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Atomistic Visualization: On-the-fly Data Extraction and Rendering. Dipesh Bhattarai Dr. Bijaya B. Karki Department of Computer Science Louisiana State University. ACMSE 2007: The 45 th ACM Southeast Conference Winston-Salem, North Carolina, USA March 23-24, 2007. Presentation Outline.
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Dr. Bijaya B. Karki
Department of Computer Science
Louisiana State University
ACMSE 2007: The 45th ACM Southeast ConferenceWinston-Salem, North Carolina, USA March 23-24, 2007
Source: Protein Data Bank
Connectivity information is implicitly assumed in a molecule.
Total Coordination Number:
Set of all the atoms that coordinated with atom i in the time period T
Partial Coordination Number: Coordination number of atoms of type α with respect to atoms of type β
Set of all the atoms of type β that coordinated with atom i of type α over the time period T
Stability of the coordination environment
A coordination environment exists only when all the bonds forming the environment exist simultaneously.
(left) spherical representation of diffusion of individual atom over the time T
(right) ellipsoidal representation of diffusion of individual atom over the time T
Coordination environmnet of Silicon(blue) atoms with respect to Oxygen (greenish) atoms: (left) number of outgoing lines from the Silicon atoms gives the coordination number of the atom, (middle) the coordination number if encoded in the Silicon atom and the bond-length between Silicon and Oxygen at also encoded, (right) stability of the coordination environment of Silicon atoms are encoded in the size of the sphere and stability of bond between Silicon and Oxygen are encoded in the width of the bond. Bonds are color-coded similar to the middle figure.
Polyhedral representation of Si-O coordination magnesium silicate liquid. The color and shapes of the polyhedra give the coordination numbers. Red spheres at the corners are Oxygen atoms involved in coordination. The size of the spheres represents the fraction of time the atom is coordinated to the Si atom, and the intensity of the polyhedral color encodes the stability of the coordination.
Polyhedral representation of Silicon and Oxygen coordination in a Magnesium Silicate (MgSiO3) system.
Even simple color coding become effective in showing the spatial distribution of Si-O coordination environment
Diffusion ellipsoids for Magnesium Oxide system at 3000 K temperature (left) and the same system at 7000 K temperature (right)
Both the system contained 64 atoms (32 Magnesium Atoms and 32 Oxygen atoms)