I am a materials scientist with a research background in solid state chemistry, condensed matter physics, pharmaceutical sciences and data science. My research focuses on applying synchrotron X-ray techniques to the study functional materials. Specifically, I have expertise in synchrotron X-ray total scattering/pair distribution functions (PDF) and inelastic X-ray scattering for probing the local structure and dynamics of materials. I also have considerable experience in small angle X-ray scattering and X-ray fluorescence imaging. The materials systems of interest span from inorganic nanoscale materials to organic crystalline/amorphous pharmaceutical compounds. In addition to experimentation, I am interested in the computer-assisted design and discovery of novel materials with advanced computing algorithms. I have written and published two software programs JRgui and xINTERPDF (more details see the CODES tab).

Class of 2015

Dr. Chenyang Shi

Department of Applied Physics and Applied Mathematics

Columbia University

Education

  1. Georgia Institute of Technology, Atlanta, 2018-2019 (expected)
    M.S., Computer Science, specialized in Machine Learning
  2. Columbia University, New York, NY, 2015
    Ph.D., Materials Science,
    Thesis: Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering
  3. Chinese Academy of Sciences, Beijing, 2011
    M.S., Materials Science,
    Thesis: A study on structure-property relationship in functional electronic ceramics
  4. Tongji University, Shanghai, 2008
    B.S.E., Materials Science and Engineering, minors in German and Japanese

Academic awards and fellowships

  1. 2015 Chinese Government Award for Outstanding Self-Financed Students Abroad
  2. 2014 Engineering Graduate Student Council Scholarship, Columbia University
  3. 2014 Poster Session Award, NSLS/NSLS-II and CFN Users' Meeting, Brookhaven
  4. 2012-2014 Energy Frontier Research Center Fellow, Columbia University
  5. 2011 President's Award, Chinese Academy of Sciences
  6. 2008 Excellent undergraduate thesis, Tongji University

Research

    Determination of onset of polymer-drug separation in ASDs (Jan. 2017 – present)

  1. Using in situ X-ray fluorescence imaging technique to determine the onset time for amorphous-amorphous phase separation (AAPS) in ritonavir-copovidone amorphous solid dispersion (ASD). This study is the first of its kind, and provides important guidance for rational formulations of ASDs, which are currently at the center of pharmaceutical research.
  2. Class of 2015

    Prediction of aqueous solubility of drug-like molecules (Jan. 2017 – present)

  3. Using group contribution methods to ab initio predict physical properties of drug-like small molecules. A graphical user interface software program JRgui was written that implements Joback & Reid method for property prediction.(JRgui program can be downloaded from https://github.com/curieshicy/JRgui)
  4. Using machine learning and deep learning algorithms to effectively predict properties of drug-like molecules through data-mining of large compiled datasets.
  5. Class of 2015

    Study of structures of crystalline and amorphous pharmaceuticals (Oct. 2015 – present)

  6. Developed and released xINTERPDF (hosted at https://github.com/curieshicy/xINTERPDF): a GUI program to extract structural information from measured X-ray pair distribution function (PDF) data for organic materials
  7. Class of 2015
  8. Synchrotron X-ray total scattering data were collected on mefenamic acid precipitated from various polymer solutions including PVP, PEG and HPMC. A novel methodology was developed to access the packing disorders in organic pharmaceutical compounds
  9. For the first time, the robust X-ray total scattering signals in transmission mode were collected on 130 micron thick indomethacin thin film deposited on the borosilicate glass substrate of equal thickness.
  10. A methodology was developed to extract X-ray scattering signal for intermolecular correlation in amorphous/crystalline organic compounds.
  11. Class of 2015

    Study of local structure and lattice dynamics of nanoparticles (Sep. 2011–Aug. 2015)

