Mathematics of Molecular and Cellular Biology

The second semester of the 2007–2008 thematic program on Mathematics of Molecular and Cellular Biology kicked-off with a superb and well attended tutorial Mathematics of Proteins, January 10-11, followed by a workshop on Protein Folding, January 14-18.

The tutorial began at 8:50 AM with a welcome by IMA director Doug Arnold, and consisted of talks on fundamental forces and molecular architecture, simulating molecular motion, and simulating protein folding by Michael Levitt, Stanford University. Patrice Koehl of University of California at Davis gave talks on the geometry of biomolecular solvation, Electrostatics,and Protein shape descriptors. There was also an introduction by Bobby Philip, Los Alamos National Laboratory, on multigrid techniques and a discussion of Geometric simulation of protein flexibility by Ileana Streinu.

The tutorial had 76 participants, and gave them an excellent introduction to the research presentations that followed.

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

For a 2-day workshop this was an unexpected success. I learned about successes/failures/directions in computational biology and gained an understanding on how my mathematics can contribute. Made at least one serious and promising new connection.

— Anonymous

The tutorial was very helpful as a preparation to the workshop the following week. In fact, it would be great if every workshop could be preceded by at least one day of tutorial.

— Peter Hinow

The IMA Workshop Protein Folding began on January 14, and ran through noon on Friday, January 18.

The workshop consisted of a mixture of 30-minute talks, and 15-minute talks. some of the highlights of the workshop were the very lively discussions held at the second chances sessions which were held at the end of lectures each day. The workshop had 136 participants.

Algorithmic Dimensionality Reduction for Molecular Structure Analysis' W.M. Brown,
S. Martin, S.N. Pollock,E.A. Coutsias and J.P. Watson, (preprint, 2008).

This was a tremendous experience. I met new people, learned new things, and had a great time. The question and answers that followed the talks were very informative. I liked the way that the organizers wrapped up the discussion at the end of each day and inspired thought about future issues.

—Greg Chirikjian

This workshop was very well designed. Speakers represented both the main thrusts in the filed and new branches, as well as interdisciplinary connections. I learned several new valuable things that I will apply in my work.

—Krzysztof Kuczera

There were 113 participants in this workshop.

I got a better idea of the variety of mathematical approaches to network problems. This was a scientifically broadening experience. I was exposed to systems biology in a coherent manner. I made new contacts both in my field and outside of it. I anticipate a collaboration will result as a consequence of attending this workshop. I learned something new about the application of Baysian nets and about root tips.

— Glenn Edwards

I made a number of new contacts, and it appears will start at least one or two collaborations from these. In particular, I may move into a new area, synthetic biology, that I've found interesting for a while, and at this workshop I met someone who has the skills that I lack in this area, and we plan to do things together in the future.

— Participant

Very good tutorial. Excellent speakers. I learned quite a lot and will probably use the knowledge in my future research.

— Beatrice Riviere

I was a first-time participant, I enjoyed the workshop very much. It allowed me to meet many other researchers (including some luminaries) in person for the first time. In some cases, I expect research collaborations to follow. I learned a lot about different approaches to systems biology, different problems, and datasets that I was not previously aware of. I got the sense that a community is beginning to form. I will definitely consider attending future meetings if invited.

— David Dill

Of all the IMA workshops this semester, the speakers in this one were best able to communicate to applied mathematiicans. Of course, that likely is because many of them themselves are mathematicians who are working on biological applications but even the experimentalists were clear about what they were doing. Put another way, at almost all the other workshops (other than tutorials), I had the sense of a applied discipline community talking mostly to themselves, and mathematicians would try to pick things up by listening in. This workshop communicated much more so within the community of applied mathematics. As such, I learned a good deal about the area. I also had substantial conversation with a couple of the speakers.

—Pete Kramer

The content of the workshop was very focused. As a graduate student, I was able to understand a large portion of the talks, and it gave me a better understanding of the different ways the community is thinking about these problems. These new insights will surely have an impact on the future directions I take in my research. Knowing which aspects of the problem are most important to this community will help me write my thesis in a way that is useful and understandable to others in the field.

— Melissa Vellela

We ended the year with these supporting remarks.

I thought the workshop was fantastic. I learned a lot and have a greater understanding of where the modeling is going. I am already exploring a collaboration with one of the participants (a mathematician). I am a cell biologist so much of the biology was not new for me, However, seeing the models that are being developed gave me many ideas to explore. My major field is neuroscience so all the contact I made were outside my field.

—DiAnna L. Hynds

This was a terrific workshop. I was only there for 2 days due to having an intensive summer school I am treaching at UBC, but the two days were absolutely critical to my future research. I met and had a very productive discussion with John Condeelis that may lead to a collaboration. This oculd not have happened had we not each heard the other's talk at IMA. We worked out essential details at dinner the same day and I am already starting to work on this project.

— Leah Edelstein-Kehset