Domain wall fermion calculation of nucleon g_A/g_V

We present a preliminary domain-wall fermion lattice-QCD calculation of isovector vector and axial charges, g_V and g_A, of the nucleon. Since the lattice renormalizations, Z_V and Z_A, of the currents are identical with DWF, the lattice ratio (g_A/g_V)^{lattice} directly yields the continuum value. Indeed Z_V determined from the matrix element of the vector current agrees closely with Z_A from a non-perturbative renormalization study of quark bilinears. We also obtain spin related quantities Delta-q/g_V and delta-q/g_V.Comment: Lattice 2000 (Hadronic Matrix Elements), 4 pages, 5 figure

Discotic liquid crystals of transition metal complexes 51(dagger): Synthesis and mesomorphism of flat-pumpkin-shaped phthalocyanine-fullerene dyads

We have synthesized a novel type of donor-acceptor liquid crystalline material, phthalocyanine-fullerene (Pc-C-60) dyad, [m,p,m'-(C14O)(3)PhO](6)PcCu-C-60 (7), and the Pc precursors, [m,p,m'-(C14O)(3)PhO](6)PcCu-OFBA (6) and [m,p,m'-(C14O)(3)PhO](6)PcCu-OH (5), and established their mesomorphism by using a polarizing optical microscope, a differential scanning calorimeter and a small angle X-ray diffractometer. Very interestingly, their corresponding previous parent Pc derivative, [m,p,m'-(C14O)(3)PhO](8)PcCu (4), shows a very wide temperature region ca. 90 degrees C of a bicontinuous Cub(Pn3m) mesophase, whereas the present children Pc precursors (5 and 6) and Pc-C-60 dyad 7 show not the Cub mesophase but a Col(ho) mesophase. It is also noteworthy that the staking distance in the Col(ho) mesophase of the Pc-C-60 dyad 7 was a very big value of ca. 9.1 angstrom, which is the biggest in discotic liquid crystals to our best knowledge. It may be originated from the biggest excluded volume caused by thermal fluctuation of peripheral long alkoxy chains at m, m'-positions. The excluded volume caused by thermal fluctuation of the peripheral long chains is so big that the molecular shape of the Pc derivative 4 and the Pc-C-60 dyad 7 very resembles a flat pumpkin.ArticleJOURNAL OF PORPHYRINS AND PHTHALOCYANINES. 18(10-11):856-868 (2014)journal articl

kGCN: a graph-based deep learning framework for chemical structures

Deep learning is developing as an important technology to perform various tasks in cheminformatics. In particular, graph convolutional neural networks (GCNs) have been reported to perform well in many types of prediction tasks related to molecules. Although GCN exhibits considerable potential in various applications, appropriate utilization of this resource for obtaining reasonable and reliable prediction results requires thorough understanding of GCN and programming. To leverage the power of GCN to benefit various users from chemists to cheminformaticians, an open-source GCN tool, kGCN, is introduced. To support the users with various levels of programming skills, kGCN includes three interfaces: a graphical user interface (GUI) employing KNIME for users with limited programming skills such as chemists, as well as command-line and Python library interfaces for users with advanced programming skills such as cheminformaticians. To support the three steps required for building a prediction model, i.e., pre-processing, model tuning, and interpretation of results, kGCN includes functions of typical pre-processing, Bayesian optimization for automatic model tuning, and visualization of the atomic contribution to prediction for interpretation of results. kGCN supports three types of approaches, single-task, multi-task, and multi-modal predictions. The prediction of compound-protein interaction for four matrixmetalloproteases, MMP-3, -9, -12 and -13, in the inhibition assays is performed as a representative case study using kGCN. Additionally, kGCN provides the visualization of atomic contributions to the prediction. Such visualization is useful for the validation of the prediction models and the design of molecules based on the prediction model, realizing “explainable AI” for understanding the factors affecting AI prediction. kGCN is available at https://github.com/clinfo

Nucleon isovector structure functions in (2+1)-flavor QCD with domain wall fermions

