Linear-scaling Quantum Gallery

Welcome to the Linear-scaling Quantum Gallery!
Below is a collection of linear-scaling semiempirical electronic structure calculations of solvated biological macromolecules.

DNA
 Ribozymes
 RNA-binding proteins
 Proteins

Click images for full-screen view with expanded legend.  For explanation of terms in the figure legends, see the Nomenclature Index at the bottom of the page.

DNA Back to top of page
Images/ABZ-DNA_thumb
Solvent-polarized ESP Maps of A-, B- and Z-form DNA (Khandogin et al., 2000) ESP Map of a long linear B-form DNA Solvent-polarized ESP Map of bent B-form DNA

Ribozymes  Back to top of page
Solvent-polarized ESP Map of the hammerhead ribozyme (Khandogin et al., 2000) Fukui density for the hammerhead ribozyme Local hardness map for the hammerhead ribozyme

RNA-binding proteins Back to top of page
Solvent-polarized ESP map of unbound HIV-1 NC protein (in SL3 -bound conformation) (Khandogin et al., 2003) Local hardness map of unbound HIV-1 NC protein (in SL3 -bound conformation) (Khandogin  et al., 2003) Solvent-polarized ESP map of unbound HIV-1 NC protein (in SL2-bound conformation)
Local hardness map of unbound HIV-1 NC protein (in SL2-bound conformation) Solvent-polarized ESP map of HIV-1 NC protein (bound to SL2) Solvent-polarized ESP map of HIV-1 NC protein (bound to SL3) (Khandogin et al., 2000) 

Proteins Back to top of page
Solvent-polarized ESP Map of phosphate-binding protein (PBP) in the open form (unbound) (Khandogin and York, 2004) Solvent-polarized ESP Map of phosphate-binding protein (PBP) in the closed form (phosphate not shown) (Khandogin and York, 2004)


Nomenclature Index
  • ESP map: A map of the electrostatic potential due to the nuclei and electronic charge distribution (calculated self-consistently using linear-scaling methods).  The map is projected onto the solvent accessible surface.  The macromolecular electron density in the quantum system will polarize and re-equilibrate upon conformational change or when subjected to different environments such as solvent, or binding of other molecules such as metal ions, small ligands, or large polynucleotides like RNA.
  • Fukui index: The approximate Fukui function, defined as the derivative of the electron density with respect to the total number of electrons, calculated using a finite-difference, frozen density matrix approximation and condensed onto atoms via a Mulliken paritioning.
  • Local hardness map: The approximate local hardness calculated as the electrostatic potential due to the approximate Fukui function projected onto the van der Waals molecular surface.
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