237 research outputs found
Canonical treatment of two dimensional gravity as an anomalous gauge theory
The extended phase space method of Batalin, Fradkin and Vilkovisky is applied
to formulate two dimensional gravity in a general class of gauges. A BRST
formulation of the light-cone gauge is presented to reveal the relationship
between the BRST symmetry and the origin of current algebra. From the
same principle we derive the conformal gauge action suggested by David, Distler
and Kawai.Comment: 11 pages, KANAZAWA-92-1
Software.ncrna.org: web servers for analyses of RNA sequences
We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individual stand-alone web servers. The servers are located at http://software.ncrna.org, along with the information for the evaluation and downloading. This website is freely available to all users and there is no login requirement
Agrobacterium-mediated transformation of kabocha squash (Cucurbita moschata Duch) induced by wounding with aluminum borate whiskers
An efficient genetic transformation method for kabocha squash (Cucurbita moschata Duch cv. Heiankogiku) was established by wounding cotyledonary node explants with aluminum borate whiskers prior to inoculation with Agrobacterium. Adventitious shoots were induced from only the proximal regions of the cotyledonary nodes and were most efficiently induced on MurashigeāSkoog agar medium with 1Ā mg/L benzyladenine. Vortexing with 1% (w/v) aluminum borate whiskers significantly increased Agrobacterium infection efficiency in the proximal region of the explants. Transgenic plants were screened at the T0 generation by sGFP fluorescence, genomic PCR, and Southern blot analyses. These transgenic plants grew normally and T1 seeds were obtained. We confirmed stable integration of the transgene and its inheritance in T1 generation plants by sGFP fluorescence and genomic PCR analyses. The average transgenic efficiency for producing kabocha squashes with our method was about 2.7%, a value sufficient for practical use
New insight into BRST anomalies in superstring theory
Based on the extended BRST formalism of Batalin, Fradkin and Vilkovisky, we
perform a general algebraic analysis of the BRST anomalies in superstring
theory of Neveu-Schwarz-Ramond. Consistency conditions on the BRST anomalies
are completely solved. The genuine super-Virasoro anomaly is identified with
the essentially unique solution to the consistency condition without any
reference to a particular gauge for the 2D supergravity fields. In a
configuration space where metric and gravitino fields are properly constructed,
general form of the super-Weyl anomaly is obtained from the super-Virasoro
anomaly as its descendant.
We give a novel local action of super-Liouville type, which plays a role of
Wess-Zumino-Witten term shifting the super-Virasoro anomaly into the super-Weyl
anomaly. These results reveal a hierarchial relationship in the BRST anoamlies.Comment: 29 pages, PHYZZ
PoSSuM: a database of similar proteināligand binding and putative pockets
Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ā¼33ā000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/
Gauge Equivalence in Two--Dimensional Gravity
Two-dimensional quantum gravity is identified as a second-class system which
we convert into a first-class system via the Batalin-Fradkin (BF) procedure.
Using the extended phase space method, we then formulate the theory in most
general class of gauges. The conformal gauge action suggested by David, Distler
and Kawai is derived from a first principle. We find a local, light-cone gauge
action whose Becchi-Rouet-Stora-Tyutin invariance implies Polyakov's curvature
equation , revealing the origin of the
Kac-Moody symmetry. The BF degree of freedom turns out be dynamically
active as the Liouville mode in the conformal gauge, while in the light-cone
gauge the conformal degree of freedom plays that r{\^o}le. The inclusion of the
cosmological constant term in both gauges and the harmonic gauge-fixing are
also considered.Comment: 30 pages, KANAZAWA 93-
Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators
The rapid development of novel procedures in medical ultrasonics, including treatment planning in therapeutic ultrasound and image reconstruction in photoacoustic tomography, leads to increasing demand for large-scale ultrasound simulations. However, routine execution of such simulations using traditional methods, e.g., finite difference time domain, is expensive and often considered intractable due to the computational and memory requirements. The k-space corrected pseudospectral time domain method used by the k-Wave toolbox allows for significant reductions in spatial and temporal grid resolution. These improvements are achieved at the cost of all-to-all communication, which are inherent to the multi-dimensional fast Fourier transforms. To improve data locality, reduce communication and allow efficient use of accelerators, we recently implemented a domain decomposition technique based on a local Fourier basis.
In this paper, we investigate whether it is feasible to run the distributed k-Wave implementation on the Salomon cluster equipped with 864 Intel Xeon Phi (Knightās Corner) accelerators. The results show the immaturity of the KNC platform with issues ranging from limited support of Infiniband and LustreFS in Intel MPI on this platform to poor performance of 3D FFTs achieved by Intel MKL on the KNC architecture. Yet, we show that it is possible to achieve strong and weak scaling comparable to CPU-only platforms albeit with the runtime 1.8Ć to 4.3Ć longer. However, the accounting policy for Salomonās accelerators is far more favorable and thus their employment reduces the computational cost significantly
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