Scope and Examples

Future Directions

Potential applications of HPC methods in UST research include MC sampling, joint MD-QC simulations, crystal-structure and band-structure calculations, and electron density analysis. Due to the complex nature of the transitional phenomena under study, experiment and theory often have to go hand in hand in unraveling details of the microscopic forces involved. Computational power of the cluster can also be used to increase both speed and accuracy of data acquisition by aiding experimental developments in many ways. Flexibility, expandability, and scalability of Beowulf architecture are expected to provide a solid ground for further experimental and theoretical developments at UST.

Selected Publications

• Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation, L. Meinhold, J. C. Smith, A. Kitao and A. H. Zewail, Proc. Natl. Acad. Sci. USA, 104, 17261-17265 (2007).

• Unfolding and melting of DNA (RNA) hairpins: The concept of structure-specific 2D dynamic landscapes, M. M. Lin, L. Meinhold, D. Shorokhov, and A. H. Zewail, Phys. Chem. Chem. Phys., DOI: 10.1039/b804675c (2008).

• 4D electron imaging: Principles and perspectives, D. Shorokhov and A. H. Zewail, Phys. Chem. Chem. Phys., 10, 2879-2893 (2008).

Overview Benchmarks

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As the performance of computers increases, theoretical methods continue to improve the prediction and rationalization, not only of gas-phase molecular structures, but also of molecular dynamics and chemical kinetics of complex systems. With our newly-designed supercomputer cluster we are now poised to explore ultrafast non-equilibrium dynamics of complex energy landscapes pertinent to physical, chemical, and biological processes. The structure interconversions which involve multiple degrees of freedom, such as conformational changes in biological macromolecules, can now be modeled, and the ensemble convergence can be achieved at increasingly longer time scales.

An example of such capability comes from our studies of the free energy landscape of a protein. An invariant description of the landscape is incomplete because fluctuations in volume, and thus in pressure, are inevitably present on the molecular length scale. To examine the impact of microscopic statistical pressure fluctuations on both the topology and the dissipation characteristics of the landscape, ns MD simulations of hen egg white lysozyme were recently carried out in this laboratory. In our simulations we investigated the dynamics of individual atoms, averaged over the whole ensemble present in the protein, thus obtaining a mean-field measure for the "local" energy landscape explored by a single atom. With the effect of anharmonic (and also solvent) dynamics implicitly included in all mode variables, the free energy landscape was further reexamined with the focus redirected to the characterization of collective dynamics. Importantly, the results suggest that the traditional, static view of a protein energy landscape should be subsumed by a fluctuating picture, and that this can potentially have functional consequences.

In order to assess the performance of our cluster, we carried out distributed (black solid line) and parallel MD simulations of unfolding dynamics of a benchmark 5’-ATCCTA-X4-TAGGAT-3’ DNA hairpin. As evidenced by the above Figure, the parallel performance of the cluster degrades significantly with the increasing number of nodes and/or CPU cores involved. However, parallel calculations have always been and remain the method of choice for large systems.

UST Supercomputer Cluster ns/day

Another area of focus at UST is that of experimental and theoretical studies of folding-unfolding dynamics. Even for a small macromolecule the complexity of the energy landscape demands these new tools of computations. Stimulated by recent observations of collapsed intermediate states for a DNA hairpin, we performed extensive MD simulations on a similar, benchmark hairpin macro-molecule. But, concurrently, we developed an analytical model of hairpin unzipping based on tabulated pairing-stacking thermodynamic parameters and loop entropy. After verifying assumptions and predictions of the model via ensemble-convergent MD simulations on the benchmark hairpin, the model was used to determine base-pairing structures of intermediates in DNA (un)folding.

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Beowulf supercomputer cluster at UST currently features 32 dual quad-core E5345 Intel Xeon compute nodes, 12 GB RAM/node, ~20 TB of network-attached disk storage, an LTO-3 tape library for easy backups, and a 1 GigE interconnection mesh. Linux-based software structure of the cluster provides an efficient control of system resources which facilitates both distributed and parallel calculations. System health and functionality are maintained and constantly monitored by HPC crew of Caltech’s IMSS. Hardware framework of the cluster can be easily expanded to accommodate up to four 42U racks fully loaded with computer equipment.

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