Related papers: Visualizing Conformations in Molecular Dynamics
A key to building functional devices on the basis of single molecule magnets in the framework of molecular electronics is the ability to deposit and study these molecules on a surface, because the structural, electronic and magnetic…
We consider a 3-dimensional lattice model of a network-forming fluid, which has been recently investigated by Girardi and coworkers by means of Monte Carlo simulations [J. Chem. Phys. \textbf{126}, 064503 (2007)], with the aim of describing…
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 review recent progress in computational methods for studying the dynamical evolution of large star clusters. After describing some highlights of a new comparison of different models, including N-body models, we mention in detail recent…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…
Spherically symmetric equal mass star clusters containing a large amount of primordial binaries are studied using a hybrid method, consisting of a gas dynamical model for single stars and a Monte Carlo treatment for relaxation of binaries…
Reorientational dynamics-motion defined by changes in the direction of a vector or tensor-determine relaxation behavior in nuclear magnetic resonance (NMR). However, if multiple processes exist that result in reorientation, then analyzing…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
We present a simulation of the SU(3) spin model with chemical potential using a recently proposed flux representation. In this representation the complex phase problem is avoided and a Monte Carlo simulation in terms of the fluxes becomes…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
A major challenge facing existing sequential Monte-Carlo methods for parameter estimation in physics stems from the inability of existing approaches to robustly deal with experiments that have different mechanisms that yield the results…
Configurations of the molecules on the wall of a vacancy, formed by removing a central and its first and second nearest-neighbor (NN) molecules in solid CO2 with the Pa3 structure, were calculated by the Monte Carlo simulation technique at…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Recently the general form of a translation-covariant quantum Boltzmann equation has been derived which describes the dynamics of a tracer particle in a quantum gas. We develop a stochastic wave function algorithm that enables full…
On large-scales, comparable to the horizon, the observable clustering properties of galaxies are affected by various general relativistic effects. To calculate these effects one needs to consistently solve for the metric, densities and…
Cyber-physical systems (CPS) are increasingly becoming driven by data, using multiple types of sensors to capture huge amounts of data. Extraction and characterization of useful information from big streams of data is a challenging problem.…
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,…
The mean-field approximation predicts pairing and shape phase transitions in nuclei as a function of temperature or excitation energy. However, in the finite nucleus the singularities of these phase transitions are smoothed out by quantal…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…