Yildirim Lab · Florida Atlantic University
RNA Force Fields
Developing and testing molecular mechanics models for accurate RNA simulations.
Revising RNA Force Fields for Molecular Mechanics Calculations
Accurate simulation of RNA requires models that can reproduce the physical interactions governing RNA structure and dynamics. Quantum mechanical calculations can guide model development, while molecular mechanics force fields make it possible to simulate larger RNA systems over biologically meaningful timescales.
The lab studies the strengths and limitations of widely used simulation models, including AMBER force fields, and works on challenging RNA systems where standard parameters may need refinement.
Key themes: AMBER, torsional parameters, base stacking, noncanonical motifs, RNA duplexes, comparison to experimental observables.
