Session T5: Simplifying Biological Complexity

Statics and dynamics of ecosystems

Understanding an ecological community represents a formidable many-body problem - one has an interacting many-body system with imperfectly known interactions and a wide range of spatial and temporal scales. In tropical forests across the globe, ecologists have been able to measure certain quantities such as the distribution of relative species abundance; the probability that two trees drawn randomly a specified distance apart belong to the same species; and the dynamics of species turnover. A simple analytic framework will be presented for describing the statics and dynamics of ecosystems and its predictions will be benchmarked against observational data. \newline \newline I. Volkov et al., Nature 424, 1035-1037 (2003); Phys. Rev. Lett. 92, 218703 (2004); Nature 438, 658-661 (2005). \newline T. Zillio et al., Phys. Rev. Lett. 95, 098101 (2005). \newline S. Azaele et al., Nature (2006) in press.   

Stretching to Understand Proteins

Mechanical stretching of single proteins has been studied experimentally for about 50 proteins yielding a variety of force patterns and values of the peak forces. We have performed a theoretical survey of 7749 proteins of known native structure and map out the landscape of possible dynamical behaviors unders stretching at constant speed. The model used is constructed based on the native geometry. It is solved by methods of molecular dynamics and validated by comparing the theoretical predictions to experimental results. We characterize the distribution of peak forces and on correlations with the system size and with the structure classification as characterized by the CATH scheme. We identify proteins with the biggest forces and show that they belong to few topology classes. We determine which protein segments act as mechanical clamps and show that, in most cases, they correspond to long stretches of parallel beta-strands, but other mechanisms are also possible. We then consider stretching by fluid flows. We show that unfolding induced by a uniform flow shows a richer behavior than that in the force clamp. The dynamics of unfolding is found to depend strongly on the selection of the amino acid, usually one of the termini, which is anchored. These features offer potentially wider diagnostic tools to investigate structure of proteins compared to experiments based on the atomic force microscopy.