Quantum Mechanical Fragment Approaches to Molecular Excited-state Dynamics

Abstract:

Electronic excitations correspond to a rearrangement of the electrons in a molecule in response to absorption of electromagnetic radiation, and are important in a wide range of systems of technological and biological interest. One molecule of particular interest is green fluorescent protein (GFP), which has revolutionized many fields of biology due its use in imaging and manipulating organisms at the sub-cellular level. A detailed understanding of the mechanism of GFP’s action, and most importantly, the competing pathways that lead to its irreversible damage, will aid greatly in the development of new fluorescent proteins with improved imaging and lifetime capabilities, and such information can in principle be gleaned from the methods of quantum chemistry. Unfortunately, standard quantum chemistry approaches to electronic excitations and dynamics are much too expensive to apply to entire systems as large as GFP due to their steep computational scaling with the number of electrons. Collaborating with Prof. Xiao He (ECNU & NYU Shanghai), we are working on overcoming this hurdle by developing an efficient linear-scaling quantum mechanical (QM) fragmentation approach to excited-states of proteins like GFP by extending the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method developed by Prof. He. EE-GMFCC is able to treat an entire protein at the quantum mechanical level by recognizing that a protein can be broken down into subunits of amino acid fragments, the energy of which can be computed rapidly and then summed appropriately to find the total energy of the entire protein. Using the Terachem quantum chemistry software package, which Prof. Glover contributes to, the method will be implemented for Graphical Processing Units (GPUs), which allow supercomputer-like performance on consumer-grade computer systems. EE-GMFCC-based excited-state dynamics simulations will be utilized to reveal the nature of electronic states involved in the photodegradation of green fluorescent proteins (GFPs) as well as their reaction pathway. Rational point mutation of GFPs in modulating their photostability will be proposed from first-principles.

NYU Shanghai STEM seminar series is a weekly seminar series on every Wednesday. Please see below schedule of STEM seminar series in 2017 Fall Semester.

• October 11: Gerard Ben Arous, Professor of Mathematics
• October 18: Gus Xia, Assistant Professor of Computer Science
• October 25: Brad Weslake, Associate Professor of Philosophy
• November 1: William Glover, Assistant Professor of Chemistry
• November 8: Chuck Newman, Professor of Mathematics & Vladas Sidorvicius, Professor of Mathematics
• November 15: Tim Byrnes, Assistant Professor of Physics
• November 29: Xing Tian, Assistant Professor of Neural and Cognitive Sciences & Zheng Zhang, Professor of Computer Science
• December 6: Yves Le Jan, Visiting Professor of Mathematics