GPU-acceleration for Moving Particle Semi-Implicit method

The MPS (Moving Particle Semi-implicit) method has been proven useful in computation free-surface hydrodynamic flows. Despite its applicability, one of its drawbacks in practical application is the high computational load. On the other hand, Graphics Processing Unit (GPU), which was originally developed for acceleration of computer graphics, now provides unprecedented capability for scientific computations. The main objective of this study is to develop a GPU-accelerated MPS code using CUDA (Compute Unified Device Architecture) language. Several techniques have been shown to optimize calculations in CUDA. In order to promote the acceleration by GPU, particular attentions are given to both the search of neighboring particles and the iterative solution of simultaneous linear equations in the Poisson Pressure Equation. In this paper, 2-dimensional calculations of elliptical drop evolution and dam break flow have been carried out by the GPU-accelerated MPS method, and the accuracy and performance of GPU-based code are investigated by comparing the results with those by CPU. It is shown that results of GPU-based calculations can be obtained much faster with the same reliability as the CPU-based ones

Prediction of 4f7-4f65d1 transition energy of Eu2+ in oxides based on first-principles calculations and machine learning

In order to establish a method to predict the 4f7-4f65d1 transition energy of Eu2+ in oxides, linear regression models were created based on first-principles calculations and machine learning. The model clusters consisting of the central Eu2+ and O2- ions closer than the nearest cation were constructed and the 4f7-4f65d1 absorption energy of Eu2+ in these clusters were calculated by first-principles many-electron calculation using the relativistic discrete variational multi-electron (DVME) method. However, the 4f7-4f65d1 absorption energies of Eu2+ in oxides calculated by relatively simple first-principles calculations tend to be overestimated by ca. 1.6 eV. In order to improve the accuracy of the prediction, we performed machine learning considering the calculated absorption energy as well as the other electronic and structural parameters as the attributes. As a result, the regression formula to predict the 4f7-4f65d1 absorption energy of Eu2+ in oxides has been created by machine learning. The 4f7-4f65d1 absorption energy predicted by this model are in good agreement with the experimental ones. Therefore, accuracy of the prediction was significantly improved compared to the simple first-principles calculations. In a similar way, a predictive model of the 4f65d1-4f7 emission energy of Eu2+ in oxides has been also create

Structural characterization of a binuclear center of a Cu-containing NO reductase homologue from Roseobacter denitrificans: EPR and resonance Raman studies

AbstractAerobic phototrophic bacterium Roseobacter denitrificans has a nitric oxide reductase (NOR) homologue with cytochrome c oxidase (CcO) activity. It is composed of two subunits that are homologous with NorC and NorB, and contains heme c, heme b, and copper in a 1:2:1 stoichiometry. This enzyme has virtually no NOR activity. Electron paramagnetic resonance (EPR) spectra of the air-oxidized enzyme showed signals of two low-spin hemes at 15 K. The high-spin heme species having relatively low signal intensity indicated that major part of heme b3 is EPR-silent due to an antiferromagnetic coupling to an adjacent CuB forming a Fe–Cu binuclear center. Resonance Raman (RR) spectrum of the oxidized enzyme suggested that heme b3 is six-coordinate high-spin species and the other hemes are six-coordinate low-spin species. The RR spectrum of the reduced enzyme showed that all the ferrous hemes are six-coordinate low-spin species. ν(Fe–CO) and ν(C–O) stretching modes were observed at 523 and 1969 cm−1, respectively, for CO-bound enzyme. In spite of the similarity to NOR in the primary structure, the frequency of ν(Fe–CO) mode is close to those of aa3- and bo3-type oxidases rather than that of NOR

Spinal cord stimulation for the treatment of pain and toe ulceration associated with systemic sclerosis: a case report

Systemic sclerosis is a complex disease characterized by extensive fibrosis, microvascular alterations, and additional sequelae. Microvascular alterations can cause painful ulcers and necrosis; however, conservative or surgical treatment is often challenging in terms of healing. The study aimed to describe a toe ulcer with systemic sclerosis and its' successful treatment with spinal cord stimulation. An 83-year-old woman, who was diagnosed with systemic sclerosis over the past decade, was distressed by a non-healing toe ulcer for an extended period of time. The patient underwent spinal cord stimulation treatment with the expectation of pain relief and an improvement in microcirculatory insufficiency. Her pain scales and microcirculation improved, and the toe ulcer healed. Furthermore, the frequency of Raynaud's symptoms was reduced, and the patient's pain decreased. There was no recurrence of the ulcer and she no longer needed a cane for walking

Early outcomes of thoracic endovascular aortic repair in treating type B aortic dissection

We evaluated the treatment results and aortic remodeling of Stanford type B aortic dissection （TBAD） following thoracic endovascular aortic repair （TEVAR） to determine the optimal timing to operate. Based on the duration from the onset of TBAD to surgery, 17 patients who underwent TEVAR for TBAD were divided into early （n＝10, TEVAR＜3 months from onset） and late （n＝7, TEVAR≥3 months from onset） groups. True- and false-lumen areas were measured at four levels （A-D） using contrast-enhanced computed tomography before and after TEVAR: A, immediately after the left subclavian artery branching; B, descending aorta at the tracheal bifurcation; C, aortic annulus; and D, diaphragm. The durations from the onset of TBAD to TEVAR were 46±25 days and 7.0±5.3 years in the early and late groups, respectively. No major intraoperative complications were observed in either group. However, the early group had one case of retrograde type A aortic dissection 54 days after TEVAR. In the early group, true-lumen area increased at all levels, except at level A, whereas false-lumen areas decreased at all levels （p＜0.05）. The late group showed no tendencies, except for an increased true-lumen area at level B. A difference in early aortic remodeling was observed—true-lumen area enlargement and false-lumen area decrease were more marked in the early group than the late group. TEVAR is useful when performed early after TBAD onset （within 3 months） and results in good aortic remodeling. In the late phase, the effect might be relatively smaller

Identification and characterization of novel components of a Ca2+/calmodulin-dependent protein kinase cascade in HeLa cells

AbstractIn this report, we cloned a novel calmodulin-kinase (CaM-KIδ) from HeLa cells and characterized its activation mechanism. CaM-KIδ exhibits Ca2+/CaM-dependent activity that is enhanced (∼30-fold) in vitro by phosphorylation of its Thr180 by CaM-K kinase (CaM-KK)α, consistent with detection of CaM-KIδ-activating activity in HeLa cells. We also identified a novel CaM-KKβ isoform (CaM-KKβ-3) in HeLa cells whose activity was highly Ca2+/CaM-independent. Transiently expressed CaM-KIδ exhibited enhanced protein kinase activity in HeLa cells without ionomycin stimulation. This sustained activation of CaM-KIδ was completely abolished by Thr180Ala mutation and inhibited by CaM-KK inhibitor, STO-609, indicating a functional CaM-KK/CaM-KIδ cascade in HeLa cells