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The hybrid Quantum Trajectory/Electronic Structure DFTB-based approach to Molecular Dynamics

Published: 13 July 2014 Publication History

Abstract

This paper describes a quantum trajectory (QT) approach to molecular dynamics with quantum corrections on behavior of the nuclei interfaced with the on-the-fly evaluation of electronic structure (ES). Nuclear wavefunction is represented by an ensemble of trajectories, concurrently propagated in time under the influence of the quantum and classical forces. For scalability to high-dimensional systems (hundreds of degrees of freedom), the quantum force is computed within the Linearized Quantum Force (LQF) approximation. The classical force is determined from the ES calculations, performed at the Density Functional Tight Binding (DFTB) level. High throughput DFTB version is implemented in a massively parallel environment using Open MP/MPI. The dynamics has also been extended to describe the Boltzmann (imaginary-time) evolution defining temperature of a molecular system. The combined QTES-DFTB code has been used to study reaction dynamics of systems consisting of up to 111 atoms.

References

[1]
D. Bohm. A suggested interpretation of the quantum theory in terms of "hidden" variables, I and II. Phys. Rev., 85:166--193, 1952.
[2]
Y. Cha, C. J. Murray, and J. P. Klinman. Hydrogen tunneling in enzyme reactions. Science, 243:1325--1330, 1989.
[3]
G. Czako, A. L. Kaledin, and J. M. Bowman. A practical method to avoid zero-point leak in molecular dynamics calculations: Application to the water dimer. J. Chem. Phys., 132:164103, 2010.
[4]
G. Czako, A. L. Kaledin, and J. M. Bowman. Zero-point energy constrained quasiclassical, classical, and exact quantum simulations of isomerizations and radial distribution functions of the water trimer using an ab initio potential energy surface. Chem. Phys. Lett., 500(46):217--222, 2010.
[5]
L. de Broglie. Interference and corpuscular light. Nature, 118:441--442, September 1926.
[6]
C. Dekker and M. A. Ratner. Electronic properties of DNA. Phys. World, 14:29--33, 2001.
[7]
M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys. Rev. B, 58:7260--7268, Sep 1998.
[8]
S. Garashchuk. Quantum trajectory dynamics in imaginary time with the momentum-dependent quantum potential. J. Chem. Phys., 132:014112, 2010.
[9]
S. Garashchuk. Quantum trajectory dynamics in imaginary time with the momentum-dependent quantum potential. J. Chem. Phys., 132:014112, 2010.
[10]
S. Garashchuk. Calculation of the zero-point energy from imaginary-time quantum trajectory dynamics in Cartesian coordinates. Theoretical Chemistry Accounts, 131:1083, 2012.
[11]
S. Garashchuk, V. A. Rassolov, and G. C. Schatz. Semiclassical nonadiabatic dynamics using a mixed wave-function representation. J. Chem. Phys., 123:174108, 2005.
[12]
S. Garashchuk and M. V. Volkov. The energy-conserving dynamics of quantum-classical systems based on quantum trajectories. Mol. Phys., 110:985--993, 2012.
[13]
S. Garashchuk and M. V. Volkov. Incorporation of quantum effects for selected degrees of freedom into the trajectory-based dynamics using spatial domains. J. Chem. Phys., 137:074115, 2012.
[14]
S. Irle. Improved DFTB parameters for Pyrene and Coronone. Private communicaton, 2013.
[15]
M. Karplus, R. D. Sharma, and R. N. Porter. Dynamics of reactive collisions - H+H2 exchange reaction. J. Chem. Phys., 40:2033, 1964.
[16]
D. R. Killelea, V. L. Campbell, N. S. Shuman, and A. L. Utz. Bond-selective control of a heterogeneously catalyzed reaction. Science, 319:790--793, 2008.
[17]
M. J. Knapp and J. P. Klinman. Environmentally coupled hydrogen tunneling - linking catalysis to dynamics. Eur. J. of Biochem., 269:3113--3121, 2002.
[18]
E. Madelung. Quantum theory in hydrodynamic form. Z. Phys., 40:322--326, 1927.
[19]
