Composing Scalable Nonlinear Algebraic Solvers

Most efficient linear solvers use composable algorithmic components, with the most common model being the combination of a Krylov accelerator and one or more preconditioners. A similar set of concepts may be used for nonlinear algebraic systems, where nonlinear composition of different nonlinear solvers may significantly improve the time to solution. We describe the basic concepts of nonlinear composition and preconditioning and present a number of solvers applicable to nonlinear partial differential equations. We have developed a software framework in order to easily explore the possible combinations of solvers. We show that the performance gains from using composed solvers can be substantial compared with gains from standard Newton-Krylov methods.Comment: 29 pages, 14 figures, 13 table

Nucleon Sigma Term and In-medium Quark Condensate in the Modified Quark-Meson Coupling Model

We evaluate the nucleon sigma term and in-medium quark condensate in the modified quark-meson coupling model which features a density-dependent bag constant. We obtain a nucleon sigma term consistent with its empirical value, which requires a significant reduction of the bag constant in the nuclear medium similar to those found in the previous works. The resulting in-medium quark condensate at low densities agrees well with the model independent linear order result. At higher densities, the magnitude of the in-medium quark condensate tends to increase, indicating no tendency toward chiral symmetry restoration.Comment: 9 pages, modified version to be publishe

Interference Fragmentation Functions and the Nucleon's Transversity

We introduce twist-two quark interference fragmentation functions in helicity density matrix formalism and study their physical implications. We show how the nucleon's transversity distribution can be probed through the final state interaction between two mesons ($\pi^+\pi^-$, $K\bar K$, or $\pi K$) produced in the current fragmentation region in deep inelastic scattering on a transversely polarized nucleon.Comment: Final version to be published in Phys. Rev. Let

In vivo transcriptional profiling of Plasmodium falciparum

BACKGROUND: Both host and pathogen factors contribute to disease outcome in Plasmodium falciparum infection. The feasibility of studying the P. falciparum in vivo transcriptome to understand parasite transcriptional response while it resides in the human host is presented. METHODS: A custom made oligonucleotide array with probes based on the P. falciparum 3D7 laboratory strain chromosome 2 sequence was used to detect in vivo P. falciparum transcripts. This study analyzed transcripts from total RNA derived from small blood samples of P. falciparum infected patients and compared the in vivo expression profile to the in vitro cultivated 3D7 strain transcriptome. RESULTS: The data demonstrated that in vivo transcription can be studied from a small blood sample, despite the abundance of human RNA. The in vivo transcriptome is similar to the 3D7 ring stage transcriptome, but there are significant differences in genes encoding a sexual stage antigen and surface proteins. CONCLUSIONS: Whole genome transcription analysis of P. falciparum can be carried out successfully and further studies in selected patient cohorts may provide insight into parasite in vivo biology and defense against host immunity

Modified Quark-Meson Coupling Model for Nuclear Matter

The quark-meson coupling model for nuclear matter, which describes nuclear matter as non-overlapping MIT bags bound by the self-consistent exchange of scalar and vector mesons, is modified by introducing medium modification of the bag constant. We model the density dependence of the bag constant in two different ways: one invokes a direct coupling of the bag constant to the scalar meson field, and the other relates the bag constant to the in-medium nucleon mass. Both models feature a decreasing bag constant with increasing density. We find that when the bag constant is significantly reduced in nuclear medium with respect to its free-space value, large canceling isoscalar Lorentz scalar and vector potentials for the nucleon in nuclear matter emerge naturally. Such potentials are comparable to those suggested by relativistic nuclear phenomenology and finite-density QCD sum rules. This suggests that the reduction of bag constant in nuclear medium may play an important role in low- and medium-energy nuclear physics.Comment: Part of the text is reordered, revised version to appear in Phys. Rev. C. 19 pages, ReVTeX, 4 figures embedde

In-medium relativistic kinetic theory and nucleon-meson systems

Within the $\sigma-\omega$ model of coupled nucleon-meson systems, a generalized relativistic Lenard--Balescu--equation is presented resulting from a relativistic random phase approximation (RRPA). This provides a systematic derivation of relativistic transport equations in the frame of nonequilibrium Green's function technique including medium effects as well as flucuation effects. It contains all possible processes due to one meson exchange and special attention is kept to the off--shell character of the particles. As a new feature of many particle effects, processes are possible which can be interpreted as particle creation and annihilation due to in-medium one meson exchange. In-medium cross sections are obtained from the generalized derivation of collision integrals, which possess complete crossing symmetries.Comment: See nucl-th/9310032 for revised version which the authors incompetently resubmitted rather than correctly replacing thi