We report on numerical lattice QCD calculations of some of the low moments of the nucleon structure functions. The calculations are carried out with gauge configurations generated by the RBC and UKQCD collaborations with (2+1)-flavors of dynamical domain wall fermions and the Iwasaki gauge action ($\beta = 2.13$). The inverse lattice spacing is $a^{-1} = 1.73$ GeV, and two spatial volumes of ((2.7{\rm fm})^3) and ((1.8 {\rm fm})^3) are used. The up and down quark masses are varied so the pion mass lies between 0.33 and 0.67 GeV while the strange mass is about 12 % heavier than the physical one. The structure function moments we present include fully non-perturbatively renormalized iso-vector quark momentum fraction, (_{u-d}), helicity fraction, (< x >_{\Delta u - \Delta d}), and transversity, (_{\delta u - \delta d}), as well as an unrenormalized twist-3 coefficient, (d_1). The ratio of the momentum to helicity fractions, (_{u-d}/_{\Delta u - \Delta d}), does not show dependence on the light quark mass and agrees well with the value obtained from experiment. Their respective absolute values, fully renormalized, show interesting trends toward their respective experimental values at the lightest quark mass. A prediction for the transversity, (0.7 _{\delta u -\delta d} < 1.1), in the (\bar{\rm MS}) scheme at 2 GeV is obtained. The twist-3 coefficient, (d_1), though yet to be renormalized, supports the perturbative Wandzura-Wilczek relation.Comment: 14 pages, 22 figures

Periostin in Allergic Inflammation

ABSTRACTPeriostin, an extracellular matrix protein belonging to the fasciclin family, has been shown to play a critical role in the process of remodeling during tissue/organ development or repair. Periostin functions as a matricellular protein in cell activation by binding to their receptors on cell surface, thereby exerting its biological activities. After we found that periostin is a downstream molecule of interleukin (IL)-4 and IL-13, signature cytokines of type 2 immune responses, we showed that periostin is a component of subepithelial fibrosis in bronchial asthma, the first formal proof that periostin is involved in allergic inflammation. Subsequently, a great deal of evidence has accumulated demonstrating the significance of periostin in allergic inflammation. It is of note that in skin tissues, periostin is critical for amplification and persistence of allergic inflammation by communicating between fibroblasts and keratinocytes. Furthermore, periostin has been applied to development of novel diagnostics or therapeutic agents for allergic diseases. Serum periostin can reflect local production of periostin in inflamed lesions induced by Th2-type immune responses and also can predict the efficacy of Th2 antagonists against bronchial asthma. Blocking the interaction between periostin and its receptor, αv integrin, or down-regulating the periostin expression shows improvement of periostin-induced inflammation in mouse models or in in vitro systems. It is hoped that diagnostics or therapeutic agents targeting periostin will be of practical use in the near future

Nucleon structure with two flavors of dynamical domain-wall fermions

We present a numerical lattice quantum chromodynamics calculation of isovector form factors and the first few moments of the isovector structure functions of the nucleon. The calculation employs two degenerate dynamical flavors of domain-wall fermions, resulting in good control of chiral symmetry breaking. Non-perturbative renormalization of the relevant quark currents is performed where necessary. The inverse lattice spacing, $a^{-1}$, is about 1.7 GeV. We use degenerate up and down dynamical quark masses around 1, 3/4 and 1/2 the strange quark mass. The physical volume of the lattice is about $(1.9{fm})^3$. The ratio of the isovector vector to axial charges, $g_A/g_V$, trends a bit lower than the experimental value as the quark mass is reduced toward the physical point. We calculate the momentum-transfer dependences of the isovector vector, axial, induced tensor and induced pseudoscalar form factors. The Goldberger-Treiman relation holds at low momentum transfer and yields a pion-nucleon coupling, $g_{\pi NN} = 15.5(1.4)$, where the quoted error is only statistical. We find that the flavor non-singlet quark momentum fraction $_{u-d}$ and quark helicity fraction $_{\Delta u-\Delta d}$ overshoot their experimental values after linear chiral extrapolation. We obtain the transversity, $_{\delta u-\delta d} = 0.93(6)$ in $\bar{\rm MS}$ at 2 GeV and a twist-3 polarized moment, $d_1$, appears small, suggesting that the Wandzura-Wilczek relation holds approximately. We discuss the systematic errors in the calculation, with particular attention paid to finite-volume effects, excited-state contamination, and chiral extrapolations.Comment: 28 pages in two columns; 37 figures, 12 table