  12. X-ray total scattering experiment in combination with atomic pair distribution function (PDF) technique were applied to investigate the local structure of various technologically relevant nanoparticles (NPs) ranging from carbon supported platinum NPs, emerging two-dimensional Ti3C2, Nb4C3 MXene materials, zirconium based ion exchangers through Co, Ni and Mn based water splitting catalysts to ferroelectric BaTiO3 and metallic ferrite NPs.
  13. Class of 2015
  14. Small angle X-ray scattering and PDF techniques were combined in a "complex modeling" to obtain robust morphological and structural parameters of CdS NPs.
  15. Class of 2015
  16. For the first time we directly mapped out the phonon density of states of three quantized grown “magic size” CdSe nanoclusters using HERIX technique at Argonne National Laboratory. Theoretically lattice dynamics was investigated by empirical force field calculation and ab initio DFT.
  17. Class of 2015

    Structure-property correlation of functional ceramics (Sep. 2008 –Jul. 2011)

  18. Structural, magnetic and dielectric properties of a wide variety of functional ceramics systems were investigated including modified multiferroics BiFeO3, Ca doped La2NiO4, Nd2NiMnO6 and colossal dielectrics Ca2TiMnO6.
  19. Class of 2015

Publication(Google Scholar)

  1. Chenyang Shi, Luxi Li, Thomas B. Borchardt and Geoff G. Z. Zhang, “Direct visualization of drug-polymer phase separation in ritonavir-copovidone amorphous solid dispersion thin film via in situ synchrotron X-ray fluorescence imaging”, submitted to J. Am. Chem. Soc.
  2. Chenyang Shi, Yan Li, Alexander N. Beecher, Bogdan M. Leu, Ayman Said, Michael Y. Hu, Jonathan S. Owen and Simon J. L. Billinge, “Size-dependent lattice dynamics of atomically precise cadmium selenide quantum dots”, Phys. Rev. Lett., 122 (2019) 026101. (Link)
  3. Chenyang Shi, “xINTERPDF: a graphical user interface for analyzing intermolecular pair distribution functions in organic compounds from X-ray total scattering data”, J. Appl. Cryst., 51 (2018) 1498-1499.(Link)
  4. Casey N. Brodsky, D. Kwabena Bediako, Chenyang Shi, Thomas P. Keane, Cyrille Costentin, Simon J. L. Billinge, and Daniel G. Nocera, “Proton–electron conductivity in thin films of a cobalt–oxygen evolving catalyst”, ACS Appl. Energy Mater., (2018) https://doi.org/10.1021/acsaem.8b00785.(Link)
  5. Chengbin Huang, Zhenxuan Chen, Yue Gui, Chenyang Shi, Geoff Zhang and Lian Yu, “Crystal nucleation rates in glass-forming molecular liquids: D-sorbitol, D-arabitol, D-xylitol, and glycerol”, J. Chem. Phys., 149 (2018) 054503. (Selected as Editor's Pick) (Link)
  6. Chenyang Shi, Simon J. L. Billinge, Eric Puma, Sun Hwi Bang, Nate Bean, J. C. de Sugny, Robert G. Gambee, Richard C. Haskell, Adrian Hightower and Todd C. Monson, “Barium titanate nanoparticles: short-range lattice distortions with long-range cubic order”, Phys. Rev. B, 98 (2018) 085421.(Link)
  7. Chenyang Shi and Thomas B. Borchardt, “JRgui: A Python program of Joback and Reid method”, ACS Omega, 2(12) (2017) 8682–8688. (Link)
  8. Maxwell W. Terban*, Chenyang Shi*, Rita Silbernagel, Abraham Clearfield and Simon J. L. Billinge, “The structure of layered nanocrystalline zirconium phosphonate-phosphate ion exchange materials and intercalation environment of Tb3+”, Inorg. Chem. 56(15) (2017) 8837-8846. (*co-first authors) (Link)
  9. Chenyang Shi, Rattavut Teerakapibal, Lian Yu, and Geoff G. Z. Zhang, “Pair distribution functions of amorphous organic thin films determined by synchrotron X-ray scattering in transmission mode”, IUCrJ, 4 (2017) 555-559. (Link)
