Group Leader:

Andreas Hanke, Assistant Professor of Physics

Mailing Address:

Department of Physics and Astronomy
The University of Texas at Brownsville
80 Fort Brown
Brownsville, TX 78520

Office Address: Engineering, Science & Technology, Office 1.318

Phone: (956) 882-6682

Fax: (956) 882-6726

e-mail: hanke@phys.utb.edu

Research Interests: Biophysics - from single molecules to biological function

I am theoretical physicist by training and have worked in the fields of mesoscopic quantum systems, soft condensed matter physics, and biological physics. My current plans are to build up a theory division in the fields of biophysics and nanoscience at the Physics Department of UT Brownsville. The scope of my research is to develop new theoretical models relevant to molecular cell biology and nanoscience and to validate these models with experimental data for systems such as cell membranes, proteins, DNA, RNA, and their interactions. My research is highly interdisciplinary in nature, involving Statistical Physics, Biology, Computer Science, and Math.

1) Studies of single biomolecules: DNA conformational changes and protein binding

Jointly with S. D. Levene (UT Dallas) and M. C. Williams (Northeastern University)

Structural transitions of DNA and docking of proteins on DNA are fundamental processes in molecular biology. Understanding these processes on a single-molecule level is essential for our understanding of gene function and control, and may find application in DNA-based sensors and other emerging nanotechnology.

Stretching on individual DNA molecules in single molecule force spectroscopy can be used to induce a helix-coil transition in double-stranded DNA. Within a certain range of stretching forces, only local denaturing of the DNA duplex, or "bubble formation", occurs. The interaction of these localized regions of unwound DNA with single-strand-specific DNA binding proteins can then be probed under a wide range of conditions using new experimental techniques. Our collaborator Mark Williams and his group at Northeastern University is able to measure the forces required to stretch single DNA molecules by using an optical tweezers instrument with high precision. In our lab at UTB we study also force-induced transitions and conformational changes caused by DNA-binding proteins. A state-of-the-art Veeco Nanoscope IV Scanning Probe Microscope with PicoForce Module is available for imaging at atomic resolution and force measurements in the piconewton range.

2) Sequence-dependent unwinding in superhelical DNA

Jointly with S. D. Levene (UT Dallas)

Sequence-dependent unwinding of DNA is an integral aspect of many biological processes such as gene regulation, DNA replication, and DNA repair.  DNA unwinding is facilitated by negative supercoiling, which provides a ubiquitous source of free energy that augments the unwinding free energy accompanying the interactions of many proteins with their cognate DNA sequences.  Although much is known about sequence-dependent unwinding in linear DNA molecules, our present understanding of the effects of supercoiling on localized, sequence-dependent melting transitions in DNA is at best semi-quantitative.

The DNA of virtually all terrestrial organisms is negatively supercoiled. Negative supercoiling is regulated in prokaryotes by DNA gyrase; eukaryotes lack gyrase but maintain negative supercoiling through winding of DNA around nucleosomes and interactions with DNA-unwinding proteins.  Large regions of mammalian chromosomes appear to be organized into negatively supercoiled, topologically independent domains. Therefore, understanding the interplay of supercoiling and local helical structure is essential to a complete understanding of biological mechanisms in higher organisms.  Recent developments in biophysical theory provide an opportunity to develop a detailed and quantitative framework for analyzing localized DNA-unwinding transitions in superhelical domains.

In our research we will use a fusion of numerical simulations of superhelical conformation and a statistical-mechanical treatment of sequence-dependent transitions in DNA to develop a comprehensive biophysical model for supercoiling-dependent DNA unwinding. The theoretical model will be validated by comparing predictions of the theory for several DNA sequences with experimental data from plasmid DNAs and supercoiled DNA minicircles that contain 2-aminopurine substitutions as spectroscopic probes of local unwinding.

Development

I wrote my diploma thesis with Prof. W. Zwerger at the Physics Department at the Ludwig Maximilians University Munich, Germany, on a topic of mesoscopic quantum systems. In my PhD thesis with Prof. S. Dietrich at the University of Wuppertal, Germany, now at the Max Planck Institute for Metal Research in Stuttgart, I studied fluctuation-induced entropic forces between colloidal particles. After my PhD I went to MIT for my post-doctoral studies where I worked with Prof. M. Kardar on problems of nanoscience and biological physics. In November and December 2001 I visited the group of Prof. M. Schick in Seattle, before I moved to a Postdoctoral Position in Prof. John Cardy's group at the University of Oxford. From October 2002 until July 2003 I worked as Research Associate in the group of Prof. U. Seifert in Stuttgart where I worked on problems of single molecule biophysics. In August 2003 I returned with a Marie Curie Fellowship to John Cardy\222s group at the University of Oxford. In March 2004 I finally moved to my present position as Assistant Professor at the Physics & Astronomy Department at The University of Texas at Brownsville. I am also Adjunct Assistant Professor at the Physics Department at The University of Texas at Dallas and member of the Institute of Biomedical Sciences and Technology (IBMST) at UT Dallas. My research includes summer appointments at the Dallas NanoTech Institute.

Teaching

Spring 2005:  PHYS 4320 - Quantum Mechanics  (Undergraduate Course)

Fall 2005:      PHYS 5322 - Electrodynamics II  (Graduate Course at UT Dallas)

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