430 research outputs found

    An hourglass-free formulation for total Lagrangian smoothed particle hydrodynamics

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    The total Lagrangian smoothed particle hydrodynamics (TL-SPH) for elastic solid dynamics suffers from hourglass modes which can grow and lead to the failure of simulation for problems with large deformation. To address this long-standing issue, we present an hourglass-free formulation based on volumetric-devioatric stress decomposition. Inspired by the fact that the artifact of nonphysical zigzag particle distribution induced by the hourglass modes is mainly characterized by shear deformation and the standard SPH discretization for the viscous term in the Navier-Stokes (NS) equation, the present formulation computes the action of shear stress directly through the Laplacian of displacement other than from the divergence of shear stress. A comprehensive set of challenging benchmark cases are simulated to demonstrate that, while improving accuracy and computational efficiency, the present formulation is able to eliminate the hourglass modes and achieves very good numerical stability with a single general effective parameter. In addition, the deformation of a practically relevant stent structure is simulated to demonstrate the potential of the present method in the field of biomechanics.Comment: 38 pages 21 figure

    Revisiting the TALE repeat

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    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33–35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13238-014-0035-2) contains supplementary material, which is available to authorized users

    An explicit multi-time stepping algorithm for multi-time scale coupling problems in SPH

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    Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step algorithm coupled with a solid dynamic relaxation scheme. The explicit scheme simplifies the equation system in contrast to the implicit scheme, while the multi-time step algorithm allows the equations of different physical processes to be solved under different time step sizes. Furthermore, an implicit viscous damping relaxation technique is applied to significantly reduce computational iterations required to achieve equilibrium in the comparatively fast solid response process. To validate the accuracy and efficiency of the proposed algorithm, two distinct scenarios, i.e., a nonlinear hardening bar stretching and a fluid diffusion coupled with Nafion membrane flexure, are simulated. The results show good agreement with experimental data and results from other numerical methods, and the simulation time is reduced firstly by independently addressing different processes with the multi-time step algorithm and secondly decreasing solid dynamic relaxation time through the incorporation of damping techniques.Comment: 37 pages 20 figure

    High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs

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    Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scientific computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We find that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of 1010 to 10310^3 depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.Comment: work presented in NYSDS 201

    A qualitative exploration of perceptions and experiences of contraceptive use, abortion and post-abortion family planning services (PAFP) in three provinces in China

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    Background: The INPAC project aims to evaluate the effectiveness of integrated post-abortion family planning (PAFP) services into existing hospital based abortion services in China. A qualitative study was conducted in three provinces to contribute to developing effective PAFP services through understanding influences on contraceptive use, experiences of abortion and existing PAFP, and their effect on future contraceptive practices from the perspective of users, in the context of social and institutional change. Methods: Twenty-nine in-depth interviews (IDIs) were undertaken with women who had experienced abortion between 1 and 6 months prior to interview, recruited from three urban and two rural facilities in each province. Thirteen IDIs were also conducted with male partners. Six focus group discussions (FGDs) were carried out with community members from different social groups, including unmarried and married women and men, urban residents and rural-to-urban migrants. Results: Social networks and norms are important in shaping attitudes and behaviour towards abortion and contraception. Widespread concerns were expressed about side-effects, reliability and effects on future fertility of some modern contraceptives. The combination of limited information and choices and a lack of person-centred counselling in PAFP with anxieties about side effects underlies the widespread use of unreliable methods. Gendered power relations significantly influence contraceptive (non) use, with several examples illustrating women's relative lack of power to decide on a method, particularly in the case of condoms. Although the availability of contraceptive information from respected providers can offer impetus for individual behaviour change, social distance from providers reduces opportunities for clients to discuss their difficulties regarding contraceptive use; particularly, but not exclusively for young, unmarried clients. Conclusions: Increased access to non-commercial, reliable information on contraceptive methods is needed. PAFP services must go beyond simple information provision to ensure that providers take a more personcentred approach, which considers the most appropriate method for individual clients and probes for the underlying influences on contraceptive (non) use. More sensitive reflection on gender norms and relationships is required during counselling and, where women choose this, efforts should be made to include their male partners. Specific attention to provider positionality and skills for counselling young, unmarried clients is needed

    Evaluation of the Ecological Quality of the Taishan Region Based on Landsat Series of Satellite Images

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    The deterioration of ecological environment has seriously restricted regional sustainable development. Taishan region is one of the ecological protection and restoration of life community of mountains-rivers-forests-farmlands-lakes-grasslands in China. Its ecological quality changes are directly related to the overall layout of ecological restoration and protection projects. In this study, the Taishan region of China was taken as study area, and the grade change, spatial distribution, and spatial temporal fluctuation of the ecological environment quality were quantified. Based on the ENVI platform, the Landsat series of three images of the Taishan region in 2005, 2013, and 2017 serve as the data source, and the remote sensing ecological index model (RSEI) was used. According to the change characteristics of land use types, the driving factors of ecological environmental quality change were analyzed. The results showed that: (1) The area ratio of the ecological environment quality above the middle level was in order from large to small: 2005 (97.37%) > 2017 (91.46%) > 2013 (84.64%). (2) The overall quality of the ecological environment declined during the period of 2005-2013. (3) The overall change ranges from 2013 to 2017 are smaller than those from 2005 to 2013. The area of the deteriorating area decreased by 44.90%, and the area of the constant area and the area of the area that improved increased by 16.17% and 28.72%, respectively. During 2013-2017, the general trend is getting better and better. The improved areas were mainly concentrated in the main urban areas (Taishan District, Daiyue District), eastern Ningyang County, and western Xintai City. The research results can provide a scientific basis for the scientific evaluation of the ecological environment quality during the development and construction of the region, and have important value in the design and application of the ecological environment quality optimization path
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