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

We will review recent progress on the generation and detection of picosecond shear acoustic waves Examples will be shown in which the transverse isotropic symmetry of the sample structure is broken in order to permit shear wave generation through sudden laser heating As an illustration of the technique, picosecond longitudinal and shear acoustic waves have been successfully employed to probe structural dynamics in nano-sized solids (gold nano-crystals assemblies) and nano-sized liquids (glycerol and water)

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Picosecond shear waves in nano-sized solids and liquids

Femtosecond transient absorption measurements have been used to study CO dissociation in three simple transition metal carbonyls, Cr(CO)6 and Mn2(CO)10 [M=Mn, Re[ in solution. In all compounds, CO dissociation is seen to occur within one picosecond. Cr(CO)6 shows subsequent solvent coordination within 2.5 ps which is consistent with previous results. All compounds show slow spectral evolution on a 10 to 50 ps timescale which is interpreted as relaxation of the resulting photoproducts.

Femtosecond time resolved absorption spectroscopy of Cr(CO)6 and Mn2(CO)10: Observation of elementary bond breakage and formation

Preliminary femtosecond time‐resolved impulsive stimulated scattering data from CS2 liquid are shown which clearly indicate an inertial component of the short‐time motion which cannot be described in terms of Debye relaxational dynamics A discussion of time‐domain and frequency‐domain light scattering techniques is given to illustrate the comparative difficulty of characterizing this type of motion by conventional methods

Preliminary observation of nonrelaxational inertial motion in CS2 liquid by femtosecond time‐resolved impulsive stimulated scattering

Erratum: Phonon-polariton excitations in photonic crystals [Phys. Rev. B 68, 075209 (2003)]

We have constructed a noncollinear optical parametric amplifier with two signal beams amplified in the same nonlinear crystal. This dual-beam design is more energy-efficient than operating two amplifiers in parallel. The cross-talk between two beams has been characterized and discussed. We have also added a second amplification stage to enhance the output of one of the arms, which is then frequency-doubled for ultraviolet generation. This single device provides two tunable sources for ultrafast spectroscopy in the ultraviolet and visible region.

/pdf/efficient-two-stage-dual-beam-noncollinear-optical-4qwxpcs1sl.pdf

Keith A. Nelson

Papers

Picosecond shear waves in nano-sized solids and liquids

Femtosecond time resolved absorption spectroscopy of Cr(CO)6 and Mn2(CO)10: Observation of elementary bond breakage and formation

Preliminary observation of nonrelaxational inertial motion in CS2 liquid by femtosecond time‐resolved impulsive stimulated scattering

Erratum: Phonon-polariton excitations in photonic crystals [Phys. Rev. B 68, 075209 (2003)]

Efficient two-stage dual-beam noncollinear optical parametric amplifier