College of Arts and Sciences

Education:

• PhD, Chemistry, University of Wisconsin-Madison
• MS, Chemistry, The Ohio State University
• BS, Chemistry, Nankai University, China

Research Interests:

• Theoretical Chemistry
• Computational Chemistry
• Chemistry Education
• Biochemistry/Biophysics
• Biomineralization
• Interfacial Chemistry
• Materials Science

Bio:

Dr. Yang Yang obtained his Ph.D. in Theoretical Chemistry from the Department of Chemistry of the University of Wisconsin-Madison (UW-Madison) under the mentorship of Prof. Qiang Cui. Afterwards, he had a joint postdoctoral training at NASA Astrobiology Institute, Department of Geoscience, and Department of Chemistry of UW-Madison under the supervisions of Profs. Nita Sahai and Qiang Cui. Dr. Yang’s research focuses on understanding (bio)molecular behaviors with theoretical and computational approaches, specifically enzymatic catalysis studies with Quantum Mechanical/Molecular Mechanical (QM/MM) methods, explorations of biomineralization processes such as organic-mediated crystal nucleation and growth, (bio)molecular interactions with minerals and biomaterials, rational drug designs with bioinformatics and physics-based approaches, and investigations on structures of aqueous solutions and ionic liquids at the electronic structure level. Dr. Yang has contributed over 130 publications, conference presentations, and seminars/talks. He published his research discoveries on Journal of Chemical Theory and Computation, Journal of Physical Chemistry, Journal of Molecular Biology, Biomaterials, Geochimica et Cosmochimica Acta, Langmuir, PLOS Computational Biology, Applied Surface Science, Physical Chemistry Chemical Physics, Journal of Computational Chemistry, and so on.

Dr. Yang loves teaching and is keen to share his understanding of chemistry with students. Prior to joining Drexel, Dr. Yang served as an Assistant Professor (Principal Investigator) at Rowan University and a Professor of Practice at Lehigh University. He has taught over 30 chemistry courses, ranging from introductory general chemistry to advanced graduate-level classes across 5 U.S. institutions, including UW-Madison, Haverford College, and The Ohio State University. Dr. Yang treasures the privilege of his dual role as a chemistry faculty, adventuring in the molecular world and elucidating its beauty and logic to his students, the community, and the general public.

Selected Publications:

• Y. Yang, Z. Xu, Q. Cui, N. Sahai (2014) “Molecular simulation of biomineral nucleation and crystal growth: modern computational challenges and approaches”, Biomineralization Sourcebook: Characterization of Biominerals and Biomimetic Materials, Eds. L. Gower and E. DiMasi, CRC Press, Taylor and Francis Group (Invited Book Chapter)
• H. Yu, Y. Yang, L. Ma and Q. Cui (2009) “Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain”, Proteins Energy, Heat and Signal Flow, Eds. D. M. Leitner and J. E. Straub, CRC Press, Taylor and Francis Group (Invited Book Chapter)

• X. Yang, M. Wang, Y. Yang, B. Cui, Z. Xu, X. Yang (2019) “Physical origin underlying the prenucleation cluster mediated nonclassical nucleation pathways for calcium phosphate”, Phys. Chem. Chem. Phys., 21, 14530-14540 (Journal Back Cover Feature)
• Q. Wei, W. Zhao, Y. Yang, B. Cui, Z. Xu, X. Yang (2018) “Method evaluations for adsorption free energy calculations at solid/water interface via metadynamics, umbrella sampling and Jarzynski’s equality”, ChemPhysChem. 19(6):690-702 (Journal Cover Feature)
  
• S. Sarkar, D. Gandla, Y. Venkatesh, P. R. Bangal, S. Ghosh, Y. Yang, S. Misra (2016), “Graphene quantum dots from graphite by liquid exfoliation showing excitation-independent emission, fluorescence upconversion and delayed fluorescence”, Phys. Chem. Chem. Phys., 18, 21278-21287 (over 100 citations)
• Z. Xu, Y. Yang, W. Zhao, Z. Wang, W. J. Landis, Q. Cui and N. Sahai (2015) “Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues”, Biomaterials, 39, 59-66 (over 100 citations)
• Y. Yang, L. Yi (2013) “Theoretical investigations of ferrocene/ferrocenium solvation in imidazolium-based room-temperature ionic liquids”, Phys. Chem. Chem. Phys., 15 (8), 2669-2683 (Journal Back Cover Feature)
• Y. Yang, Q. Cui, N. Sahai (2010) “How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations”, Langmuir, 26 (12), 9848-9859 (over 100 citation)
• Y. Yang, Q. Cui (2009) “The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state”, J. Phys. Chem. A, 113 (45), 12439-12446 (Russell M. Pitzer Festschrift)
• Y. Yang, Q. Cui (2009) “Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol”, J. Phys. Chem. B, 113 (14), 4930-4939 (Recommended by Prof. Arieh Warshel, Nobel Laureate in Chemistry 2013, at “Faculty of 1000”)
• Y. Yang, H. Yu, D. York, M. Elstner, Q. Cui (2008) “Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. parameterization”, J. Chem. Theo. Comp., 4 (20), 2067-2084 (over 100 citations)
• Y. Yang, H. Yu, Q. Cui (2008) “Extensive conformational transitions are required to turn on ATP hydrolysis in myosin”, J. Mol. Biol., 381, 1407-1420.
• Y. Yang, H. Yu, D. York, Q. Cui, M. Elstner (2007), “Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction”, J. Phys. Chem. A, 111 (42), 10861-10873 (over 300 citations)
• Y. Yang, Q. Cui (2007) “Interactions between phosphate and water in solution: a natural bond orbital based analysis in a QM/MM framework”, J. Phys. Chem. B., 111 (16), 3999-4002 (Letter)
• D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Koenig, G. Li, D. Xu, H. Guo, M. Elstner, Q. Cui (2006) “Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes”, J. Phys. Chem. B., 110 (13), 6458-6469 (Journal Cover Feature, over 300 citations)