Discovering the remarkable ability of ribonucleic acid (RNA) molecules to catalyze complex chemical transformations has profoundly impacted our understanding of the role of RNA in biology, the design of new biotechnology and the formulation of theories into the origin of life.

Here at Rutgers, we employ computational techniques to help study RNA including:

• Large-scale atomistic molecular dynamics (MD) simulations, to study the conformational landscape accessible to RNA molecules
• Graphics processing unit (GPU) -accelerated, alchemical-free energy simulations to predict metal ion and co-factor binding and to interpret experimental activity-pH profiles
• Multidimensional ab initio hybrid quantum-mechanical/molecular-mechanical (QM/MM) free-energy simulations to elucidate catalytic pathways in enzymes and ribozymes, predict reaction rates, and explain the origin of chemical modification and mutational effects.

The results of these studies provide new insights into the function of RNA enzymes, insights that can aid in the design of new biotechnology and therapeutics.

Role of Caliburn

Caliburn, with its numerous central processing unit (CPU) nodes and its fast interconnect, provides a critical enabling technology for running our production QM/MM free energy simulations, which typically involve running 20 to 30 jobs that require one node each.