Faculty
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   Steve Durbin
   David D. Nolte
   Earl Prohofsky

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*Dept of Physics
*Applied Physics
Interdepartmental Biophysics / Structural Biology
Contact: Bill Cramer



School of Science


Purdue University

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Biophysics Group

Purdue University
Department of Physics
525 Northwestern Avenue
West Lafayette, Indiana 47907-2036
Telephone:  765 - 494 - 3005    Fax:  765 - 494 - 0706



The newly formed Biophysics Group in the Department of Physics consists of faculty applying concepts and experimental methods from condensed matter physics to the understanding of x-ray dynamic scattering from proteins, laser spectroscopy of energy transfer proteins in membranes, and theoretical studies of DNA melting.


  Steve Durbin

X-ray studies of vibrational modes in biomolecules
 

While the static structures of simple proteins like myoglobin and hemoglobin are fairly well understood, their biological activity is likely to also depend on their dynamic vibrational properties. A new x-ray synchrotron technique is being exploited to measure the vibrational spectrum of iron atoms in the heme group, the major functional structure in myoglobin and several other important proteins. Utilizing the extremely high brightness of an undulator x-ray source at the Advanced Photon Source (APS) at Argonne National Laboratory, an x-ray beam whose energy is very close to the Mossbauer nuclear resonance (14.4 keV) and having meV energy resolution is incident on the Mb specimen. If a vibrational mode has an energy equal to the difference between the x-ray beam and the nuclear resonance, the resonance can be excited, with subsequent deexcitation which can be detected as Fe fluorescence. By monitoring this fluorescence as the x-ray energy is scanned through the resonance, an approximate map of the Fe vibrational density of states is obtained. This is especially important because the modes are specific to Fe, so there is no interference from the other parts of the protein; this provides an excellent complement to other Raman scattering and other vibrational probes. 

This work is done in colaboration with Tim Sage and Paul Champion of Northeastern University, and Ercan Alp and Wolfgang Sturhahn at the Advanced Photon Source. 


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  David D. Nolte

The Adaptive Optics and Biophotonics group of Prof. David Nolte has made the first depth-resolved holographic images of living tissue. They are developing holographic optical coherence imaging (OCI) as a new biomedical imaging approach that is analogous to putting on a pair of sunglasses to “see” inside tissue. It uses a photorefractive quantum well, which is the most sensitive dynamic holographic film ever developed. For a Purdue News Service item see http://www.purdue.edu/UNS/html4ever/020507.Nolte.imaging.html

Our recent advance into digital holography has made it possible to detect motion inside cells and tissue to study the effect of anti-cancer drugs.
http://news.uns.purdue.edu/x/2007a/070306NolteShimmer.html

The group has also invented and developed the BioCD. This is like a digital compact disc (CD) but is printed with antibodies instead of digital information. The goal of this research is to develop a high-speed high-throughput immunoassay for rapid screening of up to thousands of proteins in bodily fluids. For a Purdue News Service item see http://news.uns.purdue.edu/UNS/html4ever/2004/040518.Nolte.CD.html

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  Earl Prohofsky

Dynamics of the DNA Double Helix

Biological Physics deals with large systems that have very complex nonlinear interactions. Thesystems are large because biomolecules are large and have little symmetry. The interactions are highly nonlinear because associations and dissociations of segments are taking place during biological function and such gross changes in the interaction scheme are highly nonlinear. The most desirable analysis would involve description of the dynamics on an atomic scale to allow for building insight into behavior. The combination of large size and large nonlinearities form a particular challenge for theoretical investigation.
The most common approach is simulation but that runs into the problem of time scale.  Simulations of large systems over time periods of nanoseconds require heroic efforts. The interesting time scale for the processes to be investigated is, however, in the millisecond range.  The efforts of Professor Earl Prohofsky and his group have been in developing an  entirely new approach to the calculation of probabilities of certain events based on a statistical mechanics approach. The determination of equilibrium probabilities is appropriate for long time-scale events which includes dissociation probabilities etc.  It gives predictions of observed absolute melting temperatures and proper transition widths without the use of fitted parameters. The prediction of fluctuational opening rates of base pairs in the premelting regime is also in agreement with observation. The method has also been applied to the dissociation of drugs from their attachment to the DNA helix and the binding constant of two systems, daunomycin and netropsin, are also predicted from unfitted potentials. Current efforts are aimed at studying the basic stability of proteins and complexes involving proteins. The subject is often referred to as the protein folding problem.
The group is currently developing the codes to allow calculations on truly large systems. This involves diagonalization of large but sparse matrices. It will also develop methods to simplify the calculations for projecting out only the particular eigenvectors needed. The principal thrust will be to study the statistical mechanics of very large nonlinear systems at the atomic level of detail including the bonded stability. This is a problem (the analysis of large nonlinear systems) that is also important in many other areas of physics.

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