
HuaGen Yu
Chemist
Chemistry
Department
Building 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 119735000
Phone: (631) 3444367
FAX: (631) 3445815
email
GasPhase Molecular
Dynamics
Education:
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 Department, 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 Department, 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 quasibound (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:
• Twolayer 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
tetraatomic molecules before 2002. In order to overcome this difficulty, we
developed a twolayer Lanczos iterative approach using a
“divideandconquer” strategy based on the properties of the representation
of the Hamiltonian in orthogonal polyspherical coordinates. Using the
twolayer 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 CH_{4}, CH_{3}D, H_{3}O_{2}^{} and
(H_{2})_{3} systems. To the best of our knowledge, these are of the first
calculated five/sixatom 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 twolayer
Lanczos algorithm, a universal program TetraVib has been developed for
studying the rovibrational spectra of general fouratomic molecules.
Currently, we are developing a general program for fiveatom systems.
• A coherent discretevariable 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
basiscontracted Lanczos method of Wang and Carrington or our twolayer
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
discretevariable representation (ZDVR) method. In this approach, inspired
by a coherentstate 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 twodimensional 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
onedimensional (1D) potentialoptimized discrete variable representation
(PODVR) 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 Kdependent adiabatic approach to the RennerTeller (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
coupledchannel 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 radicalradical
bimolecular reactions, which are important reactions in combustion
environments. It is very challenging to study the dynamics of
radicalradical reactions because of the strong correlation energy, spin
contamination, and the sizeconsistent problem in such systems. In
particular, the sizeconsistent problem essentially excludes the possibility
of using density functional theory (DFT) or other singledeterminant methods
in most cases. In order to deal with those issues, the DualOrthGT program is
implemented with four advanced techniques: the predictorcorrector
symplectic reversible integrator of Martyna and Tuckerman for solving
Hamilton’s equations of nuclear motion, CASSCFguided (when necessary)
electronic wave functions, an accurate duallevel 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 combustionrelated
reactions such as O(^{1}D) + CH_{4}, ^{1}CH_{2} + C_{2}H_{2}, and HOCO + X (X = H, CH_{3}, O, O_{2},
OH, HO_{2}, Cl and ClO, etc.), and the photoinitiated reactions of molecules
or ions. Recently, we also used the CarParrinello 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 mechanicsbased algorithm,
it is capable of studying large polyatomic ions. The preliminary application
of this method to CH^{+}, H_{3}O^{+} and H^{+}(H_{2}O)_{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 H_{3}^{+} 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. Fulldimension quantum
calculations of vibrational spectra of sixatom molecules I. Theory and
numerical results; Yu, H.G.; J. Chem. Phys. 120, 2270 (2004).
88. Twolayer 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 + CH_{4}
«
HCl
+ CH_{3} 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:

G. Nyman and H.G. Yu,
“Quantum theory of bimolecular chemical reactions,” Rep. Prog. Phys.
63, 10011059 (2000).

G. Nyman and H.G. Yu,
“Iterative digonalization of large sparse matrix by using spectral
transformation and filter diagonalization,” J. Comp. Meth.
Sci.
Eng.
1, 29 (2001).
Books:
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
Last Modified: September 5, 2013
