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PUBLICATIONS

Submitted and Published Papers

13.   "Conical intersection accessibility dictates brightness in red fluorescent proteins", E. Pieri, A. R. Walker, M. Zhu, T. J. Martínez, J. Am. Chem. Soc., 2024, DOI: 10.1021/jacs.4c00458.

12.   "Modeling pH-dependent biomolecular photochemistry", E. Pieri, O. Weingart, M. Huix-Rotllant, V. Ledentu, M. Garavelli, N. Ferré, J. Chem. Theory Comput., 2024, DOI: 10.1021/acs.jctc.3c00980.

 

11.   "TeraChem Protocol Buffers (TCPB): Accelerating QM and QM/MM Simulations with a Client-Server Model.", V. W. D. Cruzeiro, Y. Wang, E. Pieri, E. G. Hohenstein, T. J. Martínez, J. Chem. Phys., 2023, DOI: 10.1063/5.0130886.

10.   "The Non-Adiabatic Nanoreactor: Towards the Automated Discovery of Photochemistry.", E. Pieri, D. Lahana, A. M. Chang, C. R. Aldaz, K. C. Thompson and T. J. Martínez, Chemical Science, 2021, 12, 7294-7307, DOI:10.1039/D1SC00775K.

9.    "ChemVox: Voice-Controlled Quantum Chemistry.", U. Raucci, A. Valentini, E. Pieri, H. Weir, S. Seritan and T. J. Martínez, Nature Computational Science, 2021, 1, 42-45 DOI:10.1038/s43588-020-00012-9.

8.    "Frontiers in Multiscale Modelling of Photoreceptor Proteins", M. Mroginski, S. Adam, G. Amoyal, A. Barnoy, A. Bondar, V. Borin, J. Church, T. Domratcheva, B. Ensing, F. Fanelli, N. Ferré, O. Filiba, L. González, R. González, C. González-Espinoza, R. Kar, L. Kemmler, S. Kim, J. Kongsted, A. Krylov, Y. Lahav, M. Lazaratos, Q. Eddin, I. Navizet, A. Nemukhin, Ma. Olivucci, J. Olsen, A. Pérez de Alba Ortíz, E. Pieri, A. Rao, Y. Rhee, N. Ricardi, S. Sen, I. Solov’yov, L. De Vico, T. Wesolowski, C. Wiebeler, X. Yang and I. Schapiro, Photochem. Photobiol., Invited Review, 2020, DOI:10.1111/php.13372.

7.    "Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy.", B. A. Erickson, Z.N. Heim, E. Pieri, E. Liu, T. J. Martínez and D. M. Neumark, J. Phys. Chem. A 2019, 123, 50, 10676-10684, DOI:10.1021/acs.jpca.9b08258.

 

6.    "CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum.", E. Pieri, V. Ledentu, M. Sahlin, F. Dehez, C. Chipot, M. Olivucci and N. Ferré, J. Chem. Theory Comput. 2019, 15, 8, 4535-4546, DOI:10.1021/acs.jctc.9b00221.

5.    "Mapping the Ultrafast Vibrational Dynamics of all-Trans and 13-Cis Retinal Isomerization in Anabaena Sen- sory Rhodopsin.", P. P. Roy, Y. Kato, R. Abe-Yoshizumi, E. Pieri, N. Ferré, H. Kandori and T. Buckup, Phys. Chem. Chem. Phys., 2018, 20, 30159-30173, DOI:10.1039/c8cp05469j.

4.    "Sampling the protonation states: pH-dependent UV absorption spectrum of a polypeptide dyad.", E. Pieri, V. Ledentu, M. Huix-Rotllant and N. Ferré, Phys. Chem. Chem. Phys., 2018, 20, 23252-23261, DOI:10.1039/c8cp03557a.

3.    "pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena Sensory Rhodopsin.", M. Stenrup, E. Pieri, V. Ledentu and N. Ferré, Phys. Chem. Chem. Phys., 2017, 19, 14073-14084, DOI:10.1039/c7cp00991g.

2.    "Design, synthesis and dynamics of a Green Fluorescent Protein fluorophore mimic with an ultrafast switching function.", M. Paolino, M. Gueye, E. Pieri, M. Manathunga, S. Fusi, L. Latterini, D. Pannacci, M. Filatov, J. Léonard, M. Olivucci and A. Cappelli, J. Am. Chem. Soc. 2016, 138, 31, 9807-9825, DOI:10.1021/jacs.5b10812.

1.    "Directionality of Double-Bond Photoisomerization Dynamics Induced by a Single Stereogenic Center.", G. Marchand, J. Eng, I. Schapiro, A. Valentini, L. M. Frutos, E. Pieri, M. Olivucci, J. Léonard and E. Gindensperger, J. Phys. Chem. Lett. 2015, 6, 4, 599-604, DOI:10.1021/jz502644h.

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