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Research Highlights

Femtobiology & Femtochemistry | 4D Microscopy & Diffraction | Video

Computational

Theoretical

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 (see abstracts below), and the ensemble convergence can be achieved at increasingly longer time scales.

Beowulf supercomputer cluster at our laboratory currently features 32 dual quad-core E5345 Intel Xeon compute nodes (Dell Power Edge 1950/2950), 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 [PPS handout]. 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.

Selected Publications

Dominance of misfolded intermediates in the dynamics of α-helix folding, M. M. Lin, D. Shorokhov, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2014, 111, 14424-14429.
[Web link] [Abstract] [Top of page]



Structural dynamics of free proteins in diffraction, M. M. Lin, D. Shorokhov, A. H. Zewail, J. Am. Chem. Soc. 2011, 133, 17072-17086.
[Web link] [Abstract] [Top of page]



Structural ultrafast dynamics of macromolecules: Diffraction of free DNA and effect of hydration, M. M. Lin, D. Shorokhov, A. H. Zewail, Phys. Chem. Chem. Phys. 2009, 11, 10619-10632.
[Web link] [Abstract] [Top of page]



Conformations and coherences in structure determination by ultrafast electron diffraction, M. M. Lin, D. Shorokhov, A. H. Zewail, J. Phys. Chem. A 2009, 113, 4075-4093.
[Web link] [Abstract] [Top of page]



Unfolding and melting of DNA (RNA) hairpins: The concept of structure-specific 2D dynamic landscapes, M. M. Lin, L. Meinhold, D. Shorokhov, A. H. Zewail, Chem. Phys. Phys. Chem. 2008, 10, 4227-4239.
[Web link] [Abstract] [Video] [Top of page]



Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation, L. Meinhold, J. C. Smith, A. Kitao, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2007, 104, 17261-17265.
[Web link] [Abstract] [Top of page]



Helix-to-coil transitions in proteins: Helicity resonance in ultrafast electron diffraction, M. M. Lin, D. Shorokhov, A. H. Zewail, Chem. Phys. Lett. 2006, 420, 1-7.
[Web link] [Abstract] [Top of page]