Yang Yang

Professor of Practice
610-758-3676
Seeley G. Mudd, Room 491
Research Interests: 
Theoretical Chemistry
Computational Chemistry
Biophysics/Biochemistry
Biomineralization
Interfacial Chemistry
Biomaterials
Teaching Interests: 
General Chemistry
General Chemistry Lab
Physical Chemistry
Physical Chemistry Lab

Selected Recent Publications:

X. Yang, M. Wang, Y. Yang, B. Cui, Z. Xu, X. Yang, “Physical origin underlying the prenucleation cluster mediated nonclassical nucleation pathways for calcium phosphate”, Phys. Chem. Chem. Phys., 21, 14530-14540, 2019 (Journal Back Cover Feature)

X. Wang, M. Wang, Q. Wei, X. Yang, Y. Yang, B. Cui, X. Yang, Z. Xu, “Modulation of solid-water-peptide interfacial properties towards surface adsorption/bioresistance”, Applied Surface Science, 483, 373-382, 2019

Z. Xu, W. Zhao, Z. Wang, Y. Yang, N. Sahai, “Structure analysis of collagen fibril at atomic-level resolution and its implications for intra-fibrillar transport in bone biomineralization”, Phys. Chem. Chem. Phys., 20, 1513-1523, 2018

Q. Wei, W. Zhao, Y. Yang, B. Cui, Z. Xu, X. Yang, “Method evaluations for adsorption free energy calculations at solid/water interface via metadynamics, umbrella sampling and Jarzynski’s equality”, ChemPhysChem, 19(6):690-702, 2018 (Journal Cover Feature)

S. Sarkar, D. Gandla, Y. Venkatesh, P. R. Bangal, S. Ghosh, Y. Yang, S. Misra, “Graphene quantum dots from graphite by liquid exfoliation showing excitation-independent emission, fluorescence upconversion and delayed fluorescence”, Phys. Chem. Chem. Phys., 18, 21278-21287, 2016

Z. Xu, Y. Yang, W. Zhao, Z. Wang, W. J. Landis, Q. Cui and N. Sahai, “Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues”, Biomaterials, 39, 59-66, 2015

Y. Yang, Z. Xu, Q. Cui, N. Sahai, “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, 2014 (Invited Book Chapter)

W. Zhao, Z. Xu, Y. Yang, N. Sahai, “Surface energetics of the hydroxyapatite nanocrystal-water interface: a molecular dynamics study”, Langmuir, 30(44), 13283-13292, 2014

Z. Xu, Y. Yang, Z. Wang, D. Mkhonto, C. Shang, Z. Liu, Q. Cui, N. Sahai, “Small molecule-mediated control of hydroxyapatite growth: free energy calculations benchmarked to density functional theory”, J. Comp. Chem., 35 (1), 70-81, 2014

Y. Yang, L. Yi, “Theoretical investigations of ferrocene/ferrocenium solvation in imidazolium-based room-temperature ionic liquids”, Phys. Chem. Chem. Phys., 15 (8), 2669-2683, 2013 (Journal Back Cover Feature)

Y. Yang, N. Sahai, C. S. Romanek, S. Chakraborty, “A computational study of Mg2+ dehydration in aqueous solution in the presence of HS- and other monovalent anions—insights to Dolomite Formation”, Geochim. Cosmochim. Acta, 88, 77-87, 2012

Y. Yang, D. Mkhonto, Q. Cui, N. Sahai, “Theoretical study of bone sialoprotein in bone biomineralization”, Cells Tissues Organs, 194, 182-187, 2011 (Special Issue)

Y. Yang, Q. Cui, N. Sahai, “How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations”, Langmuir, 26 (12), 9848-9859, 2010

Y. Yang, R. M. Pitzer, “Er3+ electronic energy levels in GaN”, J. Phys. Chem. A, 114 (26), 7117-7120, 2010

H. Yu, Y. Yang, L. Ma and Q. Cui, “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, 2009 (Invited Book Chapter)

Y. Yang, Q. Cui, “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, 2009 (R. M. Pitzer Festschrift)

Y. Yang, Q. Cui, “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, 2009 (Recommended by Prof. Arieh Warshel, Nobel Laureate in Chemistry 2013, at “Faculty of 1000”)

Y. Yang, H. Yu, D. York, M. Elstner, Q. Cui, “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, 2008

Y. Yang, H. Yu, Q. Cui, “Extensive conformational transitions are required to turn on ATP hydrolysis in myosin”, J. Mol. Biol., 381, 1407-1420, 2008

Y. Yang, H. Yu, D. York, Q. Cui, M. Elstner, “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, 2007

Y. Yang, Q. Cui, “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, 2007 (Letter)

H. Yu, L. Ma, Y. Yang, Q. Cui, “Mechanochemical coupling in the myosin motor domain. II. analysis of critical residues”, PLOS Comput. Biol., 3(2): e23, 0214-0230, 2007

H. Yu, L. Ma, Y. Yang, Q. Cui, “Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations”, PLOS Comput. Biol., 3(2): e21, 0199-0213, 2007

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, “Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes”, J. Phys. Chem. B., 110 (13), 6458-6469, 2006 (Journal Cover Feature)