Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Femtosecond laser machining with high-energy pulses is used for fabrication of diffractive elements in LiNbO3 crystalline samples. This permits terahertz generation, frequency dispersion, detection, and analysis within a single integrated platform that is well suited for applications in terahertz spectroscopy or signal processing.

Integrated diffractive terahertz elements

Coherent lattice vibrations are driven beyond the harmonic limit through impulsive stimulated Raman scattering excitation with intense femtosecond pulses High overtones of the fundamental lattice vibrational frequency and wave vector are observed in the time-dependent responses of the ferroelectric crystals lithium tantalate and lithium niobate The results provide controlled experimental access to anharmonic regions of lattice potential energy surfaces, including the “soft” mode or “collective reaction coordinate” paths along which ions move from their initial lattice positions toward the positions they occupy in new lattice structures, ie, new domain orientations or crystalline phases The observations represent a significant extension of coherent optical control over material behavior, and a step toward “collective mode-selective chemistry” through which cooperative structural rearrangements might be induced

Direct time-resolved measurement of anharmonic lattice vibrations in ferroelectric crystals

Femtosecond time-resolved observation of coherent molecular vibrational motion.

We have developed a femtosecond single-shot spectroscopic technique to measure irreversible changes in condensed phase materials in real time. Crossed echelons generate a two-dimensional array of time-delayed pulses with one femtosecond probe pulse. This yields 9 ps of time-resolved data from a single laser shot, filling a gap in currently employed measurement methods. We can now monitor ultrafast irreversible dynamics in solid-state materials or other samples that cannot be flowed or replenished between laser shots, circumventing limitations of conventional pump-probe methods due to sample damage or product buildup. Despite the absence of signal-averaging in the single-shot measurement, an acceptable signal-to-noise level has been achieved via background and reference calibration procedures. Pump-induced changes in relative reflectivity as small as 0.2%−0.5% are demonstrated in semimetals, with both electronic and coherent phonon dynamics revealed by the data. The optical arrangement and the space-to-time conversion and calibration procedures necessary to achieve this level of operation are described. Sources of noise and approaches for dealing with them are discussed.

Dual echelon femtosecond single-shot spectroscopy.

Impulsive stimulated thermal scattering (ISTS) studies are conducted on glycerol in the supercooled liquid range. ISTS is used to measure the Debye–Waller factor, and to characterize the structural relaxation dynamics in the range from a few nanoseconds to hundreds of microseconds. The results are compared to predictions of mode-coupling theory (MCT), and suggest that inclusion of important microscopic degrees of freedom may be needed for MCT to successfully describe hydrogen-bonded liquids like glycerol.

Keith A. Nelson

Papers

Integrated diffractive terahertz elements

Direct time-resolved measurement of anharmonic lattice vibrations in ferroelectric crystals

Femtosecond time-resolved observation of coherent molecular vibrational motion.

Dual echelon femtosecond single-shot spectroscopy.

Impulsive stimulated thermal scattering study of structural relaxation in supercooled glycerol