Submissions and Preprints
1.  J. Campos Gonzalez Angulo, R. Alberstein, R.F. Ribeiro, F.A. Tezcan and J. Yuen-Zhou. Computational methodology for a coarse-grained simulation of auxetic, two-dimensional crystal dynamics. Submitted. arXiv:1711.11574.

2.  J. Yuen-Zhou, S.K. Saikin and V. Menon. Plexciton photoluminescence: van Hove anomalies and superradiance. Submitted. arXiV:1711.11213.

3.  R. de J. León Montiel, Z. Hu and J. Yuen-Zhou. Genuinely quantum effects in nonlinear spectroscopy: vacuum fluctuations and their induced superradiance. Submitted. arXiV:1606.05717.

1.  R.F. Ribeiro, L.A. Martínez-Martínez, M. Du, J.A. Campos-González-Angulo and J. Yuen-Zhou. Polariton chemistry: controlling molecular dynamics with optical cavities. (2018) Chem. Sci. DOI:10.1039/C8SC01043A.

2.  R.F. Ribeiro and J. Yuen-Zhou. Continuous vibronic symmetries in Jahn-Teller models: local and global aspects. (2018) J. Phys. B: Condens. Matter. DOI:10.1088/1361-648X/aac89e.

3.  R.F. Ribeiro, A. D. Dunkelberger, B. Xiang, W. Xiong, B. S. Simpkins, J. C. Owrutsky and J. Yuen-Zhou. Theory for Nonlinear Spectroscopy of Vibrational Polaritons. (2018) J. Phys. Chem. Lett. 3766--3771 (2018).

4.  M. Du, L.A. Martínez-Martínez, R.F. Ribeiro, Z. Hu, V.M. Menon and J. Yuen-Zhou. Theory of polariton long-range excitation energy transfer. (2018) Chem. Sci.DOI:10.1039/C8SC00171E.

5.  B. Xiang, R.F. Ribeiro, A.D. Dunkelberger, J. Wang, Y. Li, B.S. Simpkins, J.C. Owrutsky, J. Yuen-Zhou and W. Xiong.  Two-dimensional infrared spectroscopy of vibrational polaritons. (2018) Proc. Nat. Acad. Sci. DOI:10.1073/pnas.1722063115.

6.  L.A. Martínez-Martínez, M. Du, R.F. Ribeiro, S. Kéna-Cohen and J. Yuen-Zhou. Polariton-assisted Singlet Fission in Acene Aggregates. (2018) J. Phys. Chem. Lett. 9, 8, 1951-1957.
 Selected as ACS Editor's choice.

7.  L.A. Martínez-Martínez and J. Yuen-Zhou.  Comment on 'Quantum theory of collective strong coupling of molecular vibrations with a microcavity mode'. (2018) New J. Phys. 20:018002.

8.  L.A. Martínez-Martínez, R.F. Ribeiro, J.A. Campos-González-Angulo, and J. Yuen-Zhou. Can ultrastrong coupling change ground state chemical reactions? (2018) ACS Photonics. 5(1):167–176.
1.  R.F. Ribeiro and J. Yuen-Zhou. Vibronic ground-state degeneracies and the Berry Phase: A continuous symmetry perspective. (2017) J. Phys. Chem. Lett. 9(1):242-247.
1.  J. Yuen-Zhou, S.K. Saikin, T.Zhu, M. Onbalsi, C. Ross, V. Bulovic and M. Baldo. Plexciton Dirac points and topological modes. (2016) Nature Communications. 7:11783.
1.  A. Johnson, J. Yuen-Zhou, A. Aspuru-Guzik and J.J. Krich. Practical witness for electronic coherences. (2015) Journal of Chemical Physics. 141:244109.
1.  J. Yuen-Zhou, S. Saikin, N. Yao and A. Aspuru-Guzik. Topologically protected excitons in porphyrin thin films. (2014) Nature Materials 13:1026.

2.  J. Yuen-Zhou, D. Arias, D. Eisele, J.J. Krich, C. Steiner, K.A. Nelson, and A. Aspuru-Guzik. Coherent exciton dynamics in supramolecular light-harvesting nanotubes revealed by ultrafast quantum process tomography. (2014) ACS Nano 8(6):5527.
1.  J. Yuen-Zhou and A. Aspuru-Guzik. Remarks on time-dependent [current]-density functional theory for open quantum systems. (2013) Phys. Chem. Chem. Phys. 15:12626.
 Selected as a "hot article" by the editors.
1.  I. Kassal, J. Yuen-Zhou and S. Rahim-Keshari. Does coherence enhance transport in photosynthesis? (2012) J. Phys. Chem. Lett. 4(3):362.

2.  J. Yuen-Zhou, J.J. Krich and A. Aspuru-Guzik. A witness for coherent electronic vs vibronic-only oscillations in ultrafast spectroscopy. (2012) J. Chem. Phys. 136:234501.
1.  J. Yuen-Zhou, J.J. Krich, M. Mohseni and A. Aspuru-Guzik. Quantum state and process tomography of energy transfer systems via ultrafast spectroscopy. (2011) Proc. Nat. Acad. Sci. USA. 108(43):17615.

2.  J. Yuen-Zhou and A. Aspuru-Guzik. Quantum process tomography of excitonic dimers from two-dimensional electronic spectroscopy I: General theory and application to homodimers. (2011) J. Chem. Phys. 134:134505.
 Selected for the Virtual Journal of Quantum Information, April (2011) and the Virtual Journal of Ultrafast Science, May (2011).
 Selected for J. Chem. Phys. Editor's choice (2011).
1.  J. Yuen-Zhou, D.G. Tempel, C. Rodríguez-Rosario and A. Aspuru-Guzik. Time-Dependent Density Functional Theory for Open Quantum Systems with Unitary Propagation. (2010) Phys. Rev. Lett. 104:043001.
1.  J. Yuen-Zhou, C. Rodríguez-Rosario and A. Aspuru-Guzik. Time-dependent current-density functional theory for generalized open quantum systems. (2009) Phys. Chem. Chem. Phys. 11:4509. Special Issue on TD-DFT.
 Selected as a "hot article" by the editors.
1.  J. Yuen-Zhou, J.J. Krich, I. Kassal, A. Johnson and A. Aspuru-Guzik. Ultrafast spectroscopy: quantum information and wavepackets. (2014) IOP e-book. ISBN:978-0-750-31062-8.
Book Chapters
1.  J. Yuen-Zhou, J.J. Krich, I. Kassal and A. Aspuru-Guzik. Ultrafast Spectroscopy: Quantum Information and Wave Packets. (2017) In: I. Burghardt and S. Haacke (eds) Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies. Pan Stanford Publishing. ISBN:978-981-4745-34-5.

2.  D.G. Tempel, J. Yuen-Zhou and A. Aspuru-Guzik. Open Quantum Systems: Density Matrix Formalism and Applications. (2012) In: Marques M., Maitra N., Nogueira F., Gross E., Rubio A. (eds) Fundamentals of Time-Dependent Density Functional Theory. Lecture Notes in Physics, vol 837. Springer, Berlin, Heidelberg