TITLE:

SCOUTING THROUGH VIRAL DARK MATTER FOR NOVEL PROTEIN FOLDS / POTENTIAL ENERGY SURFACE MAPPING AND VIBRATIONAL ANALYSES OF CARBON CHAIN FREE RADICALS AS DETERMINED BY THE FINITE ELEMENT METHOD

DATE:

Friday, Nov 16th, 2012

TIME:

3:30 PM

LOCATION:

GMCS 214

SPEAKER:

Victor Seguritan and Peter Zajac.
Computational Science Research Center.
San Diego State University.

ABSTRACT:

SCOUTING THROUGH VIRAL DARK MATTER FOR NOVEL PROTEIN FOLDS

While a virus is traveling between hosts, its genome is protected by a protein shell, or capsid. Capsid form has been used to identify
and establish evolutionary relationships among viruses. Because capsids mediate the initial virus-host contact, they are important for
vaccine development. However, they evolve so rapidly to counter changing host defenses that often capsid proteins cannot be recognized by
the usual methods based on their similarities. We used a new approach that includes machine learning to predict which proteins sampled from
coral reef viruses form their capsid shells, then confirmed our prediction using protein crystallography.

POTENTIAL ENERGY SURFACE MAPPING AND VIBRATIONAL ANALYSES OF CARBON CHAIN FREE RADICALS AS DETERMINED BY THE FINITE ELEMENT METHOD

A class of hydrocarbon chain free radicals, including free radicals with molecular formula HC3O and
H3C3O, exhibit potential energy surfaces with distinct, non-equivalent minima, separated by small energy
barriers. Existence of these minima is caused by a relocation of an unpaired electron from one radical
center to another coinciding with the change of molecular orbital hybridization of the center atoms,
resulting in bond angle and bond order changes without breaking any bonds. We propose to map the three
dimensional potential energy surfaces of HC3O free radical, (which has two favorable, nonequivalent
canonical structures: propynonyl (acetylenic) and propadienonyl (cumulenic)) and the H2C2HCO isomer
(with: propenalyl and propenonyl structures) at Hartree-Fock and coupled cluster (CCSD-F12a) levels of
theory with explicitly correlated basis set (cc-pVDZ-F12). Additionally we aim to analyze the vibrational
eigenvalues and reconstruct the wavefunctions of these species using the finite element method and use
them to predict the rovibrational energies which may guide experimental probes of the isomerization.

HOST:

Dr. Jose Castillo.

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