Published 6 issues per year
ISSN Print: 2152-5080
ISSN Online: 2152-5099
Indexed in
UNCERTAINTY CLASSIFICATION AND VISUALIZATION OF MOLECULAR INTERFACES
ABSTRACT
Molecular surfaces at atomic and subatomic scales are inherently ill-defined. In many computational chemistry problems, boundaries are better represented as volumetric regions than as discrete surfaces. Molecular structure of a system at equilibrium is given by the self-consistent field, commonly interpreted as a scalar field of electron density. While experimental measurements such as chemical bond and van der Waals radii do not spatially define the interface, they can serve as useful indicators of chemical and inert interactions, respectively. Rather than using these radial values to directly determine surface geometry, we use them to map an uncertainty interval in the electron density distribution, which then guides classification of volume data. This results in a new strategy for representing, analyzing, and rendering molecular boundaries that is agnostic to the type of interaction.
-
Knoll Aaron, Wald Ingo, Navratil Paul, Bowen Anne, Reda Khairi, Papka Michael E., Gaither Kelly, RBF Volume Ray Casting on Multicore and Manycore CPUs, Computer Graphics Forum, 33, 3, 2014. Crossref
-
Reda K., Febretti A., Knoll A., Aurisano J., Leigh J., Johnson A., Papka M. E., Hereld M., Visualizing Large, Heterogeneous Data in Hybrid-Reality Environments, IEEE Computer Graphics and Applications, 33, 4, 2013. Crossref
-
Knoll A., Insley J., Papka M. E., Nomura K., Kalia R. K., Nakano A., Vashishta P., Molecular Dynamics Simulation of Amorphous SiO2 Fracture, 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, 2012. Crossref
-
Reda Khairi, Knoll Aaron, Nomura Ken-ichi, Papka Michael E., Johnson Andrew E., Leigh Jason, Visualizing large-scale atomistic simulations in ultra-resolution immersive environments, 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), 2013. Crossref
-
Gyulassy Attila, Knoll Aaron, Lau Kah Chun, Wang Bei, Bremer Peer-Timo, Papka Michael E., Curtiss Larry A., Pascucci Valerio, Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials, IEEE Transactions on Visualization and Computer Graphics, 22, 1, 2016. Crossref
-
Kozlíková B., Krone M., Falk M., Lindow N., Baaden M., Baum D., Viola I., Parulek J., Hege H.-C., Visualization of Biomolecular Structures: State of the Art Revisited, Computer Graphics Forum, 36, 8, 2017. Crossref
-
Knoll Aaron, Wald Ingo, Navrátil Paul A., Papka Michael E., Gaither Kelly P., Ray tracing and volume rendering large molecular data on multi-core and many-core architectures, Proceedings of the 8th International Workshop on Ultrascale Visualization, 2013. Crossref
-
Maack Robin G.C., Raymer Michael L., Wischgoll Thomas, Hagen Hans, Gillmann Christina, A framework for uncertainty-aware visual analytics of proteins, Computers & Graphics, 98, 2021. Crossref
-
Schulz Christoph, Schatz Karsten, Krone Michael, Braun Matthias, Ertl Thomas, Weiskopf Daniel, Uncertainty Visualization for Secondary Structures of Proteins, 2018 IEEE Pacific Visualization Symposium (PacificVis), 2018. Crossref
-
Mironenko Roman M., Likholobov Vladimir A., Belskaya Olga B., Nanoglobular carbon and palladium–nanoglobular carbon catalysts for liquid-phase hydrogenation of organic compounds, Russian Chemical Reviews, 91, 1, 2022. Crossref