on applying an external driving field to the…
Classifier ensembles are pattern recognition structures composed of a set of classification algorithms (members), organized in a parallel way, and a combination method with the aim of increasing the classification accuracy of a…
Community detection is one of the most active fields in complex networks analysis, due to its potential value in practical applications. Many works inspired by different paradigms are devoted to the development of algorithmic solutions…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The Boltzmann equation is a powerful theoretical tool for modeling the collective dynamics of quantum many-body systems subject to external perturbations. Analysis of the equation gives access to linear response properties including…
The collective response of matter is ubiquitous and widely exploited, e.g. in plasmonic, optical and electronic devices. Here we trace on an attosecond time scale the birth of collective excitations in a finite system and find distinct new…
Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…
In this work we present the modular Crowd Simulation Evaluation through Composition framework (CSEC) which provides a quantitative comparison between different pedestrian and crowd simulation approaches. Evaluation is made based on the…
A generic aggregate forming system in two dimensions (2D) is studied using canonical ensemble constant temperature molecular dynamics simulation. The aggregates form due to the competition between short range attraction and long range…
In order to discern aggregation in solutions, we present a quantum mechanical analog of the photon statistics from fluorescent molecules diffusing through a focused beam. A generating functional is developed to fully describe the…
Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on…
The generalized transport equations for a consistent description of kinetic and hydrodynamic processes in dense gases and liquids are considered. The inner structure of the generalized transport kernels for these equations is established.…
Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The…
We propose a morphological multi-scale analysis of large-scale structures obtained by computer simulations and by observations. Structures are obtained at different scales by applying a wavelet transform on the observed and simulated data.…
We describe parallel Markov chain Monte Carlo methods that propagate a collective ensemble of paths, with local covariance information calculated from neighboring replicas. The use of collective dynamics eliminates multiplicative noise and…
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious information towards its understanding and control. Unfortunately,…
We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C$_{60}$ fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on…
The investigation of the dynamics of quantum many-body systems is a concerted effort involving computational studies of mathematical models and experimental studies of material samples. Some commonalities of the two tracks of investigation…