Publication List

2016

• Payam Norouzzadeh, Charles W. Myles. A first-principles lattice dynamical study of type-I, type-II, and type-VIII silicon clathrates. Journal of Materials Science (May 2016) Volume 51, Issue 9, pp 4538-4548, http://link.springer.com/article/10.1007/s10853-016-9766-1

2015

• R. Sun, C. J. Davda, J. Zhang, and W. L. Hase. Comparison of Direct Dynamics Simulations with Different Electronic Structure Methods. F^- + CH₃I with MP2 and DFT/B97-1. Physical Chemistry Chemical Physics 17, 2589-2597 (2015)

2014

• Jai, T. M., O'Boyle, M. and Fang, D.. Neural correlates of sensory enabling presentation: A fMRI study of zooming and rotation video effects on online apparel shopping. Journal of Consumer Behaviour (April 2014), http://dx.doi.org/10.1002/cb.1476
• Austin G. Meyer, Sara S. Sawyer, Andrew D. Ellington, and Claus O. Wilke. Analyzing machupo virus-receptor binding by molecular dynamics simulations. PeerJ 2:e266 (2014), http://dx.doi.org/10.7717/peerj.266
• S. Pratihar, D. G. Bhakta, S. C. Kohale, J. Laskin, and W. L. Hase. Dynamics of Energy Transfer and Soft-Landing in Collisions of Protonated Dialanine with Perfluorinated Self-Assembled Monolayer Surfaces. Physical Chemistry Chemical Physics 16, 23769-23778 (2014)
• A. K. Paul, S. C. Kohale, S. Pratihar, R. Sun, S. W. North, and W. L. Hase. A Unified Model for Simulating Liquid and Gas Phase Intermolecular Energy Transfer: N₂ + C₆F₆ Collisions. Journal of Chemical Physics 140, 194103/1-11 (2014)
• R. Sun, M. R. Siebert, L. Xu, S. D. Chambreau, G. L. Vaghjiani, H. Lischka, J. Liu, and W. L. Hase. Direct Dynamics Simulation of the Activation and Dissociation of 1,5-Dinitrobiuret (HDNB). Journal of Physical Chemistry A 118, 2228-2236 (2014)
• S. Pratihar, S. Kohale, S. A. Vázquez, W. L. Hase. An Intermolecular Potential for Binding of Protonated Peptide Ions with Perfluorinated Hydrocarbon Surfaces. Journal of Physical Chemistry B 118, 5577-5588 (2014)
• U. Lourderaj, R. Sun, S. C. Kohale, G. L. Barnes, W. A. de Jong, T. L. Windus, and W. L. Hase. The VENUS/NWChem Software Package. Tight Coupling between Chemical Dynamics Simulations and Electronic Structure Theory. Computer Physics Communications 185, 1074-1080 (2014)

