Profile

Research Interests

All macromolecules present in the cellular environment, such as nucleic acids (DNA, RNA) and proteins reside there in extremely crowded, compact and concentrated conditions. In order to perform their biological duties these macromolecules must also undergo structural transitions, modifications and processing within this crowded, highly concentrated milieu. Clearly, a variety of different conformational forms and structural states of biological molecules are required to accommodate this compaction and enable biological processing events. Naturally a number of different but intrinsic, characteristically fundamental physical and chemical properties of the macromolecules themselves are operative in facilitating these activities. Our research efforts are aimed at elucidating these fundamental physical properties and learning how they depend on primary sequence and local secondary structures. We hope to establish a quantitative basis for understanding macromolecular behaviors in the context of intrinsic biological functions and applications in bio-nanoscience. Within this theme there are two main foci of our University research program:

(1) Analytical studies of molecular transitions in biopolymers.

(2) Mesoforms of soft matter formed from biological macromolecules.

Our research program at Portland State University is purely fundamental. The expressed goal is knowledge creation through generation of research results. With this focus it is anticipated that these efforts will not necessarily yield commercial technologies. More applied DNA biophysics research, with significant commercial applications, which historically has formed the bed rock of our University research program is now conducted entirely in a private commercial entity located away from the Portland State University campus.

Representative Publications

• "Microscopic formulation of the Zimm-Bragg model for the helix-coil transition". Badasyan AV, Giacometti A, Mamasakhlisov YSh, Morozov VF, and Benight AS.  Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 81,  TBA, 2010.
• "Cellulose/DNA Hybrid Nanomaterials". Anand P. Mangalam, John Simonsen and Albert S. Benight. Biomacromolecules, 10, 497-504, March 9, 2009.
• "Electrical Detection of the Temperature Induced Melting Transition of a DNA hairpin Covalently Attached to Gold Interdigitated Microelectrodes". Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini S. Bhandiwad, David R. Evans, Raj Solanki and Albert S. Benight. Originally published online, July 15, 2008. Nucleic Acids Research, doi:10.1093/nar/gkn436, 1-11, 2008.
• "Two Scale Generalized Model of Polypeptide Chains ." A. V. Badasyan, Sh.A. Tonoyan, A.V. Tsarukyan, E. Sh. Mamasakhlisov, A. S. Benight, and V.F. Morozov. J. Chemical Physics, 128, 195101, 2008.
• Stacking Heterogeneity: A Model for the Sequence Dependent Melting Cooperativity of Duplex DNA". A.V. Girgoryan, E. Sh. Mamasakhlisov, T. Yu. Buryakina, A. V. Tsarukyan, A. S. Benight, and V.F. Morozov. J. Chemical Physics 126, 165101, 2007.
• "On the Geometrical Thermodynamics of Chemical Reactions". M. Santoro and A. S. Benight. Published on line, July 8, 2005. arXiv:math-ph/0507026v1
• "The Helix-Coil Transition in Heterogeneous Double Stranded DNA: Microcanonical Method." A.V. Badasyan, A.V. Grigoryan. E.Sh. Mamasakhlisov, A.S. Benight and V.F. Morozov. J. Chemical Physics,. 123, 194701, November 2005.
• "The Four State Model of a Linear Lattice: Applications to Lattice: Applications to Ligand Controlled Hybridization of Short Duplex DNAs". A. S. Benight, Biopolymers 69, 406 420, June, 2003.