For the 2007 part of the contract we had scheduled a two-month session covering the period August 12th-2007/October 6th-2007. The aim was to bring together young and experienced researchers interested in the field of statistical biological physics. This is the third event of a series of three, the first one (completed in 2005) devoted to Dynamical Systems, and the second one in 2006 focused on stochastic problems with emphasis on biological problems. All the three events, as planned, took place in the French village of St. Etienne de Tinée, located about 90km north of Nice, in the French Alps.
In 2007 there has been a slight modification in the arrangement: Initially the school (first two weeks) was supposed to be separated from the training period (following two weeks) and the conference (last two weeks). The first two periods were merged, however, there still remained an emphasis on the more scholarly introductory lectures during the first two to three weeks and more specialised talks during the training period. The advantage in this modification was a flexibility in the dates, that allowed us to attract better keynote speakers. Due to the limited size of the community working in biological physics this was a very important step in order to achieve an excellent program of lectures. Further the students still had lectures during the training period, which made them have regular encounters every day and fostered the networking aspect among them. The students also gave short, informal seminars on the topics of their research. Keynote speakers gave the students projects to work on and the students freely chose the project they wanted. The project was to be performed in the intermediate weeks under the supervision of the professors (either in situ or by e-mail). This way it was possible to reach a high level of activity during the whole period. Six of the young researchers were chosen to give talks during the final conference and on the projects they had successfully worked on.
The community in statistical and nonlinear biological physics in Europe is on the forefront of science. Because of the novelty of real interdisciplinary work in the field, the community is, however, rather small. It was a great satisfaction to the participants of the event to see that a huge fraction of the most important European players in the field could be won for participation. This created a series of lectures of rare high quality spanning the whole range of actual application of physical methods to the biological systems outlined in the initial plan (the cytoskeleton and the genetic regulatory networks). All of the speakers made an exceptional effort to be clear and understandable to a large audience. All of the speakers spent at least about a week with the school. Each of them gave about 5 hours of lectures.
Remarkable introductory lectures were given by Ralf Bundschuh (USA) on the statistics of RNA conformations. A lecture by Imre Derényi (Hungary) on the theory of networks with special emphasis on biological networks was an excellent introductory course on the second aspect, the genetic networks. Michael Elbaum (Israel) presenting an experimental view on cellular transport in general with particular emphasis on transport through the cell nuclear pores. Karsten Kruse (Germany) held an impressive introductory lecture on the subject of motor filament systems. This lecture complemented well an introductory lecture by Frank Jülicher, director at the Max Planck Institute for complex systems in Dresden, Germany and scientific coorganiser on molecular transport, which presented links between the Fokker Planck equation, Langevin equation and Onsager relations and from an unusual, nevertheless essential viewpoint. Bertrand Fourcade gave a lecture on cell mechanics, motility and the cytoskeleton, which spanned from fundamental statistical physics to cell molecular aspects. This ensemble of lectures was a solid bases for the more specialized talks, that were given later during the training course. Thomas Duke (GB) gave a thrilling lecture on physical aspects of hearing, opening the series of the more specialized lectures. The more specialized talks were followed by Christian Tischer (Holland) talking about microtubule dynamics and Erwin Frey (Germany) talking about the fundamentals of molecular dynamics simulation and a more specialized aspects how game theoretical problems can be mapped to a Landau Ginzburg equation, a topic of his very recent research. Jean Francois Joanny gave a very involved lecture on active gels, that is filaments such as actin combined with molecular motors. He derived a formalism, which he applied to shape formation of stereocilia, among other topics of present research. Holger Stark gave a lecture on the hydrodynamics at high Reynolds number, a lecture which greatly developed the grounds for Ray Goldstein’s lecture on Volvox and hydrodynamics of collections of bacteria, which had interesting links to aspects of pattern formation. Walter Zimmermann developed further and more general aspects of pattern formation in conjunction with Biology. Michael Lässig taught the basics of the physics of transcription regulator binding and the physics of gene regulation, an aspect of Physics, which is not only important for many bioinformatics applications but can be seen as a basis for the understanding of the evolution of gene regulatory networks. Jacques Prost gave a lecture on fundamental problems posed by Jarsinzky, which still continue to fascinate those, who are interested in thermodynamics. Albrecht Ott gave a lecture resuming experimental results on cell mechanics highlighting the experimental aspects of active gels and a lecture on problems related to DNA microarrays including aspects from information theory and DNA and RNA conformation linked to Ralf Bundschuh’s lecture. Albert Libchaber described recent experimental progress on problems related to RNA in its function as a molecule of the origin of life, which induces amino acid binding. He also talked about bacterial thermotaxis and problems related to molecular biology.
