ABOUT THIS PROJECT
This project is funded by NSF/SSE (No.5-27425), and focused on the sustainable development of a cutting-edge CG/UCG molecular simulation platform with broad applicability to the fields of chemistry, biology and the materials sciences in accordance with the National Strategic Supercomputing Initiative (e.g. Principle 1, Objective 2), and the Vision and Strategy for Software for Science, Engineering, and Education (NSF 12-113, Strategies 1-4). This software element will integrate our cutting-edge CG and UCG model generation/simulation algorithms into LAMMPS, a community-standard MD platform (see letter of collaboration from Steve Plimpton, the lead LAMMPS developer), and provide a user-driven code/data repository for public dissemination of CG/UCG models and parameters. This project therefore enables the study of sophisticated, dynamic and extremely large-scale molecular systems that were previously inaccessible to the scientific community. By definition, such an undertaking requires the integration of advanced computational techniques with a wide variety of cross-disciplinary and domain-specific knowledge to produce simple, robust and flexible software. The broad scope of CG/UCG models and methodologies strongly implies an open process for software development and model dissemination that responds to the needs of a wide user community: a single research group cannot envision the full range of problems to which these models can be applied.
What is MSCG?
The multiscale coarse-graining (MS-CG) methodology provides a systematic, bottom-up way to calculate effective CG interactions based on rigorous statistical mechanics. It seeks to approximate the many-body potential of mean force by variationally minimizing the difference between CG forces at the mapped fine-grained reference forces (a.k.a, “force matching”). This method is related to liquid state theory and the Yvon-Born-Green equation.
Recent methodological work on MS-CG has included the inclusion of three-body interactions as well as formulations for both the constant NVT and constant NPT ensembles. We have also explored center-of-charge mappings as an alternative to the more traditional center-of-mass and center-of-geometry mappings. MS-CG models have been applied to wide range of systems including common solvents (e.g., methanol, hexane, water, ionic liquids), membrane systems, carbohydrates, polyglutamine aggregation, peptide secondary structures, and larger proteins.
- Benefits to society by allowing researchers to access entire classes of problem with significant scientific and societal interest.
- The novel software we propose will be publically available under a permissive software license, fully documented and provided with example systems.
- Integrating Research and Education while Enhancing Teaching, Training and Learning.
- Dissemination from the provision of the publically accessible wiki platform, including example results from both the core developers and the wider user community.
- Broadening participation of Underrepresented Groups, such as undergraduate students from minority groups to pursue education and careers in the mathematical and natural sciences through the Leadership Alliance
The Voth Group
he research in the Voth Group involves theoretical and computer simulation studies of biomolecular, condensed phase, quantum mechanical, and materials systems. One of our goals is to develop new theory to describe such problems across multiple, connected length and time scales. Another related goal is to develop and apply new computational methods, tied to our multiscale theory, that can explain and predict complex phenomena occurring in these systems. Our methods are developed, for example, to probe protein-protein self-assembly, membrane-protein interactions, biomolecular and liquid state charge transport, complex liquids, self-assembly, and energy conversion materials. Our research is also often carried out in close collaboration with leading experimentalists from around the world. For more information, please visit our group website.