Dr. Jorge A. Morales

Principal Research Interests

 

• Simulations of Proton Cancer Therapy Reactions
• Time-Dependent, Variational, Direct, Non-Adiabatic Chemical Dynamics
• Novel Coherent-States Theory for Nuclear and Electronic Degrees of Freedom
• Coupled-Cluster Theory
• Quantum Computing for Quantum Chemistry

 

The main focus of our present research efforts is the direct, time-dependent simulation of chemical reactions. In that approach, a reaction is simulated in the same way the process evolves in “real life” (i.e. by evaluating instantaneously the reaction evolution and its acting molecular forces “on the fly”, without the cumbersome time-independent predetermination of potential energy surfaces). In the main, quantum mechanics is the theoretical framework of our simulations. However, even with the current computer technology, full quantum-mechanics descriptions of large chemical systems remain impractical and recurrences to more feasible classical-mechanics treatments are inevitable. Therefore, we advocate a generalized quantum/classical (Q/C) approach to ab initio molecular mechanics where molecular degrees of freedom and/or molecular regions are distributed into quantum and classical treatments. Degrees of freedom less critical for quantum effects (e.g. nuclear translational, rotational and vibrational motions under some circumstances) and/or a peripheral molecular region not housing quantum processes can be treated via classical mechanics with added quantum corrections.  Conversely, the central region containing quantum phenomena (e.g. tunneling) must be described quantum-mechanically.

Toward such a goal, we are developing a novel Q/C methodology that permits making transitions from quantum to classical treatments in a gradual and continuous way; we attain such flexibility by exploiting the properties of coherent states (CS). Broadly speaking, CS are sets of quantum states that permit expressing quantum dynamical equations in a classic-like format in terms of generalized positions and momenta. Some CS are also quasi-classical if their generalized positions and momenta obey classical mechanics. A CS-formulated dynamics is still quantum but in a classic-like format as close to classical mechanics as possible; furthermore, if a quasi-classical CS is employed for a molecular region and/or a degree of freedom then a classical dynamics with a quantum state is obtained and a Q/C partition is created.

A highlight of creativity in our CS efforts is the original formulation of novel types of CS to implement such a CS dynamics. Whereas nearly all previous chemical research on CS has mostly dealt with the celebrated Glauber CS to describe nuclear motions, we are  endeavoring for the creation and/or use of novel types of CS for all types of particles (nuclei and electrons) and for all types of dynamics (translational, rotational, vibrational, electronic). Our methods are implemented in our code PACE (Python-Accelerated Coherent states Electron-nuclear dynamics). PACE embodies various cutting-edge techniques in computer sciences such as a mixed programming language (Python for logic flow and Fortran and C++ for numerical calculations), intra- and internode parallelization, and the OED/ERD atomic integral package from the ACES III/IV program.

 