  10. Babak Anasori, Chenyang Shi, Eun Ju Moon, Yu Xie, Cooper A. Voigt, Paul R. C. Kent, Steven J. May, Simon J. L. Billinge, Michel W. Barsoum and Yury Gogotsi, “Control of electronic properties of 2D carbides (MXenes) by manipulating their transition metal layers”, Nanoscale Horiz., 1 (2016) 227-234. (Selected as Journal Cover) (Link)
  11. Chenyang Shi, “Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering”, PhD Dissertation, (2015). (Link)
  12. Michael Huynh, Chenyang Shi, Simon J. L. Billinge and Daniel G. Nocera, “The nature of activated manganese oxide for oxygen evolution”, J. Am. Chem. Soc., 137 (2015) 14887-14904. (Link)
  13. Amanda L. Tiano, Georgia C. Papaefthymiou, Crystal S. Lewis, Jinkyu Han, Cheng Zhang, Qiang Li, Chenyang Shi, Milinda Abeykoon, Simon J. L. Billinge, Eric Stach, Justin Thomas, Kevin Guerrero, Pablo Munayco, Jimmy Munayco, Rosa B. Scorzelli, Philip Burnham, Arthur J. Viescas and Stanislaus S. Wong, “Correlating size and composition-dependent effects with magnetic, Mössbauer, and pair distribution function measurements in a family of catalytically active ferrite nanoparticles.” Chem. Mater., 27 (2015) 3572-3592. (Link)
  14. Chenyang Shi., Majid Beidaghi, Michael Naguib, Olha Mashtalir, Yury Gogotsi and Simon J. L. Billinge, “Structure of nanocrystalline Ti3C2 MXene using atomic pair distribution function.” Phys. Rev. Lett., 112 (2014) 125501. (Link)
  15. Michael Ghidiu, Michael Naguib, Chenyang Shi, Olha Mashtalir, L. M. Pan, B. Zhang, J. Yang, Yury Gogotsi, Simon J. L. Billinge and Michel W. Barsoum, “Synthesis and characterization of two-dimensional Nb4C3 (MXene).” Chem. Comm., 50 (2014) 9517-9520. (Link)
  16. Christopher L. Farrow, Chenyang Shi, Pavol Juhas, Xiaogang Peng and Simon J. L. Billinge, “Robust structure and morphology parameters for CdS nanoparticles by combining small-angle x-ray scattering and atomic pair distribution function data in a complex modeling framework.” J. Appl. Cryst., 47 (2014) 561-565. (Selected as Journal Cover) (Link)
  17. Mengqiang Zhu, Paul Northrup, Chenyang Shi, Simon J. L. Billinge, Donald L. Sparks and Glenn A. Waychunas, “Structure of sulfate adsorption complexes on ferrihydrite.” Environ. Sci. Technol. Lett., 1 (2014) 97-101. (Link)
  18. Chenyang Shi, Erin L. Redmond, Amir Mazaheripour, Pavol Juhas, Thomas F. Fuller and Simon J. L. Billinge, “Evidence for anomalous bond softening and disorder below 2 nm diameter in carbon supported platinum nanoparticles from the temperature dependent peak width of the atomic pair distribution function.” J. Phys. Chem. C, 117 (2013) 7226-7230. (Link)
  19. Chenyang Shi, Yongmei Hao and Zhongbo Hu, “Microstructure and colossal dielectric behavior of Ca2TiMnO6 Ceramics.” Scripta Mater., 64 (2011) 272-275. (Link)
  20. Chenyang Shi, Yongmei Hao and Zhongbo Hu, “Local valence and physical properties of double perovskite Nd2NiMnO6.” J. Phys. D: Appl. Phys., 44 (2011) 245405. (Link)
  21. Chenyang Shi, Zhongbo Hu and Yongmei Hao, “Structural, magnetic and dielectric properties of La2-xCaxNiO4+δ (x=0, 0,1, 0,2, 0,3).” J. Alloys. Compd., 509 (2011) 1333-1337. (Link)
  22. Chenyang Shi, Xinzhi Liu, Yongmei Hao and Zhongbo Hu, “Structural, magnetic and dielectric properties of Bi1-ySryFe(1-y)(1-x)Sc(1-y)xTiyO3 (x=0-0.2, y=0.1-0.3) ceramics.” Mater. Res. Bull.., 46 (2011) 378-383. (Link)
  23. Chenyang Shi, Xinzhi Liu, Yongmei Hao and Zhongbo Hu, “Structural, magnetic and dielectric properties of Sc modified (1-y)BiFeO3-yBaTiO3 ceramics.” Solid State Sci., 13 (2011) 1885-1888. (Link)
  24. Chenyang Shi, Zhongbo Hu and Yongmei Hao, “Structural and magnetic properties of single perovskite Ca(Ti1/2Mn1/2)O3.” J. Magn. Magn. Mater., 323 (2011) 1973-1976. (Link)
  25. Chenyang Shi, Yongmei Hao, Yanqing Tan and Rui Song, “The magnetic properties of Bi0.9Ba0.1Fe0.81M0.09O3 solid solutions (M=Co, Mn, Sc, Al).” Mater. Res. Bull., 46 (2011) 1848-1852. (Link)