2013

• Payam Norouzzadeh, Charles W Myles and Daryoosh Vashae. Prediction of a large number of electron pockets near the band edges in type-VIII clathrate Si46 and its physical properties from first principles. J. Phys.: Condens. Matter 25 (2013) 475502
• Payam Norouzzadeh, Charles W Myles and Daryoosh Vasha e. Structural, electronic, phonon and thermodynamic properties of hypothetical type-VIII clathrates Ba8Si46and Ba8Al16Si30 investigated by first principles. J. Alloys Comp. (2013), http://dx.doi.org/10.1016/j.jallcom.2013.10.190
• Caleb D. Phillips et al. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices. Ecology and Evolution
• Caleb D. Phillips et al. Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography. Molecular Ecology
• J. I. HOFFMAN, S. M. GRANT, J. FORCADA and C. D. PHILLIPS. Bayesian inference of a historical bottleneck in a heavily exploited marine mammal. Molecular Ecology
• Christopher D. Rock. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends in Plant Science, Available online 28 August 2013, ISSN 1360-1385, http://dx.doi.org/10.1016/j.tplants.2013.07.006. (http://www.sciencedirect.com/science/article/pii/S1360138513001490)
• Ou-Yang F, Luo Q-J, Zhang Y, Richardson CR, Jiang Y-W, Rock CD. Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice. Functional & Integrative Genomics, FIGE-D-12-00099R1 in press (2013)
• Jia F, Rock CD. MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis. Plant Molecular Biology. DOI 10.1007/s11103-013-0015-6
• M. Paranjothy, R. Sun, Y. Zhuang, and W. L. Hase.  Direct Chemical Dynamics Simulations: Coupling of Classical and Quasiclassical Trajectories with Electronic Structure Theory. WIREs Computational Molecular Science 3, 296–316 (2013)
• J. Mikosch, J. Zhang, S. Trippel, C. Eichhorn, R. Otto, R. Sun, W. A. de Jong, M. Weidemüller, W. L. Hase, and R. Wester. Indirect Dynamics in a Highly Exoergic Substitution Reaction. Journal of the American Chemical Society 135, 4250-4259 (2013)
• Y. Zhuang, M. R. Siebert, W. L. Hase, K. G. Kay, and M. Ceotto. Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations. Journal of Chemical Theory and Computation 9, 54-64 (2013)
• M. Ceotto, Y. Zhuang, and W. L. Hase. Accelerated Direct Semiclassical Molecular Dynamics Using a Compact Finite Difference Hessian Scheme. Journal of Chemical Physics 138, 054116/1-13 (2013)
• J. Zhang,U. Lourderaj, R. Sun, J. Mikosch, R. Wester, and W. L. Hase. Simulation Studies of the Cl^- + CH₃I S_N2 Nucleophilic Substitution Reaction: Comparison with Ion Imaging Experiments. Journal of Chemical Physics 138, 114309/1-13 (2013)
• M. Paranjothy, R. Sun, A. K. Paul, and W. L. Hase. Models for Intrinsic Non-RRKM Unimolecular Dynamics. Decomposition of the S_N2 Intermediate Cl^----CH₃Br. Zeitschrift für Physikalische Chemie 227, 1361-1379 (2013)
• S. Pratihar, S. C. Kohale, L. Yang, P. Manikandan, K. D. Gibson, D. R. Killiea, H. Yuan, S. J. Sibener, and W. L. Hase. Chemical Dynamics Simulations of High Energy Xenon Atom Collisions with the {0001} Surface of Hexagonal Ice. Journal of Physical Chemistry C 117, 2183-2193 (2013)
• L. Yang, D. Tunega, L. Xu, N. Govind, R. Sun, R. Taylor, H. Lischka, W. A. DeJong, and W. L. Hase. Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosponate (DMMP)/TiO₂ (110) Intermolecular Interaction. Journal of Physical Chemistry C 117, 17613-17622 (2013)

2012

• M. R. Siebert, P. Manikandan, R. Sun, D. J. Tantillo, and W. L. Hase. Gas-Phase Chemical Dynamics Simulations on the Bifurcating Potential Energy Surface of the Pimaradienyl Cation Rearrangement. Role of Enzymatic Steering in Abietic Acid Biosynthesis. Journal of Chemical Theory and Computation 8, 1212-1222 (2012)
• P. Manikandan and W. L. Hase. Comparison of Classical Chemical Dynamics Simulations of the Unimolecular Decomposition of Classical and Quantum Microcanonical Ensembles. Journal of Chemical Physics 136, 184110/1-9 (2012)
• R. Sun, K. Park, W. A. de Jong, H. Lischka, T. L. Windus, and W. L. Hase. Direct Dynamics Simulation of Dioxetane Formation and Decomposition via the Singlet •O–O–CH₂–CH₂• Biradical: Non-RRKM Dynamics. Journal of Chemical Physics 137, 044305/1-11 (2012)
• M. Paranjothy, M. R. Siebert, W. L. Hase, and S. M. Bachrach. Mechanism of Thiolate-Disulfide Exchange: Addition-Elimination or Effectively S_N2? Effect of a Shallow Intermediate in Gas-Phase Direct Dynamics Simulations. Journal of Physical Chemistry A 116, 11492 11499 (2012)
• L. Yang, R. Sun, and W. L. Hase. Direct Dynamics Determination of the Reaction Pathways for the Decomposition of the Cross-Linked Epoxy Resin Constituent CH₃-NH-CH=CH-CH₃. Computational and Theoretical Chemistry 990, 62-66 (2012)
• M. R. Siebert, A. J. A. Aquino, W. A. de Jong, G. Granucci, and W. L. Hase. Potential Energy Surface for C₂H₄I₂^+• Dissociation Including Spin-Orbit Effects. Molecular Physics 110, 2599-2609 (2012) (Peter Taylor Special Issue)
• A. C. West, J. D. Lynch, B. Sellner, H. Lischka, W. L. Hase, and T. L. Windus. O + C₂H₄ Potential Energy Surface: Excited States and Biradicals at the Multireference Level. Theoretical Chemistry Accounts 131, 1123-1131 (2012)
• A. C. West, J. D. Lynch, B. Sellner, H. Lischka, W. L. Hase, and T. L. Windus. O + C₂H₄ Potential Energy Surface: Lowest-lying Singlet at the Multireference Level. Theoretical Chemistry Accounts 131, 1279 (2012)

