Related papers: Visualizing Conformations in Molecular Dynamics
Quantum Monte Carlo approaches based on the stochastic sampling of the determinant space have evolved to be powerful methods to compute the electronic states of molecules. These methods not only calculate the correlation energy at an…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Mapping conformational heterogeneity of macromolecules presents a formidable challenge to X-ray crystallography and cryo-electron microscopy, which often presume its absence. This has severely limited our knowledge of the conformations…
Coordination geometries describe how the neighbours of a central particle are arranged around it. Such geometries can be thought to lie in an abstract topological space; a model of this space could provide a mathematical basis for…
We present a method which extends Monte Carlo studies to situations that require a large dynamic range in particle number. The underlying idea is that, in order to calculate the collisional evolution of a system, some particle interactions…
We report an implementation of a program for visualizing complex-valued molecular orbitals. The orbital phase information is encoded on each of the vertices of triangle meshes using the standard color wheel. Using this program, we…
Quantum Monte Carlo is an efficient technique for finding the ground-state energy and related properties of small molecules. A major challenge remains in accurate determination of a molecule's geometry, i.e. the optimal location of its…
A range of percolation models of cluster systems of composites is discussed. In the models the parameters of the clusters of a substance and inner boundaries were obtained by the Monte Carlo method, and the possibility of affecting the…
The crystallization of a metastable melt is one of the most important non equilibrium phenomena in condensed matter physics, and hard sphere colloidal model systems have been used for several decades to investigate this process by…
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend…
We provide a one-to-one map between the spin correlations and certain three-dimensional shapes, analogous to the map between single spins and Bloch vectors, and demonstrate its utility. Much as one can reason geometrically about dynamics…
A Monte Carlo method is presented to evaluate quantum states with many particles moving in the continuum. The scattering state is generated at each time by a Monte Carlo random sampling algorithm. The same calculation are repeated until the…
Molecular simulations produce very high-dimensional data-sets with millions of data points. As analysis methods are often unable to cope with so many dimensions, it is common to use dimensionality reduction and clustering methods to reach a…
In order to find the equilibrium geometries of molecules and solids and to perform ab initio molecular dynamics, it is necessary to calculate the forces on the nuclei. We present a correlated sampling method to efficiently calculate…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
We have developed a new parallel supercomputer code based on Henon's Monte Carlo method for simulating the dynamical evolution of globular clusters. This new code allows us to calculate the evolution of a cluster containing a realistic…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…