Related papers: Visualizing Conformations in Molecular Dynamics
In this work we present some results from computer simulations of dynamical aspects of drop formation in a leaky faucet. Our results, which agree very well with the experiments, suggest that only a few elements, at the microscopic level,…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
We model shell formation of core-shell noble metal nanoparticles. A recently developed kinetic Monte Carlo approach is utilized to reproduce growth morphologies realized in recent experiments on core-shell nanoparticle synthesis, which…
We examine several currently used techniques for visualizing complex-valued functions applied to modular forms. We plot several examples and study the benefits and limitations of each technique. We then introduce a method of visualization…
The Diffusion Monte Carlo method is devoted to the computation of electronic ground-state energies of molecules. In this paper, we focus on implementations of this method which consist in exploring the configuration space with a {\bf fixed}…
Energetically minimum configurations of the first- and second-nearest neighbor (NN) CO2 molecules surrounding a vacancy, created by removing a single molecule from the Pa3 structure, were calculated by use of the Monte Carlo simulation…
The microscopic description of collectivity in heavy nuclei in the framework of the configuration-interaction shell model has been a major challenge. The size of the model space required for the description of heavy nuclei prohibits the use…
Identifying local structural motifs and packing patterns of molecular solids is a challenging task for both simulation and experiment. We demonstrate two novel approaches to characterize local environments in different polymorphs of…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
The atomic-level structure of bulk metallic glasses is a key determinant of their properties. An accurate representation of amorphous systems in computational studies has traditionally required large supercells that are unfortunately…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
This work presents some characteristics of MoNet, a digital platform for the modeling and visualization of complex systems. Emphasis is on the ideas that allowed the successful progressive development of this modeling platform, which goes…
The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed…
We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo.…
The tasks of identifying separation structures and clusters in flow data are fundamental to flow visualization. Significant work has been devoted to these tasks in flow represented by vector fields, but there are unique challenges in…
Unsupervised machine learning methods are used to identify structural changes using the melting point transition in classical molecular dynamics simulations as an example application of the approach. Dimensionality reduction and clustering…
We present a novel, generally applicable Monte Carlo algorithm for the simulation of fluid systems. Geometric transformations are used to identify clusters of particles in such a manner that every cluster move is accepted, irrespective of…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…