QCD Sum Rules for Σ\Sigma Hyperons in Nuclear Matter

Within finite-density QCD sum-rule approach we investigate the self-energies of $\Sigma$ hyperons propagating in nuclear matter from a correlator of $\Sigma$ interpolating fields evaluated in the nuclear matter ground state. We find that the Lorentz vector self-energy of the $\Sigma$ is similar to the nucleon vector self-energy. The magnitude of Lorentz scalar self-energy of the $\Sigma$ is also close to the corresponding value for nucleon; however, this prediction is sensitive to the strangeness content of the nucleon and to the assumed density dependence of certain four-quark condensate. The scalar and vector self-energies tend to cancel, but not completely. The implications for the couplings of $\Sigma$ to the scalar and vector mesons in nuclear matter and for the $\Sigma$ spin-orbit force in a finite nucleus are discussed.Comment: 20 pages in revtex, 6 figures available under request as ps files, UMD preprint #94--11

On the Road to 6G: Visions, Requirements, Key Technologies and Testbeds

Fifth generation (5G) mobile communication systems have entered the stage of commercial development, providing users with new services and improved user experiences as well as offering a host of novel opportunities to various industries. However, 5G still faces many challenges. To address these challenges, international industrial, academic, and standards organizations have commenced research on sixth generation (6G) wireless communication systems. A series of white papers and survey papers have been published, which aim to define 6G in terms of requirements, application scenarios, key technologies, etc. Although ITU-R has been working on the 6G vision and it is expected to reach a consensus on what 6G will be by mid-2023, the related global discussions are still wide open and the existing literature has identified numerous open issues. This paper first provides a comprehensive portrayal of the 6G vision, technical requirements, and application scenarios, covering the current common understanding of 6G. Then, a critical appraisal of the 6G network architecture and key technologies is presented. Furthermore, existing testbeds and advanced 6G verification platforms are detailed for the first time. In addition, future research directions and open challenges are identified for stimulating the on-going global debate. Finally, lessons learned to date concerning 6G networks are discussed

A Reference Proteomic Database of Lactobacillus plantarum CMCC-P0002

Lactobacillus plantarum is a widespread probiotic bacteria found in many fermented food products. In this study, the whole-cell proteins and secretory proteins of L. plantarum were separated by two-dimensional electrophoresis method. A total of 434 proteins were identified by tandem mass spectrometry, including a plasmid-encoded hypothetical protein pLP9000_05. The information of first 20 highest abundance proteins was listed for the further genetic manipulation of L. plantarum, such as construction of high-level expressions system. Furthermore, the first interaction map of L. plantarum was established by Blue-Native/SDS-PAGE technique. A heterodimeric complex composed of maltose phosphorylase Map3 and Map2, and two homodimeric complexes composed of Map3 and Map2 respectively, were identified at the same time, indicating the important roles of these proteins. These findings provided valuable information for the further proteomic researches of L. plantarum

Identification of autophosphorylation sites in eukaryotic elongation factor-2 kinase

eEF2K [eEF2 (eukaryotic elongation factor 2) kinase] phosphorylates and inactivates the translation elongation factor eEF2. eEF2K is not a member of the main eukaryotic protein kinase superfamily, but instead belongs to a small group of so-called α-kinases. The activity of eEF2K is normally dependent upon Ca2+ and calmodulin. eEF2K has previously been shown to undergo autophosphorylation, the stoichiometry of which suggested the existence of multiple sites. In the present study we have identified several autophosphorylation sites, including Thr348, Thr353, Ser366 and Ser445, all of which are highly conserved among vertebrate eEF2Ks. We also identified a number of other sites, including Ser78, a known site of phosphorylation, and others, some of which are less well conserved. None of the sites lies in the catalytic domain, but three affect eEF2K activity. Mutation of Ser78, Thr348 and Ser366 to a non-phosphorylatable alanine residue decreased eEF2K activity. Phosphorylation of Thr348 was detected by immunoblotting after transfecting wild-type eEF2K into HEK (human embryonic kidney)-293 cells, but not after transfection with a kinase-inactive construct, confirming that this is indeed a site of autophosphorylation. Thr348 appears to be constitutively autophosphorylated in vitro. Interestingly, other recent data suggest that the corresponding residue in other α-kinases is also autophosphorylated and contributes to the activation of these enzymes [Crawley, Gharaei, Ye, Yang, Raveh, London, Schueler-Furman, Jia and Cote (2011) J. Biol. Chem. 286, 2607–2616]. Ser366 phosphorylation was also detected in intact cells, but was still observed in the kinase-inactive construct, demonstrating that this site is phosphorylated not only autocatalytically but also in trans by other kinases