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Accurate Estimation of Diffusion Coefficients and their Uncertainties from Computer Simulation.
J Chem Theory Comput
January 2025
Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
Self-diffusion coefficients, *, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean squared displacements (MSDs) of mobile species. MSDs derived from simulations exhibit statistical noise that causes uncertainty in the resulting estimate of *. An optimal scheme for estimating * minimizes this uncertainty, i.
View Article and Find Full Text PDFLower bounds on trees and unicyclic graphs with respect to the misbalance rodeg index.
Heliyon
January 2025
Department of Computer and Information Sciences, Northumbria University, Newcastle, NE1 8ST, UK.
The Misbalance Rodeg () index stands out among the 148 discrete Adriatic indices demonstrating considerable predictive capabilities in evaluations carried out by the International Academy of Mathematical Chemistry. This index excels particularly in forecasting both the enthalpy and the standard enthalpy of vaporization for octane isomers. Despite its significant chemical applicability, the index has not been extensively explored in the literature.
View Article and Find Full Text PDFα-Amylase inhibitory potential of dihydropyrano coumarins: In silico and DFT analysis.
3 Biotech
February 2025
Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, 632014 India.
Unlabelled: Coumarin derivatives are one of the naturally occurring bioactive molecule. Dihydropyrano coumarins are one of the medicinally important derivatives of coumarin which have been reported to exhibit various bioactivity. However, there are no reports on their antihyperglycemic activities.
View Article and Find Full Text PDFTreatment options for Achilles tendinopathy: a scoping review of preclinical studies.
PeerJ
January 2025
University of Amsterdam, Amsterdam, Netherlands.
Background: Achilles tendinopathy (AT) management can be difficult, given the paucity of effective treatment options and the degenerative nature of the condition. Innovative therapies for Achilles tendinopathy are therefore direly needed. New therapeutic developments predominantly begin with preclinical animal and in vitro studies to understand the effects at the molecular level and to evaluate toxicity.
View Article and Find Full Text PDFVirseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.
PeerJ
January 2025
Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.
Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality.
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