Yingjie Wang Kolthoff Hall 63, 207 Pleasant Street SE. Minneapolis, MN 55455

Email: [email protected] Office: 612-625-5325 Cell: 612-860-1634

Summary

An independent and well-trained scientist, with extensive experiences in , multiscale modeling and data science; a fast learner and excellent , with over 6 years experiences in developing commercial and academic packages.

Experiences

2014.10-present: Postdoctoral Scholar in University of Minnesota

Advisors: Dr. Jiali Gao and Dr. Gianluigi Veglia

I. Integrate large-scale MD simulation and NMR/SAXS experiments to study protein kinase A and its oncogenic mutants: apply Markov State Model (MSM), Mutual Information Theory to characterize the conformational dynamics and allostery; perform and Replica-Exchange MD simulation with NMR and SAXS restraints to enhance the conformational sampling efficiency; compare the simulated NMR relaxation and simulated SAXS profile with experiments II. Combine MD simulation, MSM and T-jump 2D IR spectra to study Light Harvesting Complex II (LHC-II), focusing on the temperature effect on protein conformation and water-exchange dynamics. III. Design fuzzy logic and genetic algorithm to assign methyl side-chain groups from NMR spectroscopy

2011.11-2014.8: Scientific programmer in Inc.

Independent developers in deriving and implementing several QM and QM/MM schemes in Gaussian Developmental Version software package:

o Multilevel explicit polarization (X-Pol) method, an efficient and accurate fragment-based quantum mechanical potential suitable for biomolecular modeling o Block localized density functional theory (BLDFT), a well-defined form of constrained DFT, widely applied to intermolecular interaction energy decomposition analysis o Projected hybrid orbital (PHO) scheme, a general scheme in splitting covalent boundaries at the QM/MM and QM/QM interfaces

Yingjie Wang, Ph.D. Page 1 2009.9-2014.8: Research Assistant in Computational Chemistry (University of Minnesota)

o Maintain, update and parallelize X-Pol, BLDFT in the locally modified GAMESS and CHARMM software packages. o Develop QM/MM methods in CHARMM to investigate the effects of protein dynamics on enzymatic processes, focusing on proton-coupled electron transfer mechanisms of histone lysine demethylases. o Assemble shell scripts and Python to build the database and devise the genetic- algorithm parameterization on the polarized molecular orbital (PMO) method, a semiempirical model with major improvement in describing polarizability.

Education

University of Minnesota Minneapolis, MN

• Ph.D., Chemical Physics, August 2014, GPA 3.86 o Program: Top 5 nationwide o Advisor: Dr. Jiali Gao (Credited for making important contributions in the 2013 Chemistry Nobel Prize Scientific Citation) o Research: Develop Fragment-based QM and QM/MM Schemes • M.S., Chemical Physics, May 2011, GPA 3.85

Nanjing University Nanjing, China

• B.S. , Analytical Chemistry, June 2009, GPA 3.60

Computer Skills

Programming Language: Python, , Java, Shell Scripts, R

Mathematics & Statistics: Numerical Analysis, Matlab, Statistical Learning

Chemistry& Biophysics: GAUSSIAN, GAMESS, CHARMM, GROMACS, PLUMED, VMD, PYMOL

Presentations

1. “ General Implementation of Explicit Polarization (X-POL) Method in Gaussian09,” Yingjie Wang and Jiali Gao, The 243th ACS national meeting, San Diego, March 2012, Oral Presentation

2. “ Fragment-based Variational Many-body Expansion Method,” Yingjie Wang and Jiali Gao, Midwest Theoretical Chemistry Conference, Madison, June 2012, Poster

Yingjie Wang, Ph.D. Page 2 Publications

[1] A. Cembran, P. Bao, Y. Wang, L. Song, D. G. Truhlar, and J. Gao.“On the Intrafragment Exchange in the X-Pol Method.” Journal of Chemical Theory and Computation. 2010, 6, 2469

[2] Y. Wang, . Sosa, A. Cembran, D. G. Truhlar, and J. Gao.“Multilevel X-Pol: A Fragment-based Method with Mixed Quantum Mechanical Representations of Different Fragments.” Journal of Physical Chemistry B.2012, 116, 6781

[3] J. Gao, Y. Wang.“Variational Many-Body Expansion: Accounting for Exchange Repulsion, Charge Delocalization, and Dispersion in the Fragment-based X-Pol Method.” Journal of Chemical Physics. 2012, 136, 071101

[4] M. Isegawa, L. Fiedler, H. R. Leverentz, Y. Wang, S. Nachimuthu, J. Gao, and D. G. Truhlar. “Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry.” Journal of Chemical Theory and Computation. 2013, 9, 33

[5] Y. Wang, M. Liu, and J. Gao. “An ab initio Force Field for Biomacromolecular Simulation: The Explicit Polarization (X-Pol) Model.” Journal of Molecular Science (Chinese). 2013, 6, 80.

[6] M. Liu, Y. Wang, Y. Chen, M. J. Field, and J. Gao. “QM/MM Through the 1990s: The First Twenty Years of Method Development and Applications.” Israel Journal of Chemistry. 2014, 54, 1250

[7] J. Gao, D. G. Truhlar, Y. Wang, M. Mazack, P. Löffler, M. Provorse, and P. Rehak. “ Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields.” Account of Chemical Research, 2014, 47, 2837.

[8] Y. Wang, and J. Gao, “Projected Hybrid Orbitals: A General QM/MM Method.” Journal of Physical Chemistry B. 2015, 119, 1213.

[9] Y. Wang, M. J. M. Mazack, D. G. Truhlar, and J. Gao, “ Explicit Polarization Theory”, in Many-Body Effects and Electrostatics in Biomolecules, edited by Q.Cui,, M. Meuwyl, and P. Ren (Springer Verlag), In Press

[10] J. Kim, Y. Wang, G. Li, and G. Veglia. “Labeling and Assignment of Methyl Side- Chain Groups in Large Proteins.” Methods in Enzymology Review. 2015,

[11] Y. Wang, A. Karamafrooz, J. Hall, J. Gao, S.M. Simon, S.S. Talyor, G.Veglia, "Elongation of the DnaJ appendix in the DnaJ-Chimera induces conformational changes in the catalytic cores of protein kinase A." To be submitted.

Yingjie Wang, Ph.D. Page 3