Matrix diagonalization is almost always involved in computing the density matrix needed in quantum chemistry calculations. In the case of modest matrix sizes (≲4000), performance of traditional dense diagonalization algorithms on modern GPUs is underwhelming compared to the peak performance of these devices. This motivates the exploration of alternative algorithms better suited to these types of architectures. We newly derive, and present in detail, an existing Chebyshev expansion algorithm [Liang et al., J. Chem. Phys. 119, 4117-4125 (2003)] whose number of required matrix multiplications scales with the square root of the number of terms in the expansion. Focusing on dense matrices of modest size, our implementation on GPUs results in large speed ups when compared to diagonalization. Additionally, we improve upon this existing method by capitalizing on the inherent task parallelism and concurrency in the algorithm. This improvement is implemented on GPUs by using CUDA and HIP streams via the MAGMA library and leads to a significant speed up over the serial-only approach for smaller (≲1000) matrix sizes. Finally, we apply our technique to a model system with a high density of states around the Fermi level, which typically presents significant challenges.
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Matrix Biol
December 2024
Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH; Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH. Electronic address:
Obesity is a growing concern in the US and world-wide, associated with an increased risk for several cardiometabolic diseases, including metabolic associated steatotic liver disease (MASLD). Currently, therapeutic interventions to prevent and/or treat MASLD are limited, and research is needed to identify new therapeutic targets. The specific-sized 35kDa fragment of hyaluronan (HA35), has gut protective and anti-inflammatory properties and a previous pilot clinical study reported it is well tolerated in healthy individuals.
View Article and Find Full Text PDFBMC Genomics
December 2024
School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China.
Background: The subcellular localization of mRNA plays a crucial role in gene expression regulation and various cellular processes. However, existing wet lab techniques like RNA-FISH are usually time-consuming, labor-intensive, and limited to specific tissue types. Researchers have developed several computational methods to predict mRNA subcellular localization to address this.
View Article and Find Full Text PDFEpidemics
December 2024
California Department of Public Health Center for Infectious Diseases, 850 Marina Bay Parkway, Richmond, CA 94804, United States. Electronic address:
The effective reproduction number serves as a metric of population-wide, time-varying disease spread. During the early years of the COVID-19 pandemic, this metric was primarily derived from case data, which has varied in quality and representativeness due to changes in testing volume, test-seeking behavior, and resource constraints. Deriving nowcasting estimates from alternative data sources such as wastewater provides complementary information that could inform future public health responses.
View Article and Find Full Text PDFGels
December 2024
Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Medicine, University of Debrecen, 4032 Debrecen, Hungary.
Hydrogels like agarose have long been used as sieving media for the electrophoresis-based analysis of biopolymers. During gelation, the individual agarose strands tend to form hydrogen-bond mediated double-helical structures, allowing thermal reversibility and adjustable pore sizes for molecular sieving applications. The addition of tetrahydroxyborate to the agarose matrix results in transitional chemical cross-linking, offering an additional pore size adjusting option.
View Article and Find Full Text PDFSci Total Environ
December 2024
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China; Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen 361003, China. Electronic address:
Carbon black nanoparticles (CBNPs) are ubiquitous in our daily ambient environment, either resulting from tobacco combustion or constituting the core of PM. Despite the potential risk of trafficking CBNPs to the fetus, the underlying toxicity of nano-sized carbon black particles in the placenta remains unambiguous. Pregnant C57BL/6 mice received intratracheal instillation of 30 nm or 120 nm CBNPs.
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