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Source data for the paper "Atomistic simulations reveal the mechanism of photoactivation of a carotenoid-binding photoreceptor"

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Autori principali:	Arcidiacono, Amanda, Bondanza, Mattia, Cupellini, Lorenzo, Mennucci, Benedetta
Natura:	Recurso digital
Pubblicazione:	Zenodo 2025
Accesso online:	Acceder al recurso
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author	Arcidiacono, Amanda Bondanza, Mattia Cupellini, Lorenzo Mennucci, Benedetta
author_facet	Arcidiacono, Amanda Bondanza, Mattia Cupellini, Lorenzo Mennucci, Benedetta
contents	<p>The files contain the most important data from the paper "<em>Atomic simulations reveal the mechanism of photoactivation of a carotenoid-binding photoreceptor</em>". </p> <table style="border-collapse: collapse; width: 99.9732%;"><colgroup><col style="width: 28.8252%;"><col style="width: 71.1509%;"></colgroup> <tbody> <tr> <td>data_sh_cis.csv</td> <td>initial and final values for the isomerizind dihedral angles of cis-CAN@NTD</td> </tr> <tr> <td>data_sh_trans.csv</td> <td>initial and final values for the isomerizind dihedral angles of trans-CAN@NTD</td> </tr> <tr> <td>data_spectra_env_cis.csv</td> <td>values for the spectra of PPcis (in environment)</td> </tr> <tr> <td>data_spectra_env_trans.csv</td> <td>values for the spectra of PPtrans (in environment)</td> </tr> <tr> <td>data_spectra_env_ocpo.csv </td> <td>values for the spectra of OCPo (in environment)</td> </tr> <tr> <td>data_spectra_vac_cis.csv</td> <td>values for the spectra of PPcis (in vacuum)</td> </tr> <tr> <td>data_spectra_vac_trans.csv</td> <td>values for the spectra of PPtrans (in vacuum)</td> </tr> <tr> <td>data_spectra_vac_ocpo.csv</td> <td>values for the spectra of OCPo (in vacuum)</td> </tr> <tr> <td>trans_elec_map.csv</td> <td>map of average electrostatic interactions in the US-REMD (trans isomer)</td> </tr> <tr> <td>trans_lj_map.csv</td> <td>map of average non-electrostatic interactions in the US-REMD (trans isomer)</td> </tr> <tr> <td>cis_elec_map.csv</td> <td>map of average electrostatic interactions in the US-REMD (cis isomer)</td> </tr> <tr> <td>cis_lj_map.csv</td> <td>map of average non-electrostatic interactions in the US-REMD (cis isomer)</td> </tr> <tr> <td>data_usremd_cis.h5</td> <td>data (LJ and electrostatic interaction, potential energy, kinetic energy, temperature, collective variable) of each replica of the US-REMD simulations (cis isomer)</td> </tr> <tr> <td>data_usremd_trans.h5</td> <td>data (LJ and electrostatic interaction, potential energy, kinetic energy, temperature, collective variable) of each replica of the US-REMD simulations (trans isomer)</td> </tr> <tr> <td>structures.zip</td> <td> <p>representative structures from the photoproducts, US-REMD and surface hopping simulations.</p> <p>photoproduct -> representative structures from Figure 1.</p> <p>surface_hopping -> representative structures from Figure 4, initial and final conditions of the trajectories that succesfully reached the ground state in 20 ps.</p> <p>US-REMD -> representative structures from the local Free Energy minima.</p> </td> </tr> </tbody> </table> <p> </p>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_17288936
institution	Zenodo
language
publishDate	2025
publisher	Zenodo
record_format	zenodo
spellingShingle	Source data for the paper "Atomistic simulations reveal the mechanism of photoactivation of a carotenoid-binding photoreceptor" Arcidiacono, Amanda Bondanza, Mattia Cupellini, Lorenzo Mennucci, Benedetta <p>The files contain the most important data from the paper "<em>Atomic simulations reveal the mechanism of photoactivation of a carotenoid-binding photoreceptor</em>". </p> <table style="border-collapse: collapse; width: 99.9732%;"><colgroup><col style="width: 28.8252%;"><col style="width: 71.1509%;"></colgroup> <tbody> <tr> <td>data_sh_cis.csv</td> <td>initial and final values for the isomerizind dihedral angles of cis-CAN@NTD</td> </tr> <tr> <td>data_sh_trans.csv</td> <td>initial and final values for the isomerizind dihedral angles of trans-CAN@NTD</td> </tr> <tr> <td>data_spectra_env_cis.csv</td> <td>values for the spectra of PPcis (in environment)</td> </tr> <tr> <td>data_spectra_env_trans.csv</td> <td>values for the spectra of PPtrans (in environment)</td> </tr> <tr> <td>data_spectra_env_ocpo.csv </td> <td>values for the spectra of OCPo (in environment)</td> </tr> <tr> <td>data_spectra_vac_cis.csv</td> <td>values for the spectra of PPcis (in vacuum)</td> </tr> <tr> <td>data_spectra_vac_trans.csv</td> <td>values for the spectra of PPtrans (in vacuum)</td> </tr> <tr> <td>data_spectra_vac_ocpo.csv</td> <td>values for the spectra of OCPo (in vacuum)</td> </tr> <tr> <td>trans_elec_map.csv</td> <td>map of average electrostatic interactions in the US-REMD (trans isomer)</td> </tr> <tr> <td>trans_lj_map.csv</td> <td>map of average non-electrostatic interactions in the US-REMD (trans isomer)</td> </tr> <tr> <td>cis_elec_map.csv</td> <td>map of average electrostatic interactions in the US-REMD (cis isomer)</td> </tr> <tr> <td>cis_lj_map.csv</td> <td>map of average non-electrostatic interactions in the US-REMD (cis isomer)</td> </tr> <tr> <td>data_usremd_cis.h5</td> <td>data (LJ and electrostatic interaction, potential energy, kinetic energy, temperature, collective variable) of each replica of the US-REMD simulations (cis isomer)</td> </tr> <tr> <td>data_usremd_trans.h5</td> <td>data (LJ and electrostatic interaction, potential energy, kinetic energy, temperature, collective variable) of each replica of the US-REMD simulations (trans isomer)</td> </tr> <tr> <td>structures.zip</td> <td> <p>representative structures from the photoproducts, US-REMD and surface hopping simulations.</p> <p>photoproduct -> representative structures from Figure 1.</p> <p>surface_hopping -> representative structures from Figure 4, initial and final conditions of the trajectories that succesfully reached the ground state in 20 ps.</p> <p>US-REMD -> representative structures from the local Free Energy minima.</p> </td> </tr> </tbody> </table> <p> </p>
title	Source data for the paper "Atomistic simulations reveal the mechanism of photoactivation of a carotenoid-binding photoreceptor"
url	https://doi.org/10.5281/zenodo.17288936