Another Milestone for Computational Chemistry

On October 9, the Nobel Prize in Chemistry 2013 was jointly awarded to Martin Karplus, Michael Levitt and Arieh Warshel “for the development of multiscale models for complex chemical systems.” A New York Times article said the three researchers were awarded the Nobel Prize “for work that did not involve test tubes or lab coats. Instead, they explored the world of molecules virtually, with computers.”

This is another key milestone in the solidification of computational chemistry as an important discipline for current and future researchers.

It has been more than 50 years since the Nobel Prize in Chemistry was awarded to Linus Pauling “for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances.” His achievement was remarkable considering, at that time, there were no computers like the ones we have today.  His pioneering work helped scientists understand the glue that holds atoms together to form molecules. Similar achievement has been accomplished in taking very complicated theoretical concepts and turning them into a program that can be used to look at chemical properties on a computer.

One of the first milestones in recognizing the importance of turning a computer program into an everyday tool that bench chemists can use to complement their experimental work happened in 1998.  Sir John Anthony Pople was a Nobel Prize winning theoretical chemist, and was awarded the Nobel Prize in Chemistry with Walter Kohn in the year 1998.  It recognized their work in advancing the modeling of electronic structures of systems through sophisticated computer models.

Computational chemistry has rapidly evolved over the last 50 years, and has dramatically changed the way research is carried out.  Simply put, computational chemistry has brought computers into the laboratory and as a result computers have expanded our view of the world around us.  These programs allow chemists to have a “computational microscope” to look at the molecular level and accurately visualize molecules and how they fundamentally interact among each other.  Scientists have learned how to turn complex theoretical models such as quantum mechanics, molecular mechanics, classical molecular dynamics and Monte Carlo Simulations methods into sophisticated software programs.  These models, combined with the deep chemical knowledge of the research scientist, now plays a key role in today’s industrial, pharmaceutical or academic laboratory.

The methods pioneered by these Nobel Laureates have been applied to systems ranging from modern semiconductor surfaces to the understanding how the Human Immunodeficiency Virus (HIV) causes acquired immunodeficiency syndrome (AIDS).  One of the models that has been successfully used to study large molecules and the atoms that form molecules is classical molecular dynamics.  The molecules are allowed to move for a certain period of time by numerically solving the Newton’s equations of motion for a system of interacting molecules.  In this model, forces between the molecules and potential energy are defined by molecular mechanics force fields.  The nature of this method has allowed researchers to apply this model to relatively large systems of biological interest.

These pioneering methods are used every day by scientist on computers ranging from laptops to the largest supercomputers. With today’s highly advanced supercomputers, it is now possible to do highly accurate simulations of large systems that were impossible just a few years ago.

At the National Center for Supercomputing Applications at the University of Illinois, a team of researchers used a Cray supercomputer, nicknamed Blue Waters, to complete the highest resolution study of the mechanism of HIV cellular infection.  Their work appeared on the cover of the May 30, 2013 issue of Nature. Their simulations leverage methods develop by the Nobel Prize winners, such as the extensively used CHARMM force field, which was developed by Karplus and his co-workers.

Because of the groundbreaking work of Pople, Kohn, Karplus, Levitt, Warshel and many others, the chemists, biologists and physicists of today are now armed with a widening arsenal of tools to solve problems at the molecular level. New developments in scientific and software algorithms, combined with advancements in supercomputing technologies will be critical in advancing our understanding of our complex world.  We at Cray look forward to being a part of this next step, a “quantum leap” so to speak, toward the frontiers of exascale computing and exascale science.

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