Mathematics of Molecular and Cellular Biology

The 2007–2008 thematic program on Mathematics of Molecular and Cellular Biology is well underway, with the fall semester concentration on the mathematics of DNA and RNA stuctures coming to a close.

The fall semester kicked-off with a superb tutorial on Mathematics of Nucleic Acids, and then continued with two very successful workshops on Mathematics of DNA Structure, Function, and Interactions, September 16-21, and RNA in Biology, Bioengineering and Nanotechnology, October 29-November 2. Both of the these programs were well attended and well received by the participants.

The tutorial began at 8:50 AM with a welcome by IMA director Doug Arnold, and consisted of four 1-hour talks. Wilma Olson, Dept. of Chemistry, Rutgers University gave the two morning talks. The talk titles were Sequence-dependent helical structure and global responses of DNA, and Implications of base sequence-dependent structural information on larger-scale genetic control. In her talks, Wilma stressed the importance of energy considerations in computing DNA structure and protein interactions. She introduced concepts to be covered in a number of talks in the follow-on IMA Workshop, including the talks of Richard Lavery, Jonathan Widom, Victor Zhurkin, Ariel Prunell, Andrew Travers, Jason Kahn and James Maher.

David Swigon, Dept. of Mathematics, University of Pittsburgh gave the two afternoon talks. His titles were DNA topology and geometry/DNA elasticity and DNA statistical mechanics/DNA dynamics. Like Wilma, David previewed a number of concepts central to talks in the follow-on IMA workshop, including the talks of Andrzej Stasiak, Alex Vologodskii, Isabel Darcy, John Marko, Makunni Jayaram and Mariel Vazquez.

The tutorial had 87 participants, and gave them an excellent introduction to the research presentations that followed.

Luger et al. (1997)-Crystal structure of the nucleosome core particle is one of the most striking examples of protein-induced DNA deformation.

In the words of some of the participants of the tutorial:

The speakers did an excellent job making this accessible to those of us who were a bit new to aspects of the area. For those areas which I know well, I was pleased to observe that they got things right and did not get lost in details so as to obscure the critical features.

— Ken Millett

I attended the tutorial purely out of curiosity. My work at 3M has skirted some subjects in the biological sciences and I have a general ongoing interest in this area. It was also useful to hear Swigon's review of Langevin and Brownian dynamics, since this has potential impact on my work at 3M, where I do computational analysis ("modeling").

— Larry Carson

The IMA Workshop Mathematics of DNA Structure, Function and Interactions began on Sunday, September 16, and ran through noon on Friday, September 21. The organizers chose to run the workshop for 5.5 days instead of 4.5 days (the usual IMA workshop length), and to schedule the workshop immediately following the Saturday tutorial. The reason for this was to encourage maximum interaction between the scientists and mathematicians in attendance.

The workshop consisted of 21 1-hour talks, and 11 15-minute talks. The short talks were selected from abstracts submitted by workshop participants. There was a reception and poster session in Lind Hall 400 on Monday, September 17, at which 16 posters were presented. A workshop dinner for all participants was held on Tuesday evening, September 18 at Kikugawa restaurant. A dinner for the invited hour speakers was held on Wednesday evening, September 19 at the Caspian restaurant. At the dinner, De Witt Sumners led a discussion about the future publication by Springer of an IMA Workshop volume dedicated to Nick Cozzarelli, and based on the activity of the workshop. This volume will be edited by the organizers of the workshop.

Some of the highlights of the workshop were the second chances discussions held each day at the end of lectures. These were very lively events, with lots of audience participation. The workshop had 111 participants.

This was a delightful and effective meeting. There were good examples of ongoing collaborations between mathematicians, theorists, and biologists, and a number of new collaborations were potentiated at this meeting. I made new contacts both within and between fields.

—Jim Maher

I learned a great deal. I was not familiar with the field of DNA topology, nor with terms such as linking number and writhe. As a consequence of the workshop, I plan to continue discussions with Marcia Fenley and perhaps pursue a new approach on modeling DNA binding mechanisms. I also expect to work with Mariel Vazquez now that the workshop is over. The workshop helped me have a better feel for the work she has done from a topological perspective before we discuss a more graph-theoretic approach.

— Meredith Betterton

This is how Tamar Schlick,(Chem, Math, & Comp Sci, NYU), one of the organizers of this workshop described the event:

Our workshop on RNA in Biology, Bioengineering and Biotechnology brought together a broad spectrum of 132 researchers from the US and abroad that included mathematicians, biologists, computer scientists, chemists, bioengineers, and physicists. Adding to the interesting geographical mix was a blend of both experts, with extensive hands-on experience on RNA research, and novices from allied fields who were interested in this young and vibrant field of immense scientific importance. Our esteemed biopolymer subject generated exciting new themes, approaches, and problems concerning RNA structure analysis, design, and prediction, all of which were intensely discussed throughout the workshop, from the lecture room (both in the lectures and extensive discussions) to the halls, IMA offices, and during the walks and meetings surrounding the special evening events (e.g., Guthrie theater outing and US premier screening of Achieving the Unachievable).

The IMA systems group worked hard in the weeks leading up to the workshop to install the software systems. Their effort benefited not only the workshop participants, but will also be beneficial to all subsequent participants to the thematic year, as they will find their workstations equipped with the latest software tools in algebraic geometry.

Here is the input of some of the participants:

This workshop was an extraordinary experience, bringing together the very most prominent researchers in the field. In some cases, ideas for future work that I was already contemplating were solidified and in other cases, new ideas were born. As a result of this workshope, I expect to complete at least two additional projects and begin a new one. I also learned about an application of RNA that I had not considered before, namely in the arena of nanotechnology.

— Debra Knisley

The workshop was a great experience. Being a fundamental (micro)biologist, who is the end-user of computer applications, bioinformatics,etc., it gave me a first-hand glimpse of how such tools are conceived. Thus, it also gave me a perspective of the limitations of present day algorithms. I was able to network with people from diverse backgrounds and I hope to collaborate with/share RNA related expertise for better results.

—Madhan Tirumalai

This workshop was critical for the research of my group. Due to conversations with other participants, I am refining a particular RNA gene finder we are building, and we are developing applications to RNA design.

—Peter Clote