Our
research is evenly divided into two areas, molecular
biophysics and molecular electronics. The biophysics
group has the primary goal of studying the structure
and function of visual pigments and light-transducing
proton pumps. The molecular electronics group investigates
the encoding, manipulation, and retrieval of information
at a molecular level using bioelectronic and biomimetic
methods. Both groups use molecular spectroscopy and
quantum theory as the primary tools.
The Nature of Wavelength
Regulation in Cone Pigments
Our primary interest is the mechanism
of wavelength and photochemical regulation in the short
wavelength cone pigments. We use nonlinear laser spectroscopy,
vibrational spectroscopy, low temperature photocalorimetry
and site directed mutagenesis to isolate the key structural
components that characterize these unusual protein binding
sites. A recent example of this research can be found
in the following article: Photochemistry of the primary
event in short-wavelength visual opsins at low temperature,
B.W. Vought, A. Dukkipatti, M. Max, B.E. Knox and R.R.
Birge, Biochemistry 38, 11287-11297 (1999).
Molecular Electronics
and Protein-based Devices
Our research in this area emphasizes biomolecular electronics,
the use of biological molecules or biomimetic approaches
to make electronic components or systems. We use the protein
bacteriorhodopsin to make a variety of devices that exploit
the unique abilities of this protein to convert light
into a refractive index or an optical density gradient.
Current devices under study include an artificial retina,
an optical associative processor, and a three-dimensional
memory. We also use both site-directed mutagenesis and
directed evolution to optimize the protein for each application.
Protein-based associative processors and volumetric memories,
R.R. Birge, N.B. Gillespie, E.W. Izaguirre, A. Kusnetzow,
A.F. Lawrence, D. Singh, Q.W. Song, E. Schmidt, J.A. Stuart,
S. Seetharaman and K.J. Wise, J. Phys. Chem. B.
103, 10746-10766 (1999).
Molecular Orbital
Theory of Large Systems
Our theoretical research develops and
applies semiempirical procedures aimed at studying protein
structure and function using quantum chemical methods.
Our mndoci method is capable of handling the first and
second shells of protein binding sites containing many
hundreds of atoms while simultaneously carrying out
full single and double configuration interaction on
the protein-bound chromophore. This approach requires
careful parameterization coupled with transformation
procedures that provide a tractable basis set while
simultaneously treating the surrounding protein using
a full valence SCF basis set. Reparameterizing MNDO
for excited state calculations using ab initio effective
Hamiltonian theory: Application to the 2,4-pentadien-1-iminium
cation, C.H. Martin and R.R. Birge, J. Phys. Chem.
A 102, 852-860 (1998); The nature of the chromophore
binding site of bacteriorhodopsin: The potential role
of Arg-82 as a principal counterion, A. Kusnetzow, D.L.
Singh, C.H. Martin, I. Barani and R.R. Birge, Biophys.
J. 76, 2370-2389 (1999).
MathScriptor
For CHEM-393 and INTD-291 students
and otthers interested in MathScriptor, the program
is located here.
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