Q-Chem: About Q-Chem

Jing Kong, Ph.D.


CEO & Chief Scientist of Q-Chem, Inc.

 

jkong


Dr. Jing Kong is the CEO and Chief Scientist of Q-Chem. He obtained his Ph.D. degree in Theoretical Chemistry from Dalhousie University in 1996. Previously, he obtained B.S. from Nanjing University, and M.S. from Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences. He joined the company in 1996, and since 1998 has overseen the operation, code development and marketing/sales. He has also played a major role in obtaining millions of dollars of outside funding, mainly through federal SBIR (Small Business Innovative Research) grants.

In addition to managing the company, he leads a group of scientists on innovative research. The main theme of the Q-Chem group is to extend the capacity of the quantum chemistry models to the research areas where the first-principle calculations are desirable but not yet practical. He has been very fortunate to work with some very talented quantum chemists. Here are the projects that the group have worked on:

  • Efficient DFT algorithms. The more recent development is a new method called mrXC (multiresolution exchange-correlation) that combines the two types of numerical grids (uniform cubic grid and atom-centered grid) seamlessly and accelerates the numerical integration of DFT exchange-correlation terms by several times with no error. Previously, IncDFT method was developed to take advantage of small differences between iterations and Fourier Transform Coulomb (FTC) was implemented to speed up Coulomb calculation several times over the combination of CFMM and J-engine. People who have worked along this line include Drs. Shawn Brown, Laszlo Fusti-Molnar, Nick Russ, Chun-Min Chang and Yihan Shao.
    • J. Kong, S. T. Brown, and L. Fusti-Molnar, "Efficient Computation of the Exchange-Correlation Contribution in the Density Functional Theory Through Multiresolution", Journal of Chemical Physics, 124, 94109 (2006). [pdf]
    • S. T. Brown, L. Fusti-Molnar, and J. Kong, "Interpolation Density Values on a Cartesian Grid: Improving the efficiency of Lebedev Based Numerical Integration in Kohn-Sham Density Functional Algorithms", Chemical Physics Letters, 418, 490 (2006). [pdf]
    • L. Fusti-Molnar, J. Kong, "Fast Coulomb Calculations with Gaussian Functions", Journal of Chemical Physics, 122, 74108 (2005). [pdf]
    • S.T. Brown, J. Kong, "IncDFT: Improving the efficiency of density functional theory using some old tricks", Chemical Physics Letters, 408, 395 (2005). [pdf]

  • New DFT functionals. Recently, we have developed efficient implementations of Becke and Johnson’s exchange-dipole moment model (XDM) for dispersion interaction and Becke’s model functional B05 for nondynamic correlation. We have shown that the dispersion interaction can be treated perturbatively at the error of 10-5 in density matrix. The SCF implementation of B05, a so-called 4th rung functional, is especially challenging. Drs. Emil Proynov, Yihan Shao, Zhengting Gan are the main contributors to this part of work.
    • E. Proynov, Y. Shao, J. Kong, “Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method”, Chem. Phys. Lett., 493, 381 (2010). [pdf]
    • J. Kong, Z. Gan, E. Proynov, M. Freindorf, T. R. Furlani, “Efficient computation of the dispersion interaction with density functional theory”, Phys. Rev. A, 79, 042510 (2009). [pdf]
    • E. Proynov, Zhengting Gan, and J. Kong, “Analytical Representation of Becke-Roussel Exchange Functional”, Chem. Phys. Lett., 455, 103 (2008). [pdf]
    • E. Proynov, and J. Kong, “An improved meta-GGA correlation functional of the Lap family”, J. Chem. Theory Comput., 3, 746 (2007). [pdf]

  • Hybrid methods and their applications. We are actively developing new ways to mix different computational models. In particular, , a very simple QM/MM method, called YinYang Atom, is developed to separate the QM and MM regions connected through chemical bonds. Dr. Yihan Shao was the main contributor to the YinYang Atom model. In addition, we have also carried out QM/MM studies on biological systems, in collaboration with Dr. Marek Freidorf and Dr. Thomas Furlani at University at Buffalo and Bernie Brooks’ group at NIH.
    • A. Ghysels, H. L. Woodcock III, J. D. Larkin, B. T. Miller, Y. Shao, J. Kong, D. V. Van Neck, V. Van Speybroek, M. Waroquier, B. R. Brooks, “Efficient calculation of QM/MM frequencies with the Mobile Block Hessian”, J. Chem. Theor. Comp., 7, 496 (2011). [pdf]
    • H. Lee Woodcock, Wenjun Zheng, An Ghysels, Yihan Shao, Jing Kong, and Bernard R. Brooks, “Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit”, J. Chem. Phys., 129, 214109 (2008). [pdf]
    • Y. Shao, and J. Kong, “YinYang Atom: a simple combined ab initio quantum mechanical molecular mechanical model”, J. Phys. Chem. A, 111, 3661 (2007). [pdf]
    • M. Freindorf, Y. Shao, S. T. Brown, J. Kong, T. R. Furlani, “A Combined Density Functional Theory and Molecular Mechanics (QM/MM) Study of FeCO Vibrations in Carbonmonoxy Myoglobin”, Chemical Physics Letters, 419, 563 (2006). [pdf]
    • M. Freindorf, Y. Shao, T. R. Furlani, and J. Kong, "Lennard - Jones Parameters for Combined QM/MM Method Using B3LYP/6-31+G*/AMBER Potential", J.Comput.Chem. 26, 1270 (2005). [pdf]

  • Quantum chemistry on new hardware platforms. Part of constant challenge in computational chemistry to adapt the programming to new hardware paradigms. Early on, DFT and HF of Q-Chem were parallelized up to the calculation of 2nd derivatives of energy (frequencies). The memory usage is scalable in the frequency calculation, making it affordable for large structures. More recently, algorithms are being developed to implement those basic methods on GPU (graphic processing unit). People who have worked on parallelization and GPU implementation include Drs. Holger Dachsel, Prakashan Korambath, Zhengting Gan and Yihan Shao. This on-going project is in collaboration with Dr. Thomas Furlani at Center for Computational Research, University at Buffalo.we have implemented DFT and HF on parallel computers.
    • http://www.nvidia.com/content/GTC/documents/1050_GTC09.pdf
    • P.P. Korambath, J. Kong, T.R. Furlani, and M. Head-Gordon, "Parallelization of Analytical Hartree-Fock and Density Functional Theory Hessian Calculations", Molecular Physics, 100, 1755 (2002). [pdf]
    • T.R. Furlani, J. Kong, and P.M.W. Gill, "Parallel SCF calculations with Q-Chem.", Computer Physics Communications, 128, 170 (2000). [pdf]



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