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

A novel “pseudo-phasematching” scheme for THz polariton amplification is demonstrated. Nonlinear THz spectroscopy using an integrated platform for THz generation, guidance, and visualization enabled the first observations of nonlinear lattice responses from LiNbO3.

THz Polaritonics: Shaped Waveforms, Large Amplitudes and Linear and Nonlinear Spectroscopy

Multiple-quantum two-dimensional Fourier transform optical (2D FTOPT) spectroscopy was developed and conducted on GaAs quantum wells. Spatiotemporal femtosecond pulse shaping was used to control the optical phases and time delays of ultrashort pulses in multiple non-collinear beams so that fully coherent four-wave and higher-order mixing measurements could be conducted without delay stages, multiple interferometers, or any active phase control. Coherences of biexcitons, unbound but correlated exciton pairs, and excitons undergoing rephasing were observed directly.

Multiple-quantum 2D spectroscopy of many-body correlations in GaAs quantum wells

We study the excitonic coupling and homogeneous spectral line width of brick layer J-aggregate films. We begin by analysing the structural information revealed by the two-exciton states probed in two-dimensional spectra. Our first main result is that the relation between the excitonic couplings and the spectral shift in a two-dimensional structure is different (larger shift for the same nearest neighbour coupling) from that in a one-dimensional structure, which leads to an estimation of dipolar coupling in two-dimensional lattices. We next investigate the mechanisms of homogeneous broadening - population relaxation and pure dephasing - and evaluate their relative importance in linear and two-dimensional aggregates. Our second main result is that pure dephasing dominates the line width in two-dimensional systems up to a crossover temperature, which explains the linear temperature dependence of the homogeneous line width. This is directly related to the decreased density of states at the band edge when compared with linear aggregates, thus reducing the contribution of population relaxation to dephasing. Pump-probe experiments are suggested to directly measure the lifetime of the bright state and can therefore support the proposed model.

/pdf/how-two-dimensional-brick-layer-j-aggregates-differ-from-19b0whx592.pdf

How two-dimensional brick layer J-aggregates differ from linear ones: excitonic properties and line broadening mechanisms

http://link.springer.com/content/pdf/10.1007/978-3-642-59319-2_66.pdf

Automated Two-Dimensional Femtosecond Pulse Shaping and Phased-Array THz Generation

Laser-induced shock waves have been gaining attention for biological and medical applications in which shock waves influence cell permeation. However, the mechanisms of permeation remain mostly unclear because of the difficulty of observing the transient and dynamic behaviors of the shock waves and the cells. Here we present an all-optical measurement method that can quantitatively capture the pressure distribution of the propagating shock wave and simultaneously monitor the dynamic behavior of cell membranes. Using this method, we find that a sharp pressure gradient causes cell membrane permeation. Our measurement will further advance biological and medical applications of shock waves. 

Keith A. Nelson

Papers

THz Polaritonics: Shaped Waveforms, Large Amplitudes and Linear and Nonlinear Spectroscopy

Multiple-quantum 2D spectroscopy of many-body correlations in GaAs quantum wells

How two-dimensional brick layer J-aggregates differ from linear ones: excitonic properties and line broadening mechanisms

Automated Two-Dimensional Femtosecond Pulse Shaping and Phased-Array THz Generation

Investigation of laser-induced shock effects on cell membrane by ultrafast measurement of pressure distribution and membrane permeation