In this paper, we discuss the ability to numerically minimize the grand potential of hard disks in two-dimensional and of hard spheres in three-dimensional space within the framework of classical density functional and fundamental measure theory on modern graphics cards. Our main finding is that a massively parallel minimization leads to an enormous performance gain in comparison to standard sequential minimization schemes. Furthermore, the results indicate that in complex multi-dimensional situations, a heavy parallel minimization of the grand potential seems to be mandatory in order to reach a reasonable balance between accuracy and computational cost.
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http://dx.doi.org/10.1063/1.4997636 | DOI Listing |
J Biol Chem
January 2025
Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA. Electronic address:
Transient protein-protein interactions play key roles in controlling dynamic cellular responses. Many examples involve globular protein domains that bind to peptide sequences known as Short Linear Motifs (SLiMs), which are enriched in intrinsically disordered regions of proteins. Here we describe a novel functional assay for measuring SLiM binding, called Systematic Intracellular Motif Binding Analysis (SIMBA).
View Article and Find Full Text PDFMicroorganisms
January 2025
Hospital Juárez de México, Mexico City 07760, Mexico.
Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures.
View Article and Find Full Text PDFGenes (Basel)
January 2025
Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.
belongs to the unconventional myosin superfamily, and the myosin IIIa protein localizes on the tip of the stereocilia of vestibular and cochlear hair cells. Deficiencies in have been reported to cause the deformation of hair cells into abnormally long stereocilia with an increase in spacing. is a rare causative gene of autosomal recessive sensorineural hearing loss (DFNB30), with only 13 cases reported to date.
View Article and Find Full Text PDFGenes (Basel)
January 2025
Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.
Background/objectives: The gene is responsible for autosomal recessive non-syndromic sensorineural hearing loss and is assigned as DFNB18B. To date, 44 causative variants have been reported to cause non-syndromic hearing loss. However, the detailed clinical features for -associated hearing loss remain unclear.
View Article and Find Full Text PDFGenes (Basel)
December 2024
Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia.
Unlabelled: In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains.
Background/objectives: This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis.
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