MRI: Acquisition of a high-performance computer cluster for the computational study of complex chemical systems: from small molecules to biological nanomachines

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The best work in theoretical chemistry combines innovative creation of new mathematical methods, the development of new algorithms for the computational implementation of these methods, and large-scale, computer-intensive simulations on systems of key importance in chemistry in its broadest sense. Excellence in all three of these area characterizes the work of Millard Alexander, John Weeks, Daniel Kosov, Christopher Jarzynski, and Dev Thirumalai of the University of Maryland. Their work covers chemistry and chemical biology in the broadest sense, ranging from including non-adiabatic effects in small molecule dynamics (Alexander), thermodynamic properties of complex systems (Weeks), non-equilibrium electron transport through nanostructuctures and molecules (Kosov), thermodynamic properties of complex systems (Jarzynski), and the mechanism of ribosome assembly (Thirumalai). The principal investigators have already established transformational, forefront research programs in these areas. In addition, several of the principal investigators have contributed to the development of state-of-the-art software packages in their individual areas which are now being used in many research groups external to the University of Maryland. A major challenge in theoretical chemistry and chemical biology is the extension of accurate modeling to systems of larger complexity and dimensionality. The computational resources currently available to the principal investigators are either outdated or oversaturated, and thus have become insufficient for their research and training activities. The present MRI proposal will allow purchase of a new cluster, based on dual-core, multi-cpu server nodes. This insight gained from the proposed research will have potential application in many areas of chemistry and chemical biology, ranging from combustion, to atmospheric chemistry, to complex fluids and interfaces, to current flow in nanomaterials, to the understanding of thermodynamic equilibrium in complex systems and to the functioning of biological nanomachines. All of these areas are of crucial importance to our society as a whole, in particular to the development of cleaner combustion, more efficient lubrication, higher throughput fluid transport, new nano-materials and for a better understanding of fundamental biological transformations. Also, the proposed research will lead to the continued development of theoretical methods and computational codes for accurate, fast simulations in the areas described above, making use of both micro- and macro-parallelization. These codes will be freely distributed to the scientific community at large. In addition, future research scientists undergraduates, graduate students and postdoctoral fellows will be trained in the use of the latest tools in computational chemistry and biophysics and in the development of strategies for efficient use of high-performance, massively parallel computer architectures. These skills are crucial to ensure the technological leadership of the United States.