Program Codes Developed

    JRGUI: a GUI program for prediction of physicochemical properties of drug-like molecules

  1. By using the modern object-oriented programming language Python (e.g. tkinter and pandas modules) and a chemoinformatics open source library (RDKit), the classic Joback and Reid group contribution method was revisited and written into a graphical user interface program—JRgui. The underlying algorithm behind the program is explained, herein, with the users being able to operate the program in either a manual and automatic mode. In the manual mode, the users are required to determine the type and occurrence of functional groups in the compound of interest and manually enter into the program. In the automatic mode, both of these parameters can be detected automatically via user input of the compound SMILES string. An additional advantage of the automatic mode is that a large number of molecules can be processed simultaneously by parsing their individual SMILES strings into a text file which is read by the program. The resulting predicted physical properties along with approximately 200 molecular descriptors are saved in a spreadsheet file for subsequent analysis. The program is freely available from (https://github.com/curieshicy/JRgui) for Windows, Linux and macOS 64-bit operating systems. It is hoped that the current work may facilitate the creation of other user friendly programs in the chemoinformatics community by using Python.
  2. The JRgui has a main interface. Class of 2015 In mannual mode, the users have the options to input the types and occurrences of the functional groups Class of 2015 While in auto mode, only the SMILES codes are necessary from users. Class of 2015

    xINTERPDF: a GUI program to extract structural information from measured X-ray pair distribution function (PDF) data for organic materials.

  3. The program is designed for analyzing organic pair distribution function (PDF) data collected at synchrotron and/or laboratory X-ray sources. It uses DiffPy-CMI () as a backend for simulation of PDFs. Currently it supports (1) The study of intermolecular interaction (e.g. hydrogen bonds) by subtracting out the scattering signal of single molecule(s) in real space. (2) The PDF model fit of the crystalline organic compound using the method proposed by Prill et al. (J. Appl. Cryst., 48, 171-178, 2015.) (3) The phase quantification of physical mixtures of organics. (4) Generate Score/Scree plots based on Principle Component Analysis. The program is accessible via (https://github.com/curieshicy/xINTERPDF), and is distributed through Conda.
  4. The program has a main interface. Class of 2015 The interface for the study of intermolecular correlation is as follows. Class of 2015 The window for visualization of intermolecular PDF looks like Class of 2015 Below is the GUI window for PDF model fit of a crystalline organic compound. Class of 2015 A breakdown of the total fit to the organic crystalline PDF. Class of 2015 The interface for phase quantification Class of 2015 Generation of Score/Scree plots from Principle Component Analysis Class of 2015

