[HTML][HTML] Deciphering photoreceptors through atomistic modeling from light absorption to conformational response
In this review, we discuss the successes and challenges of the atomistic modeling of
photoreceptors. Throughout our presentation, we integrate explanations of the primary …
photoreceptors. Throughout our presentation, we integrate explanations of the primary …
Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment
This roadmap reviews the new, highly interdisciplinary research field studying the behavior
of condensed matter systems exposed to radiation. The Review highlights several recent …
of condensed matter systems exposed to radiation. The Review highlights several recent …
Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying
the solvation process of molecules in water at the nuclear quantum mechanical level with …
the solvation process of molecules in water at the nuclear quantum mechanical level with …
A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics
This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann
extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in …
extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in …
Taming the third order cumulant approximation to linear optical spectroscopy
L Allan, TJ Zuehlsdorff - The Journal of Chemical Physics, 2024 - pubs.aip.org
The second order cumulant method offers a promising pathway to predicting optical
properties in condensed phase systems. It allows for the computation of linear absorption …
properties in condensed phase systems. It allows for the computation of linear absorption …
Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method
This paper reports the improvement in the efficiency of embedded‐cluster model (ECM)
calculations in ORCA thanks to the implementation of the fast multipole method. Our …
calculations in ORCA thanks to the implementation of the fast multipole method. Our …
Importance of Polarizable Embedding for Computing Optical Rotation: The Case of Camphor in Ethanol
Solvation effects on optical rotation are notoriously challenging to model for computational
chemistry, as the specific rotatory power of a molecule can vary wildly going from apolar to …
chemistry, as the specific rotatory power of a molecule can vary wildly going from apolar to …
Protein-Driven Electron-Transfer Process in a Fatty Acid Photodecarboxylase
Naturally occurring photoenzymes are rare in nature, but among them, fatty acid
photodecarboxylases derived from Chlorella variabilis (Cv FAPs) have emerged as …
photodecarboxylases derived from Chlorella variabilis (Cv FAPs) have emerged as …
Investigating the Origin of Automatic Rhodopsin Modeling Outliers Using the Microbial Gloeobacter Rhodopsin as Testbed
D Barreiro-Lage, V Ledentu, J D'ascenzi… - The Journal of …, 2024 - ACS Publications
The automatic rhodopsin modeling (ARM) approach is a computational workflow devised for
the automatic buildup of hybrid quantum mechanics/molecular mechanics (QM/MM) models …
the automatic buildup of hybrid quantum mechanics/molecular mechanics (QM/MM) models …
First‐principles simulations of the fluorescence modulation of a COX‐2‐specific fluorogenic probe upon protein dimerization for cancer discrimination
Á Pérez‐Sánchez, C Curutchet… - Protein …, 2025 - Wiley Online Library
Abstract Cyclooxygenase‐2 (COX‐2) plays a crucial role in inflammation and has been
implicated in cancer development. Understanding the behavior of COX‐2 in different cellular …
implicated in cancer development. Understanding the behavior of COX‐2 in different cellular …