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Hua-Gen Yu

Hua-Gen Yu


Chemistry Division
Building 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000

Phone: (631) 344-4367
FAX:    (631) 344-5815

Gas-Phase Molecular Dynamics


B.Sc. Chemistry, Chengdu University of Sciences and Technology (presently, Sichuan University), China 1985
M.Sc. Atomic & Molecular Physics, Chengdu University of Sciences and Technology, China 1988
Ph.D. Physical Chemistry, Göteborg University, Sweden 2000

Graduate and Postdoctoral Advisors:

G. Nyman (Göteborg, Sweden); J. T. Muckerman, Brookhaven National Laboratory

Professional Employment

Brookhaven National Laboratory, Chemistry Division, Upton, NY
Chemist, 10/2007 - present
Associate Chemist, 10/2005 - 9/2007
Assistant Chemist, 8/2004 - 9/2005
Goldhaber Fellow (Research Associate), 8/2001 - 7/2004
Research Associate, 10/2000 - 7/2001

The University of Queensland, Chemistry Division, Brisbane, Australia
Visiting Scholar, 4/1996 - 08/1997

Universidade de Coimbra, Departamento de Quimica, Coimbra, Portugal
Visiting Scientist, 4/2000 - 5/2000
Visiting Auxiliary Professor, 3/1995 - 3/1996

The Chinese Academy of Sciences, Chengdu Institute of Organic Chemistry, China
Associate Professor in Research, 1/1994 - 3/1995
Assistant Professor in Research, 7/1991 - 12/1993

Selected Professional Activities

Department Seminar Committee Member, 2006 - present
Session Chair: The 62nd OSU International Symposium on Molecular Spectroscopy, Columbus, Ohio, June, 2007
Panelist: DOE Workshop on Basic Research Needs for Clean and Efficient Combustion of 21st Century Transportation Fuels, Arlington, VA, October 30 - November 1, 2006
Panelist: DOE Theory and Modeling in Nanoscience Workshop, San Francisco, CA,May 9 - 12, 2002

Selected Awards

  • The National Science and Technology Progress Prize (The Third Prize), issued by The Ministry of National Education of China, 1999
  • The Gertrude and Maurice Goldhaber Distinguished Postdoctoral Fellowship Award, Brookhaven National Laboratory, 2001

Research Interests

Theory and computation of the dynamics of chemical reactions, and the bound and quasi-bound (or resonance) rovibrational states of molecules; simulation of photodissociation processes; ab initio calculations and potential energy surfaces; direct dynamics of catalytic reactions; theoretical studies of nanostructures.

We are constantly developing methods and algorithms for computing new properties, and for making spectroscopy and dynamics calculations more accurate and more efficient.

Research Accomplishments

Two-layer Lanczos diagonalization algorithm: In variational studies of molecular spectroscopy, one challenging task is to diagonalize a huge matrix resulting from the representation of the Hamiltonian in a large basis set. Therefore, rigorous quantum dynamics (QD) calculations were limited to tetra-atomic molecules before 2002. In order to overcome this difficulty, we developed a two-layer Lanczos iterative approach using a "divide-and-conquer" strategy based on the properties of the representation of the Hamiltonian in orthogonal polyspherical coordinates. Using the two-layer Lanczos method, we are now able to carry out rigorous QD calculations of the vibrational spectra of polyatomic molecules containing up to six atoms. The algorithm has been applied to the CH4, CH3D, H3O2- and (H2)3 systems. To the best of our knowledge, these are of the first calculated five-/six-atom molecules (or ions) using a rigorous QD method without any dynamical approximations. This work was presented in an invited talk at the 225th ASC meeting (New Orleans, 2003), at a chemistry seminar at Stony Brook University (2003) and New York University (2004), and at the AMO seminar at Stony Brook University (2007) in addition to talks at the Goldhaber Symposium (BNL, 2002) and the 59th OSU International Symposium of Molecular Spectroscopy (Ohio, 2004). By implementing with the two-layer Lanczos algorithm, a universal program TetraVib has been developed for studying the rovibrational spectra of general four-atomic molecules. Currently, we are developing a general program for five-atom systems.

A coherent discrete-variable representation method: It is still impossible to perform a rigorous quantum dynamics study of systems larger than six atoms even using the advanced diagonalization algorithms such as the basis-contracted Lanczos method of Wang and Carrington or our two-layer Lanczos method owing to the huge size of the Hamiltonian matrix. One has to exploit several techniques at the same time to attack the problem. In this research, we attempted to reduce the basis size by constructing simple and compact basis functions. Toward this end, we have developed a coherent discrete-variable representation (ZDVR) method. In this approach, inspired by a coherent-state formalism in momentum and conjugate coordinates, the multidimensional quadrature pivots are obtained by diagonalizing a complex coordinate operator matrix in a finite basis set, which is spanned by the lowest eigenstates of a two-dimensional reference Hamiltonian. The orthonormal eigenvectors define a collocation matrix connecting the localized ZDVR basis functions and the finite basis set. Since the diagonalization of the new coordinate operator is exact within the selected basis set, the ZDVR method has the same convergence speed as the one-dimensional (1D) potential-optimized discrete variable representation (PO-DVR) approach. The ZDVR method provides exponential convergence and accurate energies. It is the only multidimensional PODVR method with Gaussian quadrature accuracy so far. We are currently pursuing this direction of research for constrained 2D cases such as DVRs on a sphere.

