NIC Series Volume 36:   From Computational Biophysics to Systems Biology (CBSB07) Ulrich H. E. Hansmann, Jan Meinke, Sandipan Mohanty, Olav Zimmermann (Editors)   ISBN: 978-3-9810843-2-0 URN: urn:nbn:de:0001-00422 August 2007, 330 pages

PREFACE

In 2007 the John von Neumann Institute for Computing (NIC) celebrates its 20th anniversary. During its two decades of existence, computer simulations have become an invaluable tool for researching biological systems. This was also the topic of the second annual workshop "From Computational Biophysics to Systems Biology" (CBSB07). About 110 researchers and students from all over the world met from May 2nd to May 4th, 2007 at the Research Centre Jülich and discussed physics-based approaches to systems biology. They emphasized the increasing importance of computing in Biology, Medicine and other life sciences. Complex diseases such as cancer or Alzheimer's, to name only two, can be understood only if we obtain an insight in the working of cells on the molecular level. The analysis of the huge amount of experimental data, together with the problem that some processes or molecules cannot be detected in experiments, require the use of simulations. However, the large number of components in a cell, the difficulties in understanding their dynamics, and the complex interactions between them, make such simulations extremely challenging. Problems such as the all-atom simulation of chromatin dynamics or of ribosomes and other supermolecular systems will require access to computers with hundreds of Teraflops. In a "town hall" meeting the participants emphasized the role of supercomputers in obtaining a detailed understanding of the working of cells. They agreed that further progress will require the supercomputer centers to provide both increased computing capacity and improved support and accessibility.

As in the previous year, the participants explored in scientific presentations and numerous informal discussions a wide range of topics ranging from single macromolecules to the working of entire cells. Topics included protein folding, miss-folding and aggregation; the interaction between proteins and other molecules; the assembly of nano-structures, multi-protein, protein-DNA/RNA complexes; and the modeling of cellular systems at a molecular level. This proceeding volume collects selected presentations from the 3-day long workshop that may serve as starting point for further discussions. It is divided into articles by invited speakers and such originally presented as posters or in contributed talks, as the interdisciplinary nature of the articles often defies a simple classification according to subject areas.

Besides the editors, Thomas Neuhaus, Tatjana Eitrich, Everaldo Arashiro, and Xiaolin Xiao helped organizing the workshop. For their most valuable help with the local arrangements we are greatly indebted to Helga Frank, Erika Wittig and Martina Kamps. We also wish to thank IBM for generous support.

Jülich, July 2007

U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann