Proteins and nucleic acids often act like small machines, carrying out functions in the cell such as the synthesis of additional molecules, communication/'signaling' among systems in the cell, and locomotion. Such functions typically involve significant changes to the shapes of the molecules. Computer simulation methodology for studying such molecular motions will be developed in the current project. The new methodology will combine advances in software and hardware. For example, new software is being developed to exploit the 99.9% of computer memory that goes unused in typical current simulations. The importance of this type of research can be understood in terms of biomolecular timescales: although cutting-edge simulations on special computers today can reach the microsecond scale or even beyond for small systems, it is widely appreciated that key biochemical phenomena occur at timescales of even seconds and longer - that is, one million times longer than computational capacity. Until this computing gap is bridged, it will be extremely difficult to systematically study the full range of biomolecular motions which keep cells working.
Broader impacts Besides research, the proposal targets science pedagogy in two ways. First, the principal investigator will prepare a significantly expanded second edition of his textbook, Statistical Physics of Biomolecules: An Introduction. This book is written for modern interdisciplinary graduate students (e.g., in biophysics or computational biology) who come from diverse semi-quantitative backgrounds. It explains the physical principles underlying biomolecular behavior. Second, the principal investigator will target a significant deficiency in modern science education: science writing. A new course and auxiliary web materials will be developed, geared toward modern students saturated with "new media". The complexities of today's world demand that science writing should be both informative and appealing.