Parallel-vector algorithms for particle simulations on shared-memory multiprocessors

Over the last few decades, the computational demands of massive particle-based simulations for both scientific and industrial purposes have been continuously increasing. Hence, considerable efforts are being made to develop parallel computing techniques on various platforms. In such simulations, particles freely move within a given space, and so on a distributed-memory system, load balancing, i.e., assigning an equal number of particles to each processor, is not guaranteed. However, shared-memory systems achieve better load balancing for particle models, but suffer from the intrinsic drawback of memory access competition, particularly during (1) paring of contact candidates from among neighboring particles and (2) force summation for each particle. Here, novel algorithms are proposed to overcome these two problems. For the first problem, the key is a pre-conditioning process during which particle labels are sorted by a cell label in the domain to which the particles belong. Then, a list of contact candidates is constructed by pairing the sorted particle labels. For the latter problem, a table comprising the list indexes of the contact candidate pairs is created and used to sum the contact forces acting on each particle for all contacts according to Newton’s third law. With just these methods, memory access competition is avoided without additional redundant procedures. The parallel efficiency and compatibility of these two algorithms were evaluated in discrete element method (DEM) simulations on four types of shared-memory parallel computers: a multicore multiprocessor computer, scalar supercomputer, vector supercomputer, and graphics processing unit. The computational efficiency of a DEM code was found to be drastically improved with our algorithms on all but the scalar supercomputer. Thus, the developed parallel algorithms are useful on shared-memory parallel computers with sufficient memory bandwidth.     

Measurement of angular distribution of soft X‐ray radiation from thin targets in the tabletop storage ring MIRRORCLE‐20SX

The only available tabletop electron storage rings are the machines from the MIRRORCLE series. The electrons are accelerated in a microtron and injected into the storage ring. During its circulation, each electron passes through a tiny target many times, emitting a photon beam. Both the spectrum and the angular distribution of the radiation depend on the material, the thickness and the shape of the target. In this paper measured angular distributions of the radiation from several different targets in the magnetic field of the 20 MeV storage ring MIRRORCLE‐20SX are presented. The detector comprises a 3 mm × 3 mm × 8.5 µm plastic scintillator (PS) coupled to a photomultiplier by a bundle of optical fibers. The output of the photomultiplier is digitized by an IF converter. This detector is sensitive mostly to soft X‐ray radiation, and its PS is moved by a mechanical system in a plane perpendicular to the radiation axis. The measured angular distributions for Mo and Sn targets contain an annulus which is attributed to transition radiation. The angular distributions for Al, carbon nanotube and diamond‐like carbon (DLC) targets show some suppression of the radiation along the magnetic field. This is the first evidence of observation of the angular distribution of synchrotron Cherenkov radiation, which represents Cherenkov radiation in a magnetic field. The power radiated from the DLC target is estimated.     

On almost holomorphic Lagrangian fibrations

We prove that the pull back of an ample line bundle by an almost holomorphic Lagrangian fibration is nef. As an application, we show birational semi rigidity of Lagrangian fibrations.     

Synthesis and spectroscopic study of diphenylamino-substituted phenylene-(poly)ethynylenes: remarkable effect of acetylenic conjugation modes

A series of diphenylamino-substituted phenylene-(poly)ethynylenes were successfully synthesized by a combination of Sonogashira coupling and double elimination protocol of β-substituted sulfones. When UV-light was irradiated, the amino-substituted phenylene-(poly)ethynylene emitted strong luminescence. The emission underwent a large bathochromic shift in polar solvent because of stabilization of their charge-separated excited states. Analyses of fluorescence life times of aminoacetylenes revealed that radiationless process was suppressed in the polar solvent CH₂Cl₂, resulting in high quantum yields.     

