PetaFLOP Molecular Dynamics for Engineering Applications

Molecular dynamics (MD) simulations enable the investigation of multicomponent and multiphase processes relevant to engineering applications, such as droplet coalescence or bubble formation. These scenarios require the simulation of ensembles containing a large number of molecules. We present recent advances within the MD framework ls1 mardyn which is being developed with particular regard to this class of problems. We discuss several OpenMP schemes that deliver optimal performance at node-level. We have further introduced nonblocking communication and communication hiding for global collective operations. Together with revised data structures and vectorization, these improvements unleash PetaFLOP performance and enable multi-trillion atom simulations on the HLRS supercomputer Hazel Hen. We further present preliminary results achieved for droplet coalescence scenarios at a smaller scale.BMBF, 01IH16008, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der Partikelsimulatio

Effects of Microwave Treatment on Structure, Functional Properties and Antioxidant Activities of Germinated Tartary Buckwheat Protein

Tartary buckwheat protein (TBP) has promise as a potential source of novel natural nutrient plant protein ingredients. The modulating effects of microwave pretreatment at varying powers and times on the structure, functional properties, and antioxidant activities of germinated TBP were investigated. Compared with native germinated TBP, after microwave pretreatment, the content of free sulfhydryl groups in the germinated TBP increased, and the secondary structure changes showed a significant decrease in α-helix and an increase in random coil contents, and the intensity of the ultraviolet absorption peak increased (p < 0.05). In addition, microwave pretreatment significantly improved the solubility (24.37%), water-holding capacity (38.95%), emulsifying activity index (17.21%), emulsifying stability index (11.22%), foaming capacity (71.43%), and foaming stability (33.60%) of germinated TBP (p < 0.05), and the in vitro protein digestibility (5.56%) and antioxidant activities (DPPH (32.35%), ABTS (41.95%), and FRAP (41.46%)) of germinated TBP have also been improved. Among different treatment levels, a microwave level of 300 W/50 s gave the best results for the studied parameters. Specifically, microwave pretreatment could be a promising approach for modulating other germinated plant protein resources, as well as expanding the application of TBP

Indoor High-Precision 3D Positioning System Based on Visible-Light Communication Using Improved Whale Optimization Algorithm

Visible-light communication (VLC) is a promising method for indoor positioning. The received signal strength algorithm is the most widely used localization algorithm in visible-light positioning (VLP) systems. However, in a VLP system, the photodiode (PD) will have a small rotation angle during movement, which will result in a massive positioning error ignoring the angle. In this study, a three-dimensional (3D) indoor VLP system using an improved whale optimization algorithm (IWOA) is proposed to reduce the error caused by the PD rotation. Firstly, the model of the VLC system with the PD rotation angles is introduced. Secondly, a novel IWOA with an elite opposition-based learning strategy and Lévy flight strategy is proposed. The convergence speed and accuracy of the WOA are improved. Lastly, the IWOA algorithm is efficiently utilized to address the problem with the PD rotation in the indoor VLP system. Simulation results show that the average error of 3D positioning is 2.14 cm with no PD rotation. When the PD has a rotation angle, the average positioning error estimated by ignoring the rotation angle is 27.14 cm, while that estimated by considering the rotation angle is 7.85 cm. In the VLP system, the positioning error with the PD rotation angle is effectively reduced by the proposed algorithm, which can be applied in a variety of indoor location scenes

Indoor High-Precision 3D Positioning System Based on Visible-Light Communication Using Improved Whale Optimization Algorithm

Visible-light communication (VLC) is a promising method for indoor positioning. The received signal strength algorithm is the most widely used localization algorithm in visible-light positioning (VLP) systems. However, in a VLP system, the photodiode (PD) will have a small rotation angle during movement, which will result in a massive positioning error ignoring the angle. In this study, a three-dimensional (3D) indoor VLP system using an improved whale optimization algorithm (IWOA) is proposed to reduce the error caused by the PD rotation. Firstly, the model of the VLC system with the PD rotation angles is introduced. Secondly, a novel IWOA with an elite opposition-based learning strategy and Lévy flight strategy is proposed. The convergence speed and accuracy of the WOA are improved. Lastly, the IWOA algorithm is efficiently utilized to address the problem with the PD rotation in the indoor VLP system. Simulation results show that the average error of 3D positioning is 2.14 cm with no PD rotation. When the PD has a rotation angle, the average positioning error estimated by ignoring the rotation angle is 27.14 cm, while that estimated by considering the rotation angle is 7.85 cm. In the VLP system, the positioning error with the PD rotation angle is effectively reduced by the proposed algorithm, which can be applied in a variety of indoor location scenes

