This award will enable an international collaboration for software development in computational chemistry between researchers in the United States and the United Kingdom. This international collaboration arose from a joint NSF/EPSRC workshop on Software Development for Grand Challenges in the Chemical Sciences held in Oxford, United Kingdom in June 2011. This award will provide travel for project team members to attend plenary and planning meetings, and for exchange visits to catalyze initial subprojects. The project will lead to the develop of new software capabilities for the study of protein systems across multiple resolutions. The collaboration will include the sharing of large datasets and the development of computational infrastructure for controlling simulations. Outcomes of this award will include software for computational chemistry and improved international collaboration in support of sustainable software for science and engineering. Interdisciplinary training of young researchers is an important consideration for this work.
The understanding of cooperative processes in biomolecular systems (such as protein dynamics, folding, and self-assembly) poses outstanding challenges both for theory and experiment. The definition and identification of global, collective variable to describe and charcaterize these systems is still an outstanding problem in and beyond molecular biophysics. Advancements on this front could allow to extract the essential information from a complex biomolecular system, partition it in time and space, and integrate the different levels of resolution to understand biological function at the molecular level. During the last decade, different groups in UK and US have worked on different aspects of this problem, proposing new theoretical tools, practical approaches, and computational algorithms. The goal of this grant was to support the exchange between these researchers to initiate new collaborations on this problem. Two meetings were supported by this grant, the first one in Nottingham, UK, and the second one at Rice University in Houston, TX. All the researchers involved in this grant presented at these meetings. Several different collaborative projects started as a result of the exchange supported by this grant. The main outcome of these collaborations has been the packaging and release of a new software, LSDMap, to define collective variables from molecular simulation data. The software is now available to the community via SourceForge: http://sourceforge.net/projects/lsdmap/. Additional results from the collaborations are still very preliminary have been used as the starting point for a NSF-SI2 grant proposal that has been recently submitted by a subgroup of the researchers involved in this grant. The main findings emerging from these collaborations concern the possibility of using collective coordinates to enhance the sampling of complex macromolecular systems. Both the mathematical foundation and the practical implementation of these ideas are under current investigation.
