An efficient and extensible format,library, and API for binary trajectory data from molecular simulations

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high‐performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost‐efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present “Trajectory Next Generation” (TNG)—a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state‐of‐the‐art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. © 2013 Wiley Periodicals, Inc.     

Parallel electromembrane extraction in the 96-well format

The repeatability and extraction recoveries of parallel electromembrane extraction (Pa-EME) was thoroughly investigated in the present project. Amitriptyline, fluoxetine, and haloperidol were isolated from eight samples of pure water, undiluted human plasma, and undiluted human urine, respectively; in total 24 samples were processed in parallel. The repeatability was found to be independent of the different sample matrices (pure water samples, human plasma, and water) processed in parallel, although the respective samples contained different matrix components. In another experiment seven of the 24 wells were perforated. Even though the perforation caused the total current level in the Pa-EME setup to increase, the intact circuits were unaffected by the collapse in seven of the circuits. In another approach, exhaustive extraction of amitriptyline, fluoxetine, and haloperidol was demonstrated from pure water samples. Amitriptyline and haloperidol were also isolated exhaustively from undiluted human plasma samples; the extraction recovery of fluoxetine from undiluted human plasma was 81%. Finally, the sample throughput was increased with the Pa-EME configuration. The extraction recoveries were investigated by processing 1, 8, 68, or 96 samples in parallel in 10 min; neither the extraction recoveries nor the repeatability was affected by the total numbers of samples. Eventually, the Pa-EME was combined with ultra performance liquid chromatography (UPLC) to combine high-throughput sample preparation with high-throughput analytical instrumentation. The aim of the present investigation was to demonstrate the potential of electromembrane extraction as a high throughput sample preparation platform; and hopefully to increase the interest for EME in the bioanalytical field to solve exisiting and novel analytical challenges.     

可调谐半导体激光吸收光谱技术的调制参量影响及优化选择

为获得较好的谐波信号,完成不同测量目的,以DFB-760.77nm波长处氧气监测为例,通过改变扫描锯齿信号和调制正弦信号的频率和幅值,讨论了调制参量对二次谐波信号峰-峰值、对称性、谐波信号展宽和信号完整性等判别依据的影响和变化.结果表明:Sinmulink模拟值和实验值相关性较高,当正弦调制信号和锯齿扫描信号频率比值为1 000倍时,可以获得较好的二次谐波信号.该研究为实验系统中调制参量的选取和调制度及系统准确度、稳定性、重复性等性能的优化提供了一定帮助.     

Reduction of four-wave mixing noises in FDM optical fiber transmission systems with quaternary bit-phase arranged return-to-zero

To reduce four-wave mixing (FWM) noises in long-haul frequency-division-multiplexing optical fiber transmission systems, quaternary bit-phase arranged return-to-zero (Q-BARZ) is proposed as a modulation format, and FWM noises are analyzed by considering pulse overlapping in both time and frequency regions. It is found that FWM noises with channel frequencies are drastically reduced in Q-BARZ.     

Linearized harmonic balance based derivation of slow flow for some class of autonomous single degree of freedom oscillators

In this paper we exploit the embedding of linearization in the harmonic balance method developed by Wu and its collaborators to propose an approach for deriving the slow flow for some class of damped autonomous single degree of freedom oscillators. The linearized harmonic balance method is used to compute the coefficients of the harmonics of an assumed form of the solution and to derive a system of two coupled ordinary differential equations related to the slow flow. A power series procedure is next used to decouple the coupled system and to obtain the slow flow. Two examples provided to illustrate the proposed procedure show excellent results.     

Theoretical and experimental analysis of RGBW display based on OLEDs/PLEDs

Flat panel display (FPD) with a novel RGBW sub-pixel format utilizing organic/polymer light-emitting devices (OLEDs/PLEDs) was analyzed theoretically and experimentally. Using the fitting curves of the OLEDs/PLEDs’ electroluminescent (EL) characteristics, RGBW sub-pixel display is clearly shown to be more energy efficient than traditional RGB sub-pixel display when the calculation is based on uniform luminance color space, especially as the efficiency of the OLEDs/PLEDs is getting higher. The relationship between the area proportion of the primary sub-pixels and the power consumption of the RGBW display panel was also investigated to further reduce the energy waste, and an optimized area proportion of blue and white primaries in RGBW display panel was presented.     

Spontaneous modulation instability in a noninstantaneous self-defocusing medium within a cavity longer than the coherence length

We study, theoretically and experimentally, the spontaneous pattern formation of modulation instability (MI) in a non-instantaneous self-defocusing medium, which is placed in a cavity longer than the coherence length of the circulating light. The delayed response of the nonlinearity can amplify the noise of certain spatial and temporal frequencies. Although it lacks the resonance condition resulted from the interference between different cycles, the cavity can still select one specific frequency. A pattern of this frequency can emerge spontaneously if its gain from the nonlinearity is larger than the total cavity loss.     

模板法测量图像传感器调制传递函数方法研究

在干涉条纹投射法测量的基础上，提出了利用正弦模板法测量图像传感器调制传递函数的新方法.通过将一定空间频率的正弦模板直接投射在图像传感器上，获得了同频率光强呈正弦分布的图像，通过计算求出图像传感器的调制传递函数.讨论了其具体实现方法，并用空间频率为50l/mm的计量光栅做了近似实验，采用了相应的数据处理方法，获得了较为满意的调制传递系数.