J. Mazzuca, S. Garashchuk, and J. Jakowski. Description of proton transfer in soybean lipoxygenase-1 employing approximate quantum trajectory dynamics. Chem. Phys. Lett., 542:153--158, 2012.
[20]
J. W. Mazzuca, S. Garashchuk, and J. Jakowski. QTES-DFTB dynamics study on the effect of substrate motion on quantum proton transfer in soybean lipoxygenase-1. Chem. Phys. Lett., Submitted 2014.
[21]
N. D. Mermin. Thermal properties of the inhomogeneous electron gas. Phys. Rev. A, 137:1441, 1965.
[22]
W. H. Miller, S. D. Schwartz, and J. W. Tromp. Quantum mechanical rate constants for biomolecular reactions. J. Chem. Phys., 79:4889--4898, 1983.
[23]
T. J. Park and J. C. Light. Quantum flux operators and thermal rate constant: collinear H + H2. J. Chem. Phys., 88:4897--4912, 1988.
[24]
E. Pollak. The symmetrized quantum thermal flux operator. J. Chem. Phys., 107:64--69, 1997.
[25]
D. Porezag, T. Frauenheim, T. Köhler, G. Seifert, and R. Kaschner. Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon. Phys. Rev. B, 51:12947, 1995.
[26]
W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. Numerical Recipes: The Art of Scientific Computing. Cambridge University Press, Cambridge, 2 edition, 1992.
[27]
O. V. Prezhdo and C. Brooksby. Quantum backreaction through the Bohmian particle. Phys. Rev. Lett., 86:3215--3219, 2001.
[28]
V. A. Rassolov, S. Garashchuk, and G. C. Schatz. Quantum trajectory dynamics in arbitrary coordinates. J. Phys. Chem. A, 110:5530--5536, 2006.
[29]
K. W. Rickert and J. P. Klinman. Nature of Hydrogen Transfer in Soybean Lipoxygenase 1: Separation of Primary and Secondary Isotope Effects. Biochemistry, 38:12218--12228, 1999.
[30]
J. C. Slater and G. F. Koster. Simplified lcao method for the periodic potential problem. Phys. Rev., 94(6):1498--1524, Jun 1954.
[31]
J. Sokoloff. Some consequences of the thermal hartree-fock approximation at zero temperature. Ann. Phys., 45:186--190, 1967.
[32]
S. J. Stuart, D. Nugawela, B. Hadri, J. Jakowski, P. Krstic, S. Garashchuk, and S. Irle. Optimization of Density Functional Tight-Binding and Classical Reactive Molecular Dynamics for High-Throughput Simulations of Carbon Materials. In Conference proceedings of XSEDE12, 2012.
[33]
C. J. Trahan and R. E. Wyatt. An arbitrary Lagrangian-Eulerian approach to solving the quantum hydrodynamic equations of motion: Equidistribution with "smart" springs. J. Chem. Phys., 118:4784--4790, 2003.
[34]
W. Zhang, H. Kawamata, and K. Liu. CH Stretching Excitation in the Early Barrier F + CHD3 Reaction Inhibits CH Bond Cleavage. Science, 325:303--306, 2009.
[35]
G. Zheng, M. Lundberg, J. Jakowski, T. Vreven, M. J. Frisch, and K. Morokuma. Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method. Int. J. Quantum Chem., 109:1841--1854, 2009.
[36]
X. Zhu, P. Lopes, and A. D. MacKerell. Recent developments and applications of the CHARMM force fields. Wiley interdisciplinary reviews -- Computational Molecular Science, 2:167--185, 2012.

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Published In

cover image ACM Other conferences
XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment
July 2014
445 pages
ISBN:9781450328937
DOI:10.1145/2616498
  • General Chair:
  • Scott Lathrop,
  • Program Chair:
  • Jay Alameda
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

In-Cooperation

  • NSF: National Science Foundation
  • Drexel University
  • Indiana University: Indiana University

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 July 2014

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Author Tags

  1. ACM proceedings
  2. Density Functional Tight Binding
  3. Dynamics
  4. Electronic Structure
  5. Quantum Trajectory
  6. Scientific-computing

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XSEDE '14

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XSEDE '14 Paper Acceptance Rate 80 of 120 submissions, 67%;
Overall Acceptance Rate 129 of 190 submissions, 68%

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