Optogenetics is a recent field where optics and genetic engineering are used to understand and ultimately control biomolecular processes. Opsins are light-gated ion channels that, upon light absorption at specific wavelengths, respond by opening or closing, conducting the flow of ions into or out of the cells (typically neurons), resulting in their activation or inhibition. The system of study in this project will be mainly channelrhodopsin-2 (ChR2), which is a subfamily of microbial-type rhodopsins [1]. It consists of seven transmembrane helices, with a covalently bound retinal as chromophore [2]. The conformer Des480 contains all-trans retinal and is non-conductive to any ions ("basal state"). Light absorption is followed by the photoisomerization of the all-trans retinal to the 13-cis configuration, driving cyclic conformational changes of the molecule, namely a photocycle, which consists of several intermediates such as P520, intermediate conductive to cations ("open sate", see the two-photocycle model of Channelrhodopsin 2 proposed in Ref. [3]). This project will perform simulations using recently developed quantum mechanics (QM)/molecular mechanics (MM) advanced methods on the ChR2 embedded in a lipid membrane. Well-parallelized codes will be employed, effectively making use of computational resources provided by Dardel. Classical molecular dynamics calculations will be performed with GROMACS [4] initially, for (a) the thermodynamic equilibration of ChR2 embedded in a POPC lipid membrane. This will be the less computationally demanding part of the project. Enhanced sampling simulations will be performed to reach metastable conformations of the system that would otherwise be inaccessible via classical MD. Some of the methods explored would be the on-the-fly probability enhanced sampling method (OPES) [5]. Through this technique, we plan to enhance the MD simulation to reach configurations corresponding to the P520 and P390 conformers. Once identified the metastable configurations, we will use QM/MM MD (Born-Oppenheimer) simulations on each of these conformations using the CPMD code [6] interfaced with a recent release of the MiMiC multiscale modeling framework [7], which allows simultaneous and on-the-fly communication with the CPMD code for the QM region and GROMACS for the MM subsystem. This will be the computationally more demanding part of the project. The obtention of the spectra will be retrieved by advanced QM/MM methods such as polarizable embedding, which allows for the polarization of the MM by the QM and vice-versa, providing a high-quality embedding potential key to providing accurate results on spectroscopic properties. The latter properties will be obtained by linear and quadratic response theory running the latest released VeloxChem code [8] on relevant snapshots, as well as for the obtention of averaged spectra and other properties, post-processing and analysis. References: [1] Science 296, 2395–2398 (2002) [2] Nature 482, 369–374 (2012) [3] Biophysics and Physicobiology, 2017, Vol. 14, 13−22. [4] J. Chem. Theory Comput. 2008, 4, 435−447 [5] The Journal of Physical Chemistry Letters 2020, 11 (7), 2731-2736 [6] CPMD, Copyright MPI für Festkörperforschung, Stuttgart, 1997−2001. http://www.cpmd.org/ [7] J. Chem. Phys. 14 July 2024; 161 (2): 022501. [8] WIREs Comput Mol Sci. 2020; 10:e1457.