Representative Publications

• Temporally Stable Rotational Coherent States for Molecular Simulations I. Spherical and Linear Rotor Cases, C. Stopera and J. A. Morales, Journal of Physical Chemistry152, 134112 (2020).
• Electron Nuclear Dynamics with Plane Wave Basis Sets: Complete Theory and Formalism, E. S. Teixeira and J. A. Morales, Theoretical Chemistry Accounts139, 73 (2020). 
• Symmetry-Breaking Effects on Time-Dependent Dynamics: Correct Differential Cross Sections and Other Properties in H⁺ + C₂H₄ at E_Lab = 30 eV, P. M. McLaurin, R. Merritt, J. C. Dominguez, E. S. Teixeira, and J. A. Morales, Physical Chemistry Chemical Physics (2019). 
• Non-Adiabatic Molecular Dynamics Simulations of Non-Charge-Transfer and Charge-Transfer Scattering in H⁺ + CO₂ at E_Lab = 30 eV, Y. Yan and J. A. Morales, Chinese Journal of Chemical Physics (2018). 
• Electron Nuclear Dynamics Simulations of Proton Cancer Therapy Reactions: Water Radiolysis and Proton- and Electron-Induced DNA Damage in Computational Prototypes, E. S. Teixeira, K. Uppulury, A. Privett, C. Stopera, P. M. McLaurin, and J. A. Morales, Cancers10(5), 136 (2018). 
• Benchmark Coupled-Cluster g-Tensor Calculations with Full Inclusion of the Two-Particle Spin-Orbit Contributions, A. Perera, J. Gauss, P. Verma, and J. A. Morales, Journal of Chemical Physics146, 164104 (2017).
• Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H⁺ + (H₂O)_1-6, A. Privett, E. S. Teixeira, C. Stopera and J. A. Morales, PLOS ONE 12(4): e0174456 (2017).
• "New Massively Parallel Linear-Response Coupled-Cluster Module in ACES III: Application to Static Polarizabilities of Closed-Shell Molecules and Oligomers and of Open-Shell Radicals", P. Verma, A. Perera and J. A. Morales, Molecular Physics (2016). http://dx.doi.org/10.1080/00268976.2015.1126367
• "Implementation of a Parallel Linear-Response Coupled-Cluster-Theory Module in ACES III: First Application to the Static Polarizabilities of the C₂₀ Isomers and of the Biphospholylidene Dioxide and Disulfide Oligomers", A. Perera and J. A. Morales, Advances in Quantum Chemistry, Vol. 72, Chapter 3, Pages: 29-60 (2016), ISSN 0065-3276, ISBN 9780128039847,http://dx.doi.org/10.1016/bs.aiq.2015.06.008, http://www.sciencedirect.com/science/article/pii/S0065327615000350
• "In Honor of N. Yngve Öhrn: Surveying Proton Cancer Therapy Reactions with Öhrn's Electron Nuclear Dynamics Method. Aqueous Clusters Radiolysis and DNA-Bases Damage by Proton Collisions", P. M. McLaurin, A. Privett, C. Stopera, T. V. Grimes, A. Perera and J. A. Morales, Molecular Physics 113, 297-313 (2015). http://dx.doi.org/10.1080/00268976.2014.938709
• "Electron Nuclear Dynamics of Proton Collisions with DNA/RNA Bases at ELab =80 keV: A Contribution to Proton Cancer Therapy Research", A. Privett and J. A. Morales, Chemical Physics Letters 603, 82-88, (2014)
• "Structure and Photochemistry of a Bio-inspired Model for Photocatalytic H2O Splitting: Improved Calculations of the Sobolewski and Domcke's Chl-Im-Q Model Complex", S. A. Perera and J. A. Morales, Molecular Physics, 112, 863-867 (2014)
• "Massively Parallel Implementations of Coupled-Cluster Methods for Electron Spin Resonance Spectra I: Isotropic Hyperfine Coupling Tensors in Large Radicals", P. Verma, A. Perera and J. A. Morales, Accepted for Publication in The Journal of Chemical Physics (2013)
• "Some Recent Developments in the Simplest-Level Electron Nuclear Dynamics Method: Theory, Code Implementation, and Applications to Chemical Dynamics", C. Stopera, T. V. Grimes, P. M. Mclaurin, A. Privett and J. A. Morales,  Advances in Quantum Chemistry, Vol. 66, Chapter 3, 113-194 (2013)
• "Dynamics of H⁺ + NO(v_i= 0)=NO(v_f (0-2) at E_Lab = 30 eV with Canonical and Morse Coherent States",C. Stopera, B. Maiti, and J. A. Morales,  Chemical Physics Letters, 551, 42-49 (2012)
• "Dynamics of H⁺ + CO at E_Lab = 30 eV", C. Stopera, B. Maiti, T. V. Grimes, P. M. McLaurin and J. A. Morales,  Journal of Chemical Physics, 136, 054304 (2012)
• "Dynamics of H⁺ + N₂ at E_Lab = 30 eV", C. Stopera, B. Maiti, T. V. Grimes, P. M. McLaurin and J. A. Morales, Journal of Chemical Physics, 134, 224308 (2011)
• "Some Coherent-States Aspects of the Electron Nuclear Dynamics Theory: Past and Present", J. A. Morales, Molecular Physics, 108, 3199-3211 (2010)
• "Time-Dependent Density-Functional Theory Method in The Electron Nuclear Dynamics Framework", S. A. Perera, P. M. McLaurin, T. V. Grimes, and J. A. Morales, Chemical Physics Letters, 496, 188-195 (2010)
• "Valence-Bond/Coherent-States Approach to The Charge Equilibration Model I. Valence-Bond Models for Diatomic Molecules", J. A. Morales, Journal of Physical Chemistry A, 113, 6004-6015 (2009)
• "A Theoretical Investigation on Fullerene-like Phosphorus Clusters", J. G. Han and J. A. Morales, Chemical Physics Letters, 396/1-3, 27 (2004)
• "The Onset of Dissociation in The Aqueous LiOH Clusters: A Solvation Study with the Effective Fragment Potential Model and Quantum Mechanics Methods", A. Yoshikawa and J. A. Morales, Journal of Molecular Structure (Theochem), 681, 27 (2004)
• "New Approach to Reactive Potentials with Fluctuating Charges: Quadratic Valence-Bond Model", J. A. Morales and T. J. Martinez, Journal of Physical Chemistry A, 108, 3076 (2004)
• "On The Rotational Coherent State in Molecular Quantum Dynamics", J. A. Morales, E. Deumens and Y. Öhrn, Journal of Mathematical Physics, 40(2), 766 (1999)
• "Electron Nuclear Dynamics of H⁺ + H₂ Collisions at E_Lab = 30 eV", J. A. Morales, A. Diz, E. Deumens and Y. Öhrn, Journal of Chemical Physics, 103, 9968 (1995)
• "Perturbation Theory without Functions for the Zeeman Effect in Hydrogen", F. M. Fernandez and J. A. Morales, Physics Review A, 46, 318 (1992)