Objectives of proposal

In summary, these are the objectives of the proposal:

1. Multiscale algorithms for molecular dynamics of large biological molecules. These algorithms will overcome some of the limitations of current atomistic simulation methodologies. They will allow longer time steps using multiple time stepping by overcoming stability barriers using mollified MTS integrators and semi-implicit methods.

2. Scalable biased hybrid Monte Carlo algorithms for statistical sampling. They will retain efficiency as the system size grows. These methods will be tested first in small systems, and then tried in large biomolecular systems.
3. Dissemination of methods and software for research and educational purposes, through a scalable and user-friendly software infrastructure called PROTOMOL. It will be file compatible with popular MD programs such as AMBER [95], CHARMM [12], NAMD [53]. It is not their direct competitor, but rather a powerful complementary tool.

4. Collaborative applications of these methods and software in the context of the study of ion channels dynamics and functions, and the effectiveness of anti breast cancer drugs. This will facilitate interdisciplinary supervision of students and junior researchers at all levels, undergraduate, graduate, and postdoctoral, and helping all of these enter the field of biomolecular modeling. This proposal will not directly fund these collaborative subprojects, but they are closely connected to the overall goals of the project.