A K-dependent adiabatic approach to the Renner-Teller (RT) effect for triatomic molecules: We have developed a new adiabatic approach for studying the rovibronic spectra of triatomic molecules with the consideration of the RT effect. This method is an extended version of the BDD (Barrow, Dixon and Duxbury) adiabatic approximation that removes the assumption that K is a good quantum number, and uses hyperspherical coordinates and the coupled-channel method. The algorithm makes it possible to accurately compute the rovibronic energy levels of the third kind of RT molecules for which the barrier to linearity is very large for the lower electronic state of the RT pair. In collaboration with Trevor Sears and Gregory Hall (BNL), the algorithm has been successfully applied to the HCCl and HCBr molecules. Six articles have been published.

Direct ab initio molecular dynamics: In this project, we have developed an accurate and efficient direct ab initio molecular dynamics program, DualOrthGT. The program is applicable to the study of radical-radical bimolecular reactions, which are important reactions in combustion environments. It is very challenging to study the dynamics of radical-radical reactions because of the strong correlation energy, spin contamination, and the size-consistent problem in such systems. In particular, the size-consistent problem essentially excludes the possibility of using density functional theory (DFT) or other single-determinant methods in most cases. In order to deal with those issues, the DualOrthGT program is implemented with four advanced techniques: the predictor-corrector symplectic reversible integrator of Martyna and Tuckerman for solving Hamilton's equations of nuclear motion, CASSCF-guided (when necessary) electronic wave functions, an accurate dual-level ab initio method (either ab initio methods or basis sets) for electronic structure calculations, and a graph theory procedure for identifying instantaneous molecular fragment identities throughout the trajectory. The program has been successfully applied to the study of several atmospheric and/or combustion-related reactions such as O(1D) + CH4, 1CH2 + C2H2, and HOCO + X (X = H, CH3, O, O2, OH, HO2, Cl and ClO, etc.), and the photo-initiated reactions of molecules or ions. Recently, we also used the Car-Parrinello molecular dynamics (CPMD) method to study the behavior of complex systems such as boron nitride nanotubes.

Dissociative recombination: We have developed a spherical electron cloud hopping (SECH) molecular dynamics method for studying the product branching ratios in the dissociative recombination (DR) of polyatomic ions with electrons. The method consists of a direct ab initio technique, the surface hopping method, and the SECH model. The SECH model is designed to mimic the quantum delocalization of the scattered electron in a classical mechanic manner. Since the SECH MD method is a classical mechanics-based algorithm, it is capable of studying large polyatomic ions. The preliminary application of this method to CH+, H3O+ and H+(H2O)3 is very promising. Computed branching fractions of products are in excellent agreement with experiments. We expect that we can now realistically simulate the product branching ratios of DR of polyatomic ions beyond H3+ and its isotopic ions. Although quantum dynamics approaches have been widely used for calculating the rate coefficients of DR, they are infeasible for the study of product branching ratios of general polyatomic molecular ions. This work has been presented at a BNL Chemistry Colloquium (2008), the Telluride Workshop on Spectroscopy and Dynamics (2008), and the BNL Goldhaber Symposium (2008).

Key Publications

114.    A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination; Yu, H.-G.; J. Chem. Phys. 128, 194106 (2008).

102.    A coherent discrete variable representation method for multidimensional systems in physics; Yu, H.-G.; J. Chem. Phys. 122, 164107 (2005).

100.   Ab initio and direct dynamics studies of the reaction of singlet methylene with acetylene and the lifetime of the cyclopropene complex; Yu, H.-G. and Muckerman, J.T.; J. Phys. Chem. A 109, 1890 (2005).

99.    Full-dimension quantum calculations of vibrational spectra of six-atom molecules I. Theory and numerical results; Yu, H.-G.; J. Chem. Phys. 120, 2270 (2004).

88.    Two-layer Lanczos iteration approach to molecular spectroscopic calculation; Yu, H.-G.; J. Chem. Phys. 117, 8190 (2002).

67.    A 4D quantum scattering study of the Cl + CH4 « HCl + CH3 reaction via spectral transform iteration; Yu, H.-G. and Nyman, G.; J.Chem. Phys. 110, 7233 (1999).

60.    The calculation of vibrational eigenstates by MINRES filter diagonalization; Yu, H.-G. and Smith, S.C.; Ber. Buns. Phys. Chem. 101, 400 (1997) (invited).

Invited Reviews

  1. G. Nyman and H.-G. Yu, "Quantum theory of bimolecular chemical reactions," Rep. Prog. Phys. 63, 1001-1059 (2000).
  2. G. Nyman and H.-G. Yu, "Iterative digonalization of large sparse matrix by using spectral transformation and filter diagonalization," J. Comp. Meth. Sci. 29 (2001).


1. Z. H. Zhu and H.-G. Yu, Molecular Structure and Potential Energy Functions (in Chinese), (Science Press of China, Beijing, 1997)

Full Publication List