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The Road to Enlightenment

Knots in Biological Sciences
A Workshop sponsored by CIMAT, UT Dallas, and UT Southwestern Medical Center

The University of Texas at Dallas, April 28, 2005

Participation

11:00 a.m. Welcome Reception

12:00 p.m. Luncheon

2:00 - 5:00 p.m. Workshop

South Engineering and Computer Science Building (ECSS), Room 3.503

Participants

1. Jose Carlos Gomez (CIMAT)
What is Knot Theory all about?

Dr. Jose Carlos Gomez Larranaga is General Director of the Research Center for Mathematics of the Mexican Council of Science and Technology (CIMAT). Under his direction, the center has concentrated its efforts in organizing several national meetings with the Mexican Society of Mathematics as well as joint meetings with the American Society of Mathematics. Dr. Gomez Larranaga holds a B.A. in Actuarial Sciences and M.S. in Mathematic Sciences from the National University of Mexico (UNAM) and a Ph.D. in Mathematics from the University of Cambridge, England. He has taught at CIMAT, Institute of Mathematics of the National University of Mexico (UNAM) and was a visiting professor in Ruhr- Universitat, in Bochum, Germany.
Among his most recent publications are: 3-Manifolds that are covered by two open bundles, coauthored with F.J. Gonzalez and W. Heil in Boletín de la Sociedad Matemática Mexicana (2004), Seifert unions of solid tori in Math Z. 240 (2002) and Seifert unions and spaces of graphs in S3 coauthored with W. Heil in J. Knot Theory Ramifications 11 (2002). Dr. Gomez Larranaga has participated in international conferences such as: The 3rd Reunion Japan-Mexico Joint Meeting on Topology and its Applications in Oaxaca, Mexico; Geometric Topology, in Xian, China and Lusternick - Schnirelmann Category in the New Millenium in South Hadley, Massachussets, USA.
Dr. Gomez Larranaga was the Secretary of the Institute of Mathematics of the National University of Mexico and the President of the Mexican Society of Mathematics. Under Dr. Gomez Larranaga's leadership, CIMAT has consolidated its internationalization, collaborating with institutions of great academic prestige such as University of Berlin, Rice University, University of Texas at Dallas, and Florida State University, among others. Dr. Gomez Larranaga is member of the Research Advisory Board of the Vice-Presidency for Research and Graduate Studies of the University of Texas at Dallas.

2. Isabel K. Darcy (Univ of Iowa)
A first order model for protein-DNA complexes.

Dr. Isabel Darcy is an Assistant Professor of Mathematics at the University of Iowa. She earned her Ph.D. in Mathematics from Florida State University in 1997 where she was a fellow of the Program in Mathematics and Molecular Biology. She also spent two years at UT Austin as a post-doc/lecturer. She is currently a member of the American Mathematical Society committee on Science Policy. She currently works on modeling the shape of DNA bound by proteins. When modeling protein-DNA reactions, frequently the general shape of the protein-bound DNA is unknown. By using the experimental technique of difference topology from the Jayaram-Harshey lab at UT Austin and the computer program described in this talk, it is possible to determine the shape of DNA within any stable protein-DNA complex. This research is funded by an NIH grant from the Joint DMS/NIGMS Initiative to Support Research in the Area of Mathematical Biology.

3. Stephen D. Levene (UT Dallas)
Topology in biology: from DNA mechanics to enzymology.

Stephen Levene is Associate Professor of Molecular and Cell Biology at The University of Texas at Dallas. Dr. Levene received his Ph.D. in Chemistry from Yale University in 1985 and was an American Cancer Society postdoctoral fellow with Bruno Zimm at University of California, San Diego until 1989. He then spent one year as a staff scientist at the Human Genome Center at Lawrence Berkeley Laboratory and was a Program in Mathematics and Molecular Biology Fellow at University of California, Berkeley in Nicholas Cozzarelli's laboratory. Dr. Levene's research interests are in the area of nucleic-acid structure and flexibility, mechanisms of DNA recombination, the structural organization of human telomeres, and applications of these areas in biotechnology. He is recipient of an Obermann Interdisciplinary Research Fellowship, is a member of the Institute of Biomedical Sciences and Technology and the Biophysical Society, and has served on NIH study sections BBCA and SSS1. In addition to scientific pursuits, Dr. Levene is an avid snow skier and cyclist, having previously competed in both sports.

4. Ray Baughman (UT Dallas)
Knotty Carbon Nanotube Yarns.

Ray Baughman became the Robert A. Welch Professor of Chemistry and Director of NanoTech Institute at the University of Texas in Dallas in August 2001, after 31 years in industry. He is a Fellow of the American Physical Society, the American Institute of Chemists, and the World Innovation Foundation, an Academician of the Russian Academy of Natural Sciences, an Honorary Professor of three universities in China, and on editorial and advisory boards of Science, Synthetic Metals, the International Journal of Nanoscience, and the Encyclopedia of Nanoscience and Nanotechnology. Ray has 57 US patents and over 230 publications. He received the Chemical Pioneer Award of the American Institute of Chemists (1995) and the Cooperative Research Award in Polymer Science and Engineering (American Chemical Society, 1996).

5. John Luecke (UT Austin)
Exotic knot theoretic solutions to an experiment by Pathania,Jayaram, and Harshey

John Luecke is a mathematician working in knot theory and topology. He is currently a professor at the University of Texas at Austin. His involvement with knot theory and biology came from participating in a joint seminar between mathematicians and biologists held in the lab of UT molecular biologist Makuni Jayaram.

6. Hugo Cabrera Ibarra (IPICyT)
A family of solutions to the action of the Gyn enzime.

Hugo Cabrera Ibarra obtained his bachelor degree as a Mathematician at Universidad Autónoma de San Luis Potosí in 1995; master degree at Centro de Investigación en Matemáticas (CIMAT) in 1997, and his PhD at CIMAT in 2001. He has been an associated researcher at the Applied Mathematics and Computational Sciences Division, IPICyT since 2001. His research interests have been primarily in the areas of topology and knot theory and their applications to problems in biological sciences.

7. Rama Ranganathan (UT Southwestern)
Evolutionary Rules for Building a Protein

Dr. Ranganathan is associate professor in the Pharmacology department at the University of Texas Southwestern Medical Center at Dallas received his Ph.D. and M.D. degrees from University of California, San Diego in 1994. He is a fellow of the Howard Hughes Medical Institute and in 2001 was honored as a Edward Mallickrodt, Jr. Foundation Scholar.

8. Mieczyslaw K. Dabkowski (UT Dallas)
Tangle Replacement Moves on Links

Mieczyslaw K. Dabkowski is Assistant Professor of Mathematics at The University of Texas at Dallas. Dr. Dabkowski received his Ph.D. in Mathematics from The George Washington University in 2003.

5:00 - 6:00 p.m. Conclusions

7:00 p.m. Dinner for participants, hosted by the Office of the Vice Presidency of Research and Graduate Education

Website donated by Center for U.S.-Mexico Studies. 

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