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

The term photonic crystals appears because of the analogy between electron waves in crystals and the light waves in artificial periodic dielectric structures. During the recent years the investigation of one-, two-and three-dimensional periodic structures has attracted a widespread attention of the world optics community because of great potentiality of such structures in advanced applied optical fields. The interest in periodic structures has been stimulated by the fast development of semiconductor technology that now allows the fabrication of artificial structures, whose period is comparable with the wavelength of light in the visible and infrared ranges.

http://ieeexplore.ieee.org/iel5/6354/16969/00781867.pdf

Photonic crystals

Sensitive optical biosensors for unlabeled targets: a review.

Microfabrication of graphene devices used in many experimental studies currently relies on the fact that graphene crystallites can be visualized using optical microscopy if prepared on top of Si wafers with a certain thickness of SiO2. The authors study graphene’s visibility and show that it depends strongly on both thickness of SiO2 and light wavelength. They have found that by using monochromatic illumination, graphene can be isolated for any SiO2 thickness, albeit 300nm (the current standard) and, especially, ≈100nm are most suitable for its visual detection. By using a Fresnel-law-based model, they quantitatively describe the experimental data.

/pdf/making-graphene-visible-4fjbh75lug.pdf

Making graphene visible

We present a novel waveguide geometry for enhancing and confining light in a nanometer-wide low-index material. Light enhancement and confinement is caused by large discontinuity of the electric field at highindex-contrast interfaces. We show that by use of such a structure the field can be confined in a 50-nm-wide low-index region with a normalized intensity of 20 mm 22 . This intensity is approximately 20 times higher than what can be achieved in SiO2 with conventional rectangular waveguides. © 2004 Optical Society of America OCIS codes: 030.4070, 130.0130, 130.2790, 230.7370, 230.7380, 230.7390, 230.7400. Recent results in integrated optics have shown the ability to guide, bend, split, and f ilter light on chips by use of optical devices based on high-index-contrast waveguides. 1–5 In all these devices the guiding mechanism is based on total internal ref lