This article presents an optimized and scalable semi-Lagrangian solver for the Vlasov–Poisson system in six-dimensional phase space. Grid-based solvers of the Vlasov equation are known to give ...accurate results. At the same time, these solvers are challenged by the curse of dimensionality resulting in very high memory requirements, and moreover, requiring highly efficient parallelization schemes. In this article, we consider the 6-D Vlasov–Poisson problem discretized by a split-step semi-Lagrangian scheme, using successive 1-D interpolations on 1-D stripes of the 6-D domain. Two parallelization paradigms are compared, a remapping scheme and a domain decomposition approach applied to the full 6-D problem. From numerical experiments, the latter approach is found to be superior in the massively parallel case in various respects. We address the challenge of artificial time step restrictions due to the decomposition of the domain by introducing a blocked one-sided communication scheme for the purely electrostatic case and a rotating mesh for the case with a constant magnetic field. In addition, we propose a pipelining scheme that enables to hide the costs for the halo communication between neighbor processes efficiently behind useful computation. Parallel scalability on up to 65,536 processes is demonstrated for benchmark problems on a supercomputer.
Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a ...few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2 -only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the methylomes of Dnmt2 -only organisms at single-base resolution. Our results show that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in Dnmt2 -deficient flies. Furthermore, genetically modified Dnmt2 -only mouse embryonic stem cells lost the DNA methylation patterns found in wild-type cells. Our results thus uncover fundamental differences among animal methylomes and suggest that DNA methylation is dispensable for a considerable number of eukaryotic organisms.
The square halophilic archaeon Haloquadratum walsbyi dominates NaCl-saturated and MgCl2 enriched aquatic ecosystems, which imposes a serious desiccation stress, caused by the extremely low water ...activity. The genome sequence was analyzed and physiological and physical experiments were carried out in order to reveal how H. walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress.
A rich repertoire of proteins involved in phosphate metabolism, phototrophic growth and extracellular protective polymers, including the largest archaeal protein (9159 amino acids), a homolog to eukaryotic mucins, are amongst the most outstanding features. A relatively low GC content (47.9%), 15-20% less than in other halophilic archaea, and one of the lowest coding densities (76.5%) known for prokaryotes might be an indication for the specialization in its unique environment
Although no direct genetic indication was found that can explain how this peculiar organism retains its square shape, the genome revealed several unique adaptive traits that allow this organism to thrive in its specific and extreme niche.
Abstract
Chemical short-range order (CSRO) refers to atoms of specific elements self-organising within a disordered crystalline matrix to form particular atomic neighbourhoods. CSRO is typically ...characterized indirectly, using volume-averaged or through projection microscopy techniques that fail to capture the three-dimensional atomistic architectures. Here, we present a machine-learning enhanced approach to break the inherent resolution limits of atom probe tomography enabling three-dimensional imaging of multiple CSROs. We showcase our approach by addressing a long-standing question encountered in body-centred-cubic Fe-Al alloys that see anomalous property changes upon heat treatment. We use it to evidence non-statistical B
2
-CSRO instead of the generally-expected D0
3
-CSRO. We introduce quantitative correlations among annealing temperature, CSRO, and nano-hardness and electrical resistivity. Our approach is further validated on modified D0
3
-CSRO detected in Fe-Ga. The proposed strategy can be generally employed to investigate short/medium/long-range ordering phenomena in different materials and help design future high-performance materials.
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, ...we use the Bayesian inference of EM (BioEM) formalism. By ranking structural models using posterior probabilities calculated for individual images, BioEM in principle addresses the challenge of working with highly dynamic or heterogeneous systems not easily handled in traditional EM reconstruction. However, the calculation of these posteriors for large numbers of particles and models is computationally demanding. Here we present highly parallelized, GPU-accelerated computer software that performs this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI parallelization combined with both CPU and GPU computing. The resulting BioEM software scales nearly ideally both on pure CPU and on CPU+GPU architectures, thus enabling Bayesian analysis of tens of thousands of images in a reasonable time. The general mathematical framework and robust algorithms are not limited to cryo-electron microscopy but can be generalized for electron tomography and other imaging experiments.
Program Title: BioEM.
Program Files doi:http://dx.doi.org/10.17632/d2jjs2wdhv.1
Licensing provisions: GNU GPL v3.
Programming language: C++, CUDA.
Nature of problem: Analysis of electron microscopy images.
Solution method: GPU-accelerated Bayesian inference with numerical grid sampling.
External routines/libraries: Boost 1.5, FFTW 3, MPI.
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