Public Research Seminar by Advanced Materials Thrust - Coarse-Grained Molecular Dynamics Simulations of The Large-Scale Biomolecular Conformational Dynamics

10:00am - 11:00am
ZOOM (ID: 933 6418 1701; Password: 951229)

Biomolecules, such as proteins and DNA, are soft matter nanoscale machines that maintain the vital activities of the cells. Biomolecules exert function relying on their well-defined three-dimensional structures. The precise measurements and determinations of the structures and the structural changes in biomolecules during the functional processes are the keys to unravel the mysterious relationship between the structure and function. However, these tasks are quite challenging from the experimental aspect. Here, we employed a computational microscope, the so-called molecular dynamics simulation, to explore a wide variety of biomolecular processes, including protein folding, protein-protein/DNA flexible recognition and chromosome structural reorganization. To overcome the limits of the spatial-temporal scales existing in the all-atom simulations, we focused on the coarse-grained modeling strategy. By invoking the statistical energy landscape theory, we developed a series of coarse-grained models and applied them to practical studies. We demonstrated that the large-scale biomolecular conformational dynamics, which may have been underestimated in previous research, should join the play of the elegant structure-function duo in molecular biology.

Event Format
Speakers / Performers:
Dr. Xiakun Chu
Stony Brook University

Dr. Chu obtained his Bachelor’s degree in Department of Physics, Jilin University. Then he stayed in the same department and pursued his PhD degree in theoretical physics under the supervision of Prof. Jin Wang. His PhD thesis mainly focused on using molecular dynamics simulation to assess the energy landscape theory and its applications to study protein binding-folding. After PhD graduation in 2014, he moved to Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, where he performed several practical protein studies. In 2015, he started his first postdoc in IMDEA-Nanoscience Institute in Madrid, Spain, working with Prof. Victor Muñoz, who is a pioneering experimentalist in the fast-folding downhill protein research. In Spain, Dr. Chu focused on studying the conformational mechanisms of downhill proteins and their relations to function from the theoretical perspective and through close collaboration with experiments. In 2018, he moved to US and conducted his second and current postdoc research with his PhD supervisor Prof. Jin Wang at Stony Brook University. At Stony Brook, he expanded his research targets to a different but higher and more complex level than his previous research, including the multi-domain proteins and chromosomes. He has published 21 papers and one book chapter, including 11 papers as first and co-first author on reputable journals, such as PNAS, Applied Physics Reviews, Advanced Science, eLife, etc. He is currently serving as a guest associated editor in Frontiers in Molecular Biosciences journal.

Language
English
Recommended For
Faculty and staff
PG students
UG students
Organizer
Function Hub, HKUST(GZ)
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