Selected Oral and Poster Presentations

  1. Invited talk at Spring Pharmaceutical Synchrotron XRPD workshop, Purdue University, West Lafayette, May 6-8, 2018.
  2. Formulation department talk at AbbVie, April, 2018, “Application of Synchrotron X-ray techniques and in silico modeling to pharmaceutical research.”
  3. Joint DPD, MST and PRD poster session at AbbVie, August 10th, 2017, “Applications of synchrotron X-ray techniques and in silico modeling in pharmaceutical research.” (Poster)
  4. American Association of Pharmaceutical Scientists (AAPS) conference, 2016, Denver. “Investigation on Molecular Packing of Pharmaceutical Compounds by Synchrotron X-ray Total Scattering Technique.” (Poster).
  5. Invited Talk at School of Pharmacy, University of Wisconsin at Madison, August 11th, 2016.
  6. Interview talk at Drug Product Development, AbbVie, September, 2015.
  7. Interview talk at JILA, University of Colorado at Boulder, July 15th, 2015.
  8. Interview talk at Chemical and Engineering Materials Division, Oak Ridge National Lab, July 1st, 2015.
  9. Interview talk at Materials Science and Technology Division, Oak Ridge National Lab, May 4th, 2015.
  10. Talk at Engineering Graduate Student Council Scholar Showcase, Columbia University, Feb. 26th, 2015.
  11. Nanoscience NY symposium, City University of New York, Feb. 19th, 2015. “Structure of Ti3C2 and Nb4C3 MXenes using atomic pair distribution function.” (Poster).
  12. NSLS/NSLS-II DOE Triennial Review, Brookhaven National Lab, Sep. 23rd, 2014 “Structure of Ti3C2 and Nb4C3 MXenes using atomic pair distribution function.” (Poster).
  13. Organizer of “1st Structure in the City Symposium”, Columbia University, August 18th, 2014. “Validation on lattice dynamics methodologies: Testing on bulk CdSe as an initial step.” (Oral).
  14. NSLS/NSLS-II and CFN Users' Meeting, Brookhaven National Lab, May 2014. “Structure of nanocrystalline Ti3C2 MXene using atomic pair distribution function.” (Poster).
  15. APAM research conference, Columbia University, March 2014. “Lattice dynamics study on size dependent CdSe clusters through PDF, Raman, IXS coupled with MD and DFT calculations.” (Oral).
  16. NSLS/NSLS-II and CFN Users' Meeting, Brookhaven National Lab, May 2013. “Extracting thermodynamic and structure-function properties of small nanoparticles from the atomic pair distribution function.” (Poster).
  17. American Conference on Neutron Scattering, Washington D.C. June 2012. “Size dependent Debye temperatures of platinum nanoparticles extracted from temperature dependent peak width of atomic pair distribution function.” (Poster).
  18. National School on Neutron and X-ray Scattering, Argonne and Oak Ridge National Lab, August 12th-15th, 2012. “Powder neutron diffractometer (POWGEN).” (Oral).

References

  1. Prof. Simon Billinge

    Department of Applied Physics and Applied Math,
    Columbia University in the City of New York,
    Email: sb2896@columbia.edu; Phone: 1-212-854-2918
  2. Prof. Yury Gogotsi

    Charles T. and Ruth M. Bach Professor,
    Distinguished University and Trustee Chair Professor,
    Department of Materials Science and Engineering,
    Drexel University,
    Email: gogotsi@drexel.edu; Phone: (215)-895-6446
  3. Prof. Lian Yu

    School of Pharmacy and Department of Chemistry,
    University of Wisconsin - Madison,
    Email: lian.yu@wisc.edu; Phone: (608)-263-2263
  4. Prof. Richard Haskell

    Department of Physics,
    Harvey Mudd College,
    Email: haskell@g.hmc.edu; Phone: 909-607-2768