2011

• Jacek Jonca-Jasinski. Volume of Inter- and Intra-hemispheric Connections Relates to the Efficiency of Higher Cognitive Processing. Dissertation (August, 2011)
• M. R. Siebert, J. Zhang, S. V. Addepalli, D. J. Tantillo, and W. L. Hase. The Need for Enzymatic Steering in Abietic Acid Biosynthesis: Gas-Phase Chemical Dynamics Simulations of Carbocation Rearrangements on a Bifurcating Potential Energy Surface. Journal of the American Chemical Society 133, 8335–8343 (2011)
• L. Yang, R. Sun, and W. L. Hase. Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths and
  Arrhenius Parameters for Large Molecules. Journal of Chemical Theory and Computation 7, 3478-3483 (2011)
• G. L. Barnes, K. Young, L. Yang, and W. L. Hase. Fragmentation and Reactivity in Collisions of Protonated Diglycine with Chemically Modified Perfluorinated Alkylthiolate-Self-Assembled Monolayer Surfaces. Journal of Chemical Physics 134, 094106/1-13 (2011)
• P. Manikandan, J. A. Carter, D. D. Dlott, and W. L. Hase. Effect of Carbon Chain Length on the Dynamics of Heat Transfer at a Gold/Hydrocarbon Interface. Comparison of Simulation with Experiment. Journal of Physical Chemistry C 115, 9622-9628 (2011)
• M. R. Siebert, P. Manikandan, R. Sun, D. J. Tantillo, and W. L. Hase.

2010

• H. Wu, M. Rahman, J. Wang, U. Lourderaj, W. L. Hase, and Y. Zhuang. Higher-Accuracy Schemes for Approximating the Hessian from Electronic Structure Calculations in Chemical Dynamics Simulations. Journal of Chemical Physics 133, 074101/1-10 (2010)
• K. Park, A. West, E. Raheja, B. Sellner, H. Lischka, T. L. Windus, and W. L. Hase. Singlet and Triplet Potential Energy Surfaces for the O₂ + C₂H₄ Reaction. Journal of Chemical Physics 133, 184306/1-13 (2010)
• Y. Zhang, G. L. Barnes, T. Yan, and W. L. Hase. Model Non-Equilibrium Molecular Dynamics Simulations of Heat Transfer from a Hot Gold Surface to an Alkylthiolate Self-Assembled Monolayer. Physical Chemistry Chemical Physics 12, 4435-4445 (2010)
• J. Zhang, J. Mikosch, S. Trippel, R. Otto, M. Weidemüller, R. Wester, and W. L. Hase. F^- + CH₃I FCH₃ + I^- Reaction Dynamics. Non-Traditional Atomistic Mechanisms and Formation of a Hydrogen-Bonded Complex. Journal of Physical Chemistry Letters 1, 2747-2752 (2010)
• J. Zhang and W. L. Hase. Electronic Structure Theory Study of the F^- + CH₃I FCH₃ + I^- Potential Energy Surface. Journal of Physical Chemistry A 114, 9635–9643 (2010) (Schinke Festschrift)