The development of accurate and fast computational procedures for the calculation of X-ray spectroscopies is paramount to facilitate theoretical analysis of modern X-ray experiments on molecules. Herein, we present the extension of Cluster Perturbation theory to comprehend the calculation of core excited states and core ionization potentials using the core-valence separation approximation, which has seen widespread success for various quantum chemistry methods. We derive the theoretical framework for introducing core-valence separation into Cluster Perturbation series for excitation energies and display the performance of the methodology in S(D) orbital excitation spaces. The obtained core excitation energies on a test set of medium sized organic molecules show that carbon, nitrogen, and oxygen K-edge excitation energies can be determined with errors below 2 eV relative to the CCSD reference results using the developed CPS(D) excitation energy models which can be used for systems way beyond the reach of conventional CCSD.
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Sci Rep
December 2024
Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada.
Hoxa5 plays numerous roles in development, but its downstream molecular effects are mostly unknown. We applied bulk RNA-seq assays to characterize the transcriptional impact of the loss of Hoxa5 gene function in seven different biological contexts, including developing respiratory and musculoskeletal tissues that present phenotypes in Hoxa5 mouse mutants. This global analysis revealed few common transcriptional changes, suggesting that HOXA5 acts mainly via the regulation of context-specific effectors.
View Article and Find Full Text PDFEBioMedicine
December 2024
CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Centre for Physiology and Pharmacology, Medical University of Vienna; Vienna, Austria. Electronic address:
Background: High content imaging-based functional precision medicine approaches have been developed and successfully applied in the field of haemato-oncology. For rheumatoid arthritis (RA), treatment selection is still based on a trial-and-error principle, and biomarkers for patient stratification and drug response prediction are needed.
Methods: A high content, high throughput microscopy-based phenotyping pipeline for peripheral blood mononuclear cells (PBMCs) was developed, allowing for the quantification of cell type frequencies, cell type specific morphology and intercellular interactions from patients with RA (n = 65) and healthy controls (HC, n = 33).
Biochem Biophys Res Commun
December 2024
Department of Biological Chemistry, School of Pharmacy and Biochemistry, University of Buenos Aires and Institute of Chemistry and Biological Physical Chemistry (IQUIFIB, UBA-CONICET), Junin 956, 1113, Buenos Aires, Argentina. Electronic address:
Here we explore the interplay between physical and chemical perturbants to unravel links among native folding, amorphous and ordered aggregation scenarios in IFABP (rat intestinal fatty acid binding protein). This small beta-barrel protein undergoes amyloid-like aggregation above 15 % v/v trifluoroethanol. Our aim was to address the influence of sub-aggregating TFE concentrations on the unfolding transitions of IFABP.
View Article and Find Full Text PDFPhys Rev Lett
December 2024
Department of Astronomy, Cornell University, Ithaca, New York 14853, USA.
We present a new perturbative full-shape analysis of BOSS galaxy clustering data, including the full combination of the galaxy power spectrum and bispectrum multipoles, baryon acoustic oscillations, and cross-correlations with the gravitational lensing of cosmic microwave background measured from Planck. Assuming the ΛCDM model, we constrain the matter density fraction Ω_{m}=0.3138±0.
View Article and Find Full Text PDFBiophys J
December 2024
Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, TX 77843, USA,; Department of Nutrition, Texas A&M University, College Station, TX 77843, USA,; CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX 77843, USA,. Electronic address:
Cholesterol-enriched plasma membrane domains are known to serve as signaling platforms in a diverse array of cellular processes. However, the link between cholesterol homeostasis and mutant APC-KRas-associated colorectal tumorigenesis remains to be established. Thus, we investigated the impact of Apc-Kras on (i) colonocyte plasma membrane cholesterol homeostasis, order, and receptor nanoclustering, (ii) colonocyte cell proliferation, and (iii) whether these effects are modulated by select membrane active dietaries (MADs).
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