Forming Model Optimization and Microstructural Analysis of Medical Biological Porous Scaffolds Fabricated by Selective Laser Melting (SLM)

Optimally designed bone implants with a suitable porous structure have similar mechanical properties to bone tissue and at the same time have good biocompatible and excellent bioactivity. The preparation of medical biological porous scaffolds by metal 3D printing technology is one of the most promising and attractive biomedical applications. The traditional regular porous and self-growing porous scaffolds were established by using CAD and C4D software, and the different scaffolds of three-dimensional models in similar porosity was obtained. A three-dimensional model of a scaffold with a porous structure was designed, and the porous scaffold was prepared by selective laser melting (SLM) technique, and its microstructure and mechanical properties were analysed. Under the similar porosity, the average hardness of the surface of the self-growing structure porous scaffold reached 236.5HV, and the stress at 5% compressive strain after heat treatment was close to 75 MPa. The original surface of the 316L porous scaffold made by SLM has the potential to effectively promote the differentiation of MG63 cells into osteoblasts. At the same time, the surface morphology and structure of the self-growth scaffold are similar to human cancellous bone, which is conducive to cell attachment and growth, so it is more suitable for repairing diseased parts of human bones

Supplementary document for General phase-shifting algorithm for hybrid errors suppression using variable-frequency fringes - 6720911.pdf

Detailed description of the proposed algorithm in Section 2.

Visualization of Cell Membrane Tension Regulated by the Microfilaments as a “Shock Absorber” in Micropatterned Cells

The extracellular stress signal transmits along the cell membrane–cytoskeleton–focal adhesions (FAs) complex, regulating the cell function through membrane tension. However, the mechanism of the complex regulating membrane tension is still unclear. This study designed polydimethylsiloxane stamps with specific shapes to change the actin filaments’ arrangement and FAs’ distribution artificially in live cells, visualized the membrane tension in real time, and introduced the concept of information entropy to describe the order degree of the actin filaments and plasma membrane tension. The results showed that the actin filaments’ arrangement and FAs’ distribution in the patterned cells were changed significantly. The hypertonic solution resulted in the plasma membrane tension of the pattern cell changing more evenly and slowly in the zone rich in cytoskeletal filaments than in the zone lacking filaments. In addition, the membrane tension changed less in the adhesive area than in the non-adhesive area when destroying the cytoskeletal microfilaments. This suggested that patterned cells accumulated more actin filaments in the zone where FAs were difficult to generate to maintain the stability of the overall membrane tension. The actin filaments act as shock absorbers to cushion the alternation in membrane tension without changing the final value of membrane tension

HBXIP blocks myosin-IIA assembly by phosphorylating and interacting with NMHC-IIA in breast cancer metastasis

Tumor metastasis depends on the dynamic balance of the actomyosin cytoskeleton. As a key component of actomyosin filaments, non-muscle myosin-IIA disassembly contributes to tumor cell spreading and migration. However, its regulatory mechanism in tumor migration and invasion is poorly understood. Here, we found that oncoprotein hepatitis B X-interacting protein (HBXIP) blocked the myosin-IIA assemble state promoting breast cancer cell migration. Mechanistically, mass spectrometry analysis, co-immunoprecipitation assay and GST-pull down assay proved that HBXIP directly interacted with the assembly-competent domain (ACD) of non-muscle heavy chain myosin-IIA (NMHC-IIA). The interaction was enhanced by NMHC-IIA S1916 phosphorylation via HBXIP-recruited protein kinase PKCβII. Moreover, HBXIP induced the transcription of PRKCB, encoding PKCβII, by coactivating Sp1, and triggered PKCβII kinase activity. Interestingly, RNA sequencing and mouse metastasis model indicated that the anti-hyperlipidemic drug bezafibrate (BZF) suppressed breast cancer metastasis via inhibiting PKCβII-mediated NMHC-IIA phosphorylation in vitro and in vivo. We reveal a novel mechanism by which HBXIP promotes myosin-IIA disassembly via interacting and phosphorylating NMHC-IIA, and BZF can serve as an effective anti-metastatic drug in breast cancer