Recent Research News

Linear-scaling Electronic Structure Methods for Biological Macromolecules in Solution

The York Group has recently demonstrated linear scaling for quantum mechanical calculations of biomolecules in solution.  "Linear scaling" means that the costs of the calculations increase as the first power of the size of the system, whereas traditional methods increase as the third or higher power.  The method allows chemical reactions to be studied with a full quantum mechanical description of the entire enzyme in solution (thousands of atoms) using linear-scaling electronic structure theory (Fig. 1).  This method has been combined with a new semiempirical d-orbital specific reaction parameter Hamiltonian for modeling of phosphate hydrolysis reactions that provides accuracy comparable to expensive ab initio methods for less than 1/1000 the computational cost.  These advances lay the groundwork for the application of new hybrid quantum mechanical/molecular mechanical potentials to study reactions of biological macromolecules in solution.

Fig. 1: CPU scaling for linear-scaling semiempirical method for several protein and DNA systems in the gas phase (solid line) and in solution (dotted line).