Alkylative Carbocyclization of ω‐Iodoalkynyl Tosylates with Alkynyllithium Compounds Through a Carbenoid‐Chain Process Leading to (1‐Iodoprop‐2‐ynylidene)tetrahydrofurans and ‐cyclopropanes

Alkylative carbocyclization reactions of ω‐iodoalkynyl tosylates with alkynyllithium compounds to give products with incorporated iodine atoms are described. Slow addition of 2‐(3‐iodoprop‐2‐ynyloxy)ethyl tosylates to 1‐alkynyllithium compounds in tetrahydrofuran at 40 °C followed by additional stirring at this temperature gives (Z)‐3‐(1‐iodoprop‐2‐ynylidene)tetrahydrofurans stereoselectively in good to moderate yields. Under similar conditions at 0 °C, 4‐iodobut‐1‐ynyl tosylates react with 1‐alkynyllithium compounds to give (1‐iodoprop‐2‐ynylidene)cyclopropanes. The carbocyclization reactions are proposed to proceed through a new carbenoid‐chain process involving the exo cyclization of a lithium acetylide intermediate and the vinylic substitution of the resulting TsO,Li‐cycloalkylidenecarbenoids (Ts=tosyl) by 1‐alkynyllithium compounds.     

High resolution‐HMBC (HR‐HMBC), a new method for measuring heteronuclear long‐range coupling constants

A useful pulse sequence for measuring long‐range C? H coupling constants (J_{C? H}) named high resolution‐HMBC (HR‐HMBC) has been developed. In this pulse sequence, the J‐scaling pulse [(nt₁)/2? 180° (H/C) ? (nt₁)/2] is incorporated after the spin evolution period, and then followed by an ¹H 180° pulse to reverse the magnetization of J_{C? H} couplings. As a result, splittings of the cross peaks due to the long‐range J_{C? H} are realigned with separations of nJ_{C? H} along the F₁ dimension, and thus even the small long‐range J_{C? H} values can easily be determined. The efficiency of measuring the long‐range J_{C? H} using the proposed pulse sequences has been demonstrated in application to the complicated natural product, portmicin. Copyright © 2010 John Wiley & Sons, Ltd.     

Commutativity in special unitary groups at odd primes

It is a classical result by Bott that SU(s) and SU(t) homotopy commute in SU(n) if and only if s+t?n. We consider the p-localization analog of this problem and give an answer at odd primes.     

Steady-State and Time-Resolved Fluorescence Spectroscopic Studies on Interaction of the N-terminal Region with the Hairpin Loop of the Phytocystain Scb

The steady-state and time-resolved fluorescece spectroscopy is one of the most powerful method to detect and analyze subtle conformation change and interaction between peptide elements in protein. Phytocystatin Scb isolated from sunflower seeds includes a single Trp residue at position 85. In an attempt to investigate the interaction of the N-terminal region of Scb with the first and second hairpin loops by fluorescence spectroscopy of Trp residue, two Scb mutants in which single Trp locates at position 52 and 58, respectively, and their N-terminal removed mutants were generated. The N-terminal truncation changed the fluorescence decay kinetics of Trp52 from the triple exponential to double. Furthermore, the time-resolved fluorescence anisotropy residue indicated that the segmental motion of Trp52 was significantly enhanced by its N-terminal truncation. In contrast, Trp58 and Trp85 had little influence. The N-terminal successive truncations of Scb and its mutants resulted in the weaken inhibitors to papain. These results suggested that the N-terminal region of Scb interacts with the peptide segment preceding the first hairpin loop, thereby stabilizing the conformation of the hairpin loop structure.     

Synthesis of 1H‐quinazoline‐2,4‐diones from 2‐aminobenzonitriles by fixation of carbon dioxide with amidine moiety supported polymer at atmospheric pressure

1H‐Quinazoline‐2,4‐diones, which are key intermediates in the synthesis of medicines, were successfully synthesized from 2‐aminobenzonitriles by the fixation of CO₂ in the presence of a polystyrene derivative bearing amidine moiety [poly(amidine)]. A model reaction, that is, the reaction of 2‐aminobenzonitrile ( 1a ) with CO₂ in the presence of N‐methyltetrahydropyrimidine ( MTHP ) revealed that a catalytic amount of MTHP afforded 1H‐quinazoline‐2,4‐dione ( 2a ) quantitatively at atmospheric pressure. Several 1H‐quinazoline‐2,4‐diones ( 2a ‐ 2c ) were successfully synthesized from the corresponding 2‐aminobenzonitriles ( 1a ‐ 1c ) in the presence of poly(amidine). The poly(amidine) could easily be separated from the reaction mixture by filtration and reused in subsequent reactions owing to the heterogeneous system. These demonstrated that poly(amidine) is a useful heterogeneous polymer‐supported reagent for the synthesis of 1H‐quinazoline‐2,4‐diones from CO₂. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 653–657, 2009