A5016042457- Photoreceptor and optogenetics research
- Neural dynamics and brain function
- Molecular Communication and Nanonetworks
- Machine Learning in Materials Science
- Neuroscience and Neuropharmacology Research
- Spectroscopy and Quantum Chemical Studies
- Nicotinic Acetylcholine Receptors Study
- DNA and Nucleic Acid Chemistry
- bioluminescence and chemiluminescence research
- Organic Electronics and Photovoltaics
- Receptor Mechanisms and Signaling
- Advanced Fluorescence Microscopy Techniques
- Chemical Synthesis and Analysis
- Photochromic and Fluorescence Chemistry
- Luminescence and Fluorescent Materials
- Molecular Junctions and Nanostructures
- Molecular spectroscopy and chirality
- Advanced Chemical Physics Studies
- CO2 Reduction Techniques and Catalysts
- Force Microscopy Techniques and Applications
- Photosynthetic Processes and Mechanisms
University of Siena
2021-2024
University of Perugia
2024
We present a deep learning model able to predict excited singlet–triplet gaps with mean absolute error (MAE) of ≈20 meV obtain potential inverted (IST) candidates. exploit cutting-edge spherical message passing graph neural networks designed specifically for generating 3D representations in molecular learning. In nutshell, the takes as input list unsaturated heavy atom Cartesian coordinates and atomic numbers, producing output. exploited available large data collections train on ≈40,000...
Abstract The understanding of how the rhodopsin sequence can be modified to exactly modulate spectroscopic properties its retinal chromophore, is a prerequisite for rational design more effective optogenetic tools. One key problem that establishing rules satisfied achieving highly fluorescent rhodopsins with near infrared absorption. In present paper we use multi-configurational quantum chemistry construct computer model recently discovered natural rhodopsin, Neorhodopsin, displaying such...
Abstract RNA‐based tools for biological and pharmacological research are raising an increasing interest. Among these, RNA aptamers whose activity can be controlled via illumination with specific wavelengths represent important target. Here, we report on a proof‐of‐principle study supporting the viability of systematic use Morita‐Baylis‐Hillman adducts (MBHAs) synthesis light‐responsive building blocks. Accordingly, acetylated MBHA derivative was employed in functionalization four natural...
Abstract The lack of a theory capable connecting the amino acid sequence light-absorbing protein with its fluorescence brightness is hampering development tools for understanding neuronal communications. Here we demonstrate that can be established by constructing quantum chemical models set Archaerhodopsin reporters in their electronically excited state. We found experimentally observed increase yield proportional to computed decrease energy difference between fluorescent state and nearby...
Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions invariably triggered by the photoisomerization of a single retinal chromophore.
We compare the performance of three different multiconfigurational wave function-based electronic structure methods and two implementations spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The study is characterized by features: (i) it uses a small set quantum-classical trajectories rather than potential energy surface mapping, (ii) focuses, exclusively, on photoisomerization retinal protonated Schiff base models, (iii) probes effect both methyl substitution increase in length...
We present a computational protocol for the fast and automated screening of excited-state hybrid quantum mechanics/molecular mechanics (QM/MM) models rhodopsins to be used as fluorescent probes based on automatic rhodopsin modeling (a-ARM). Such "a-ARM fluorescence protocol" is implemented through general Python-based driver, PyARM, that also proposed here. The implementation performance are benchmarked using different sets variants whose absorption and, more relevantly, emission spectra...
Abstract Color tuning in animal and microbial rhodopsins has attracted the interest of many researchers, as color their common retinal chromophores is modulated by amino acid residues forming chromophore cavity. Critical cavity are often called “color switches”, rhodopsin effectively tuned through substitution. Well-known switches L/Q A/TS located C G helices structure respectively. Recently, we reported on a third G/P switch F helix light-driven sodium pumps KR2 Js NaR causing substantial...
A protocol combining molecular dynamics, density functional theory, machine learning, and kinetic Monte Carlo accurately predicts the dependence of charge mobility on mechanical deformations for organic semiconductors.
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that mechanistic details this process are drastically different depending on whether takes place gas phase, acetonitrile, or water. However, such results been produced using quantum chemical methods did not incorporate both static dynamic electron correlation. In order...
The mixed covalent/charge transfer character of the excited state AR-3 allows to introduce an isomerization-blocking barrier, ideal for engineering fluorescent mutants.
In recent years, the importance of intrinsic disorder in organic semiconductors has gained increasing attention as a factor limiting transport properties these substrates. particular, presence low-frequency phonon modes modulating questions adoption harmonic approximation theoretical descriptions such modes, since large displacements from equilibrium positions are expected. Herein, we have analyzed process several using combination molecular dynamics simulations based on quantum mechanically...