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The theoretical prediction of molecular electronic spectra by means of quantum mechanical (QM) computations is fundamental to gain a deep insight into many photophysical and photochemical processes. A computational strategy that is attracting significant attention is the so-called Nuclear Ensemble Approach (NEA), that relies on generating a representative ensemble of nuclear geometries around the equilibrium structure and computing the vertical excitation energies (Δ) and oscillator strengths () and each transition with a line-shaped function with empirical full-width δ. Frequently, the choice of δ is carried out by visually finding the trade-off between artificial vibronic features (small δ) and over-smoothing of electronic signatures (large δ). Nevertheless, this approach is not satisfactory, as it relies on a subjective perception and may lead to spectral inaccuracies overall when the number of sampled configurations is limited due to an excessive computational burden (high-level QM methods, complex systems, solvent effects, etc.). In this work, we have developed and tested a new approach to reconstruct NEA spectra, dubbed GMM-NEA, based on the use of Gaussian Mixture Models (GMMs), a probabilistic machine learning algorithm, that circumvents the phenomenological broadening assumption and, in turn, the use of δ altogether. We show that GMM-NEA systematically outperforms other data-driven models to automatically select δ overall for small datasets. In addition, we report the use of an algorithm to detect anomalous QM computations (outliers) that can affect the overall shape and uncertainty of the NEA spectra. Finally, we apply GMM-NEA to predict the photolysis rate for HgBrOOH, a compound involved in Earth's atmospheric chemistry.
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http://dx.doi.org/10.1021/acs.jctc.2c00004 | DOI Listing |
PLoS One
September 2025
Center for Radiological Research, Columbia University Irving Medical Center, New York, New York, United States of America.
In the event of a large-scale radiological or nuclear emergency, a rapid, high-throughput screening tool will be essential for efficient triage of potentially exposed individuals, optimizing scarce medical resources and ensuring timely care. The objective of this work was to characterize the effects of age and sex on two intracellular lymphocyte protein biomarkers, BAX and p53, for early radiation exposure classification in the human population, using an imaging flow cytometry-based platform for rapid biomarker quantification in whole blood samples. Peripheral blood samples from male and female donors, across three adult age groups (young adult, middle-aged, senior) and a juvenile cohort, were X-irradiated (0-5 Gy), and biomarker expression was quantified at two- and three-days post-exposure.
View Article and Find Full Text PDFJ Chem Theory Comput
September 2025
Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany.
Intrinsically disordered proteins (IDPs) pose a challenge for structural characterization, as experimental methods lack the subnanometer/subnanosecond resolution to capture their dynamic conformational ensembles. Molecular dynamics (MD) simulations can, in principle, provide this information, but for the simulation of IDPs, dedicated protein and water force fields are needed, as traditional MD models for folded proteins prove inadequate for IDPs. Substantial effort was invested to develop IDP-specific force fields, but their performance in describing IDPs that undergo conformational changes─such as those induced by molecular partner binding or changes in solution environment─remains underexplored.
View Article and Find Full Text PDFClin Nucl Med
September 2025
Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland.
Background: Non-small cell lung cancer (NSCLC) is a complex disease characterized by diverse clinical, genetic, and histopathologic traits, necessitating personalized treatment approaches. While numerous biomarkers have been introduced for NSCLC prognostication, no single source of information can provide a comprehensive understanding of the disease. However, integrating biomarkers from multiple sources may offer a holistic view of the disease, enabling more accurate predictions.
View Article and Find Full Text PDFEcol Evol
September 2025
Research Institute on Terrestrial Ecosystems, National Research Council Porano Italy.
is an endemic tree species native to the Southern Italian Apennines and north-eastern Corsica, renowned for its ecological significance. Climate change projections for the Mediterranean basin indicate range shifts and increased fragmentation for many forest trees, including . Hybridization with the sympatric in the central part of its Italian native range may also influence the genetic structure and conservation priorities for .
View Article and Find Full Text PDFChemPhotoChem
March 2025
Max Planck Research Group, Faculty of Chemistry and Pharmacy, Universidad del Atlántico, Barranquilla, 081007, Colombia.
Azocompounds are among the most important group of molecular photoswitches due to their multiple applications in various scientific areas. We studied the thermal and photochemical reactions of an azocompound with photo-induced antibiotic properties using calculations based on Kohn-Shan, Spin-Flip and time-dependent Density Functional Theory. Our primary goal is to understand the absorption spectra and isomerization pathways governing the molecule's light-controlled antibiotic activity.
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