Darrin M. York, Principal Investigator

New Methods for Molecular Simulation and Quantum Mechanical Studies of Biomolecules

This research group designs and applies new computational methods to study biomolecules in aqueous solution. Their particular focus is on four main areas:

• Molecular simulation
• Combined quantum mechanical/molecular mechanical (QM/MM) methods
• Linear-scaling electronic structure methods
• A new density functional theory-based many-body force field

The methods target one of the most challenging areas of computational biochemistry: the accurate atomic-level modeling of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and their interactions with metal ions. Systems of particular interest are the hammerhead ribosome, a small self-cleaving RNA catalyzed by bound Mg2+ ions. To study the reaction using accurate hybrid QM/MM methods, the group has proposed a new semi-empirical d-orbital specific reaction parameter Hamiltonian. Moreover, they introduced new quantum indices for macromolecular characterization using linear-scaling electronic structure methods applied to DNA and RNA systems. Finally, the group is performing density-functional calculations of electronic polarizabilities of biological molecules and secondary structural motifs in order to create a benchmark data set for the design of new polarizable force field models.

Research Group

Vanessa Audette, Graduate Student Researcher
Timothy Giese, Graduate Student Researcher
Brent Gregersen, Graduate Student Researcher
Anguang Hu, Supercomputing Institute Research Scholar
Jill Johnson, Graduate Student Researcher
Jana Khandogin, Graduate Student Researcher
Xabier Lopez, Supercomputing Institute Research Scholar
Evelyn Mayaan, Graduate Student Researcher
Kwamgho Nam, Graduate Student Researcher
Peter Oman, Undergraduate Student Researcher
Kevin Range, Graduate Student Researcher
Helen Smagin, Undergraduate Student Researcher
Jack T. Surek, Graduate Student Researcher
Zeb Thomas, Staff
Sacha Zlatkova, Staff