Overall the speakers were asked to give a thorough introduction to each of the lectures. It was a relief to see that the speakers chose complementary introductions and topics. This way a whole repertoire of approaches to active biological materials as well as problems linked to gene transcription and genetic networks were given. These problems gave a good overview on the current state of current edge research on the cytoskeleton and genetic networks.
During the last week, a conference was organized, many established, but still young researchers were invited. The talks were:
K. Kruse: Active Gels
T. Franosch: Suppression of Diffusion by Disorder
E. Bodenschatz: Cardiac Dynamics
E. Bodenschatz: Intracellular Signalling
P. Martin: Hearing
D. Braun: Why DNA moves from hot to cold
H. Isambert: RNA switches
B. Maier: Mechanics and control of molecular motors in living cells
U. Schwarz: How mechanics and biochemistry couple in cell adhesion
J. Berg: Non-equilibrium dynamics of gene expression
M. Falcke: Waiting time distributions for clusters of complex molecules and cells as hierarchical stochastic systems
R. Hermsen: The Logic of Transcription Regulation
H. Isambert: Evolution of biological networks
These talks were accompanied by student talks as explained in the following.
All of the young researchers were asked to give at least one seminar on the subject they had worked on. In practice starting from the third week of the eight week training there was at least one informal seminar given by each student. These seminars often gave rise to a discussion making the seminar last for typically for more than one hour. For every keynote talk, which was not on slides but on the blackboard, two students were asked to take notes, some of the notes are exposed on the PhysBio Website. Among the student lectures, there were among others, Michael Assaf on: “Rare events and modelling using the Schrödinger Equation” and Karin Wolff: “Protein Structure calculation”. Franziska Lautenschläger: “On cell mechanical measurements”, Moritz Kreysing: “On the construction of a fiber based optical tweezer in order to impose controlled rotation on objects held in the trap”. Yung Chin Oei gave a talk on “Microtuble instability”. Sebastian Sanderius gave a talk on “ Computer simulations on networks of viscoelastic elements, that mimic cell elastic behavior”. Christoph Erlenkämper gave an interesting talk on “Microtubule based transport”. Cejkova Jitka on “Pattern formation in Dictiostelium”, A. Czovek on and V. Kubitskkyi on ”Numerical simulations in liquid crystal systems”, Natalia Denisova on “Thermal fields as a function on boundary conditions”. It must be said that all of the reasearchers made a strong effort in delivering their seminar in a clear way.
The keynote lecturers provided about 20 problems for the students to work on. They remained in contact with the students at least per email. These problems varied a lot in subject and difficulty. They spanned from more experimental thinking (such as to give simple possible mechanisms in order to explain a cell mechanical result) to numerical simulations and also very abstract theoretical questions such as coupled oscillators in various conditions. The problems created a good link between the lecturers and the young participants.
During the conference the young reseracher's talks on preliminary results of their work on problems posed to them at the beginning, were particularly well received. There were the talks of Christian Westendorf on”Small scale network regulation”, Andreas Czovek and Moatzadeh Beidokhti on” Motor Filament Systems and a simple model for "RNA-Polymerase Against the Nucleosome" , Katrin Wolff on “RNA glass transitions” and Michael Assaf on “Coupled oscillators”. In spite of the little time, that these young researchers had had, there were already first interesting results to present.
Besides the fact that most participants (students and professors) did have their own laptop computer, we made available (with the help from Nice university) a network of Macintosh computers. These computers were extensively used for the projects and numerical simulations. The computers were completely transparent and two printers were shared by all of them providing network access to printing. Most of the activities took place in the "Salle de Fetes" a large hall belonging to the Town Hall of St. Etienne de Tinée that was large enough to accommodate the conferences. In some cases, the hall was used for non-academic activities, such as movie-showing in the evening. These come-together activities have also been an important ingredient in order to establish the necessary unity within the group. Some excursions in the mountains were also self-organized, helping to increase the human relations between the members of the school. There was a program during every week-end of outdoor activities such as hiking, biking, bus trips and so on as well as a Friday night event. The participants could receive a picknik lunch in order to spend the day in the mountains. During the week there was a common lunch involving seniors and young researchers in order to foster communication. The lectures were taking place in the morning (except for the first two weeks) and the day closed with a seminar at 18h00. This way many of the participants remained in the lecture hall and had discussions on the talks or on the problems they worked on. It was not unusual to find people still working after dinner and even after midnight. As a result of the contact making efforts the group of young researchers got to know each other very well, most of the group met again during the Christmas holidays in Prague. We believe that the event has been very positive, both from the scientific side but also from the personal side of the participants.