Supercomputing Institute Principal Investigator, Professor Darrin York of the Chemistry Department at
the University of Minnesota, along with his Quantum Modeling and Simulation group are developing and
applying new multi-scale quantum methods to study large biological systems. These efforts include the
design of linear-scaling electronic structure methods that allow large protein and DNA/RNA systems in
solution to be studied with quantum mechanical models. Graduate Researcher Jana Khandogin is working to develop
these methods and apply them to study quantum mechanical electrostatic
potentials and polarization responses of biological macromolecules in solution (Figure 1). These
methods complement ongoing studies in the laboratory led by Graduate Researcher Jill Johnson focused
on metal-ion catalyzed phosphate hydrolysis reactions such as the self-cleavage mechanism of
hammerhead ribozyme (Figure 2) using hybrid quantum mechanical/molecular mechanical methods.
Professor York, together with Supercomputing Institute Research Scholar Dr. Anguang Hu,
have developed integrated multi-level quantum and empirical models that can be used in concert to
construct realistic environments to study important chemical processes. As an example, Figure 3 shows
a (UO2)2+(H2O)4 ion in an aqueous environment. This ion is important from an environmental
perspective and is often found to interact with biomolecules. Heavy metals such as uranium require a
special quantum treatment that includes relativistic effects, because the core electrons are moving at
speeds comparable to the speed of light. The water molecules close to the ion (shown in blue) can be
modeled using less computationally intensive density-functional methods, and the effect of bulk water
(shown in red) can be modeled by a simple molecular mechanical force field. Consequently, modeling
this system in a realistic solvent environment requires the integration of multiple levels of
theoretical treatment, each designed to balance accuracy with system size and combined to provide an
accurate description of a complex environment.
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Figure 3: Multi-level quantum model of a solvated (UO2)2+
(H2O)4 ion. The (UO2)2+(H2O)4
complex was modeled with an all-electron scalar relativistic quantum method, the inner 10 Å shell of
145 waters were modeled with a gradient-corrected density-functional method, and the outer 10-12 Å
shell of 1,154 waters were modeled by a molecular mechanics force field.
(Click the picture for a larger version.)
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