The fully analytic gradient of the second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity (RI) approximation in the fragment molecular orbital (FMO) framework is derived and implemented using a hybrid multilevel parallel programming model, a combination of the general distributed data interface (GDDI) and the OpenMP API. The FMO/MP2 analytic gradient contains three parts, i.e., the internal fragment component, the electrostatic potential (ESP) component, and the response terms. The RI approximation is applied to the internal fragment MP2 gradient term, whose MP2 densities and monomer MP2 Lagrangians are shared with the ESP and the response terms. The FMO/RI-MP2 analytic gradient implementation is validated against the numerical gradient (with errors ∼10-10 Hartree/Bohr) and the energy conservation in molecular dynamics (MD) simulations using NVE ensembles. The RI approximation introduces an error of ∼10 Hartree/Bohr with a speedup of 4.0-8.0× compared with the currently available GDDI FMO/MP2 gradient. The node linear scaling of the fragmentation framework due to multilevel parallelism is well-preserved and is demonstrated in single-point gradient calculations of large water clusters (e.g., 1120 and 2165 molecules) using 300-800 KNL compute nodes with a parallel efficiency of more than 90%.
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Ultrasonics
January 2025
Department of Robotics and Mechatronics, AGH University of Krakow, 30-059 Krakow, Poland. Electronic address:
Ultrasound shear wave elastography (SWE) is widely used in clinical applications for non-invasive measurements of soft tissue viscoelasticity. The study of tissue viscoelasticity often involves the analysis of shear wave phase velocity dispersion curves, which show how the phase velocity varies with frequency or wavelength. In this study, we propose an alternative method to the two-dimensional Fourier transform (2D-FT) and Phase Gradient (PG) methods for shear wave phase velocity estimation.
View Article and Find Full Text PDFAdv Appl Bioinform Chem
January 2025
Department of Information Technology, Mutah University, Al-Karak, Jordan.
Purpose: The incidence of cancer, which is a serious public health concern, is increasing. A predictive analysis driven by machine learning was integrated with haematology parameters to create a method for the simultaneous diagnosis of several malignancies at different stages.
Patients And Methods: We analysed a newly collected dataset from various hospitals in Jordan comprising 19,537 laboratory reports (6,280 cancer and 13,257 noncancer cases).
Sci Rep
January 2025
Department of Nephrology, Kanazawa Medical University, 1-1 Daigaku, Uchinada, 920-0293, Ishikawa, Japan.
To decrease the number of chronic kidney disease (CKD), early diagnosis of diabetic kidney disease is required. We performed invariant information clustering (IIC)-based clustering on glomerular images obtained from nephrectomized kidneys of patients with and without diabetes. We also used visualizing techniques (gradient-weighted class activation mapping (Grad-CAM) and generative adversarial networks (GAN)) to identify the novel and early pathological changes on light microscopy in diabetic nephropathy.
View Article and Find Full Text PDFJ Pharm Biomed Anal
January 2025
Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China. Electronic address:
Radix Rehmanniae (RR) is a widely used herb in traditional Chinese Medicine with properties of tonifying the kidneys and nourishing the blood. Both raw and processed RR are effective for the treatment of diabetes in clinical practice. Oligosaccharides and iridoid glycosides are the primary active components responsible for the anti-diabetic effects of RR.
View Article and Find Full Text PDFEur J Popul
January 2025
Stockholm University Demography Unit, Department of Sociology, Stockholm University, Stockholm, Sweden.
Research has shown that married individuals live longer lives than unmarried women and men. A smaller number of studies have included non-marital cohabitation and have found that their mortality falls between the married and other unmarried groups. There are indications that the cohabiting population is diverse in terms of mortality risk, yet very little is known about how the association is related to age and stages of the life course.
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