There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.

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SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

Summary form only given. We have observed nearly complete, (99%) pump depletion in single pass SHG in an annealed proton exchanged waveguide formed in PPLN. Pump depletion is examined as a function of pump power launched into the waveguide, along with a calculation using the same values of propagation losses and normalized efficiency used in the low power fit. Good agreement with theory is observed, with pump depletion reaching 99% at an input power of 2.8 W.

Observation of 99% pump depletion in single pass SHG in a PPLN waveguide

High energy femtosecond pulse amplification is demonstrated in a simple and compact arrangement using periodically poled LiNbO3 (PPLN) as a parametric amplifier and employing chirped pulse amplification. A single-pass gain of 40 dB is observed for 5 mJ 0.5 ns pump pulses at 786 nm in a 5-mm-long PPLN crystal, generating 1 mJ 680 fs amplified optical pulses at 1555 nm.

High-energy chirped pulse amplification using a quasi-phase-matched parametric amplifier

OPOs are often grouped by their temporal characteristics, and recently 10 – 30 ns pulse, 100 fs - 1 ps pulse, and CW OPOs have received the most attention. Here, we report on a mid-infrared OPO driven by a unique pump architecture producing pulses in the 0.1 – 1 μs regime. This temporal regime offers the potential of narrower linewidths without the complexities associated with CW OPOs.

Long Pulse Optical Parametric Oscillator based on Bulk Periodically-Poled LiNbO3

Large energy intersubband transitions are necessary for extending intersubband applications to the near-infrared (≤ 2μm wavelength) where compact diode laser based sources are available. By growing high indium content InGaAs / AlGaAs quantum wells (QWs) on GaAs substrates with linearly graded InGaAs buffers, we have demonstrated peak intersubband absorption energies as high as 580meV (2.1μm wavelength). We have also demonstrated intersubband absorption at 580meV in asymmetric coupled InGaAs / AlAs QWs. These are the largest bound-to-bound intersubband transition energies to date. Experimental studies of buffer and QW growth parameters for optimized intersubband absorption have been performed. The well width dependence of intersubband transition energies in both In0.5Ga0.5As / Al0.45Ga0.55As QWs and In0.5Ga0.5As / AlAs QWs have been measured and theoretically modelled.

Large Energy Intersubband Transitions in High Indium Content InGaAs / AlGaAs Quantum Wells

Silicon is a common material for photonics due to its favorable optical properties in the telecom and mid-wave IR bands, as well as compatibility with a wide range of complementary metal-oxide semiconductor (CMOS) foundry processes. Crystalline inversion symmetry precludes silicon from natively exhibiting second-order nonlinear optical processes. In this work, we build on recent work in silicon photonics that break this material symmetry using large bias fields, thereby enabling $\chi^{(2)}$ interactions. Using this approach, we demonstrate both second-harmonic generation (with a normalized efficiency of $0.2\,\%\,\mathrm{W^{-1} cm^{-2}}$) and, to our knowledge, the first degenerate $\chi^{(2)}$ optical parametric amplifier (with relative gain of $0.02\,\mathrm{dB}$ using $3\,\mathrm{mW}$ of pump power on-chip at a pump wavelength of $1196\,\mathrm{nm}$) using silicon-on-insulator waveguides fabricated in a CMOS-compatible commercial foundry. We expect this technology to enable the integration of novel nonlinear optical devices such as optical parametric amplifiers, oscillators, and frequency converters into large-scale, hybrid photonic-electronic systems by leveraging the extensive ecosystem of CMOS fabrication.

Martin M. Fejer

Papers

Observation of 99% pump depletion in single pass SHG in a PPLN waveguide

High-energy chirped pulse amplification using a quasi-phase-matched parametric amplifier

Long Pulse Optical Parametric Oscillator based on Bulk Periodically-Poled LiNbO3

Large Energy Intersubband Transitions in High Indium Content InGaAs / AlGaAs Quantum Wells

Degenerate optical parametric amplification in CMOS silicon