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

Electromagnetic homogenization approximation calculates an effective refractive index of a composite material as a weighted average of its components, and has found uses in gradient refractive index and transformation optics devices. However, the utility of the homogenization approximation is hindered by uncertainty in its range of applicability. Harnessing the capability of time-resolved imaging provided by the terahertz polaritonics platform, we determined the dispersion curves of slab waveguides with periodic arrays of holes, and we quantified the breakdown of the homogenization approximation as the period approached the terahertz wavelength and the structure approached the photonic bandgap regime. We found that if the propagation wavelength in the dielectric waveguide was at least two times as large as the Bragg condition wavelength, the homogenization approximation held independent of the detailed geometry, propagation direction, or fill fraction. This value is much less demanding than the estimate of 10:1 often assumed for homogenization. We further used the experimental capabilities to extract the effective refractive index of the photonic crystals in the homogenization approximation limit, and we used this to analyze the predictive strength of analytical formulas. These formulas enabled rapid design of a Luneburg lens and a bi-directional cloak in a waveguide platform without the need for numerical simulations. Movies of terahertz waves interacting with these structures, which were fabricated using femtosecond laser machining, reveal excellent performance. The combination of an analytical formula and confidence in the homogenization approximation will aid in fast design and prototyping of gradient index devices.

/pdf/the-homogenization-limit-and-waveguide-gradient-index-12spri0x19.pdf

The homogenization limit and waveguide gradient index devices demonstrated through direct visualization of THz fields

Ultrafast Pulse Generation and Spectroscopy

A non-contact and non-destructive laser-based acoustic technique called impulsive stimulated thermal scattering (ISTS) is used to measure thicknesses of films in single-layer and multilayer assemblies such as W/Si, Ti/Si, and Ti/SiO 2 /Si structures. Thicknesses are determined to within a few percent accuracy with a laboratory version of the measurement apparatus, using conventional large-frame lasers and optics, and in a commercial prototype using compact diode-pumped and diode lasers and optics which all fit onto a 1-ft × 2-ft breadboard. ISTS and conventional measurements (profilometry, SEM, and 4-point resistance) are made on the same samples and the results are found to compare favorably.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1946427400282286

Microelectronic Film Thickness Determination Using a Laserbased Ultrasonic Technique

Erratum: “A direct test of the correlation between elastic parameters and fragility of ten glass formers and their relationship to elastic models of the glass transition” [J. Chem. Phys. 130, 064502 (2009)]

We explored the use of the optically transparent semiconductor indium tin oxide (ITO) as an alternative to optically opaque metals for the fabrication of photonic structures in terahertz (THz) near-field studies. Using the polaritonics platform, we confirmed the ability to clearly image both bound and leaky electric fields underneath an ITO layer. We observed good agreement between measured waveguide dispersion and analytical theory of an asymmetric metal-clad planar waveguide with TE and TM polarizations. Further characterization of the ITO revealed that even moderately conductive samples provided sufficiently high quality factors for studying guided and leaky wave behaviors in individual transparent THz resonant structures such as antennas or split ring resonators. However, without higher conductive ITO, the limited reflection efficiency and high radiation damping measured here both diminish the applicability of ITO for high-reflecting, arrayed, or long path-length elements.

Keith A. Nelson

Papers

The homogenization limit and waveguide gradient index devices demonstrated through direct visualization of THz fields

Ultrafast Pulse Generation and Spectroscopy

Microelectronic Film Thickness Determination Using a Laserbased Ultrasonic Technique

Erratum: “A direct test of the correlation between elastic parameters and fragility of ten glass formers and their relationship to elastic models of the glass transition” [J. Chem. Phys. 130, 064502 (2009)]

Visualization of guided and leaky wave behaviors in an indium tin oxide metallic slab waveguide.