Related papers: Visualizing Conformations in Molecular Dynamics
The new approach outlined in Paper I (Spurzem \& Giersz 1996) to follow the individual formation and evolution of binaries in an evolving, equal point-mass star cluster is extended for the self-consistent treatment of relaxation and close…
The main idea of this work is that the quantum-classical isomorphism is a suitable framework for a generalization of the notion of detailed balance. The quantum-classical isomorphism is used in order to develop a Monte Carlo simulation with…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
We describe the development of a new object kinetic Monte Carlo code where the elementary defect objects are off-lattice atomistic configurations. Atomic-level transitions are used to transform and translate objects, to split objects and to…
A variant of the Direct Simulation Monte Carlo method is used to study the behavior of a granular gas, in two and three dimensions, under varying density, restitution coefficient, and inelasticity regimes, for realistic vibrating wall…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
In cluster tomography, we propose measuring the number of clusters $N$ intersected by a line segment of length $\ell$ across a finite sample. As expected, the leading order of $N(\ell)$ scales as $a\ell$, where $a$ depends on microscopic…
We consider a theoretical model for a binary mixture of colloidal particles and spherical emulsion droplets. The hard sphere colloids interact via additional short-ranged attraction and long-ranged repulsion. The droplet-colloid interaction…
A general method to obtain a representation of the structural landscape of nanoparticles in terms of a limited number of variables is proposed. The method is applied to a large dataset of parallel tempering molecular dynamics simulations of…
We present a case study investigating feature descriptors in the context of the analysis of chemical multivariate ensemble data. The data of each ensemble member consists of three parts: the design parameters for each ensemble member, field…
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…
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also…
Quantum Monte Carlo methods find fruitful application in large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in a fluctuating one-body field;…
We report an experimental approach to control the position of molecular aggregates on surfaces by vacuum deposition. The control is accomplished by regulating the molecular density on the surface in a confined area. The diffusing molecules…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Inducing and controlling the ultrafast molecular rotational dynamics using shaped laser fields is essential in numerous applications. Several approaches exist that allow following the coherent molecular motion in real-time, including…