This project aims to use JPL's Spatial Operator Algebra (SOA) computational framework to develop advanced Internal Coordinate Molecular Dynamics (ICMD) techniques, for long-time scale simulation of the dynamics of bio-molecules. The resulting ICMD’s computational complexity would increase linearly with the number of degrees of freedom (which is much more efficient than conventional cubic power ordering).
JPL will develop the GNEIMO algorithms, methodology, and software, for the internal coordinate molecular dynamics of bio-molecular systems. Research areas for this project include algorithm formation, algorithm applications, efficient conformation sampling, and methods and algorithms integration with the NAMD massively parallel molecular dynamics simulation package.
JPL is partnering with the City of Hope to conduct this research.
Abhinandan Jain - Jet Propulsion Laboratory