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

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

Carbon dots (CDs) with tunable photoluminescence (PL) and a quantum yield of up to 35% in water were hydrothermally synthesized in one pot and separated via silica column chromatography. These separated CDs emitted bright and stable luminescence in gradient colors from blue to red under a single-wavelength UV light. They exhibited high optical uniformity; that is, every sample showed only one peak in the PL excitation spectrum, only one peak in the excitation-independent PL emission spectrum, and similar monoexponential fluorescence lifetimes. Although these samples had similar distributions of particle size and graphite structure in their carbon cores, the surface state gradually varied among the samples, especially the degree of oxidation. Therefore, the observed red shift in their emission peaks from 440 to 625 nm was ascribed to a gradual reduction in their band gaps with the increasing incorporation of oxygen species into their surface structures. These energy bands were found to depend on the surfac...

Full-Color Light-Emitting Carbon Dots with a Surface-State-Controlled Luminescence Mechanism.

A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.

https://iopscience.iop.org/article/10.1088/0034-4885/76/4/046602/pdf

Anomalous transport in the crowded world of biological cells.

Have you ever felt that the very title, Progress in Optics, conjured an image in your mind? Don’t you see a row of handsomely printed books, bearing the editorial stamp of one of the most brilliant members of the optics community, and chronicling the field of optics since the invention of the laser? If so, you are certain to move the bookend to make room for Volume 16, the latest of this series. It contains seven chapters on widely diverging topics, written by well-known authorities in their fields. These are: 1) Laser Selective Photophysics and Photochemistry by V. S. Letokhov, 2) Recent Advances in Phase Profiles (sic) Generation by J. J. Clair and C. I. Abitbol, 3 ) Computer-Generated Holograms: Techniques and Applications by W.-H. Lee, 4) Speckle Interferometry by A. E. Ennos, 5 ) Deformation  Invariant, Space-Variant Optical  Pattern Recognition by D. Casasent and D. Psaltis, 6) Light Emission from High-Current Surface-Spark Discharges by R. E. Beverly, and 7) Semiclassical Radiation  Theory within a  QuantumMechanical Framework by I. R. Senitzkt. The  breadth of topic  matter  spanned  by  these  chapters makes it impossible, for this reviewer at least, to pass judgement on the comprehensiveness, relevance, and completeness of every chapter. With an editorial board as prominent as that of Progress in Optics, however, it seems hardly likely that such comments should be necessary. It should certainly be possible to take the authority of each author as credible. The only remaining judgment to be  made on these chapters is their readability. In short, what are they like to read? The first sentence of the first chapter greets the eye with an obvious typographical error: “The creation of coherent laser light source, that have tunable radiation, opened the . . . .” Two pages later we find: “When two types of atoms or molecules of different isotopic composition ( A and B ) have even one spectral line that does not overlap with others, it is pos-

Progress in optics

We present a new method to measure absolute diffusion coefficients at nanomolar concentrations with high precision. Based on a modified fluorescence correlation spectroscopy (FCS)-setup, this method is improved by introducing an external ruler for measuring the diffusion time by generating two laterally shifted and overlapping laser foci at a fixed and known distance. Data fitting is facilitated by a new two-parameter model to describe the molecule detection function (MDF). We present a recorded MDF and show the excellent agreement with the fitting model. We measure the diffusion coefficient of the red fluorescent dye Atto655 under various conditions and compare these values with a value achieved by gradient pulsed field NMR (GPF NMR). From these measurements we conclude, that the new measurement scheme is robust against optical and photophysical artefacts which are inherent to standard FCS. With two-focus-FCS, the diffusion coefficient of 4.26 x 10(-6) cm2s(-1) for Atto655 in water at 25 degrees C compares well with the GPF NMR value of 4.28 x 10(-6) cm2s(-1).

Two-Focus Fluorescence Correlation Spectroscopy: A New Tool for Accurate and Absolute Diffusion Measurements

Fluorescence correlation spectroscopy (FCS) has become an important tool for measuring diffusion, concentration, and molecular interactions of cellular components. The interpretation of FCS data critically depends on the measurement set-up. Here, we present a rigorous theory of FCS based on exact wave-optical calculations. Six of the most important optical and photophysical factors that influence FCS are studied: fluorescence anisotropy, cover-slide thickness, refractive index of the sample, laser-beam geometry, optical saturation, and pinhole adjustment. Our theoretical framework represents a general attempt to link all relevant parameters of the experimental set-up with the measured correlation function.

Performance of Fluorescence Correlation Spectroscopy for Measuring Diffusion and Concentration

Fluorescence correlation spectroscopy (FCS) is an important technique for studying low concentrations of analyte molecules in solution. The core molecular characteristic that can be addressed by FCS is the translational diffusion coefficient of the analyte molecules, which can be used for i.e. studying molecular binding and reactions, or conformational changes of macromolecules. The present paper discusses several possible optical and photophysical effects that can influence the outcome of a FCS measurement and thus can bias the value of the derived diffusion coefficient.

Art and artefacts of fluorescence correlation spectroscopy.

We introduce a pattern-matching technique for efficient identification of fluorophore ratios in complex multidimensional fluorescence signals using reference fluorescence decay and spectral signature patterns of individual fluorescent probes. Alternating pulsed laser excitation at three different wavelengths and time-resolved detection on 32 spectrally separated detection channels ensures efficient excitation of fluorophores and a maximum gain of fluorescence information. Using spectrally resolved fluorescence lifetime imaging microscopy (sFLIM), we were able to visualize up to nine different target molecules simultaneously in mouse C2C12 cells. By exploiting the sensitivity of fluorescence emission spectra and the lifetime of organic fluorophores on environmental factors, we carried out fluorescence imaging of three different target molecules in human U2OS cells with the same fluorophore. Our results demonstrate that sFLIM can be used for super-resolution multi-target imaging by stimulated emission depletion (STED).

Multi-target spectrally resolved fluorescence lifetime imaging microscopy

An efficient algorithm for pattern matching has been developed based on least-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three-dimensional molecule orientations in defocused single-molecule images. The developed algorithm exploits the excellent agreement between electrodynamic calculations of single-molecule emission and experimentally measured images. The procedure is found to be reliable and simple and can be applied to any kind of pattern recognition where the patterns to be recognized are precisely known a priori. The procedure works well even for noisy and low-intensity signals as usually encountered in single-molecule experiments.

/pdf/image-analysis-of-defocused-single-molecule-images-for-three-3dyhcyehd6.pdf

Ingo Gregor

Papers

Two-Focus Fluorescence Correlation Spectroscopy: A New Tool for Accurate and Absolute Diffusion Measurements

Performance of Fluorescence Correlation Spectroscopy for Measuring Diffusion and Concentration

Art and artefacts of fluorescence correlation spectroscopy.

Multi-target spectrally resolved fluorescence lifetime imaging microscopy

Image Analysis of Defocused Single-Molecule Images for Three-Dimensional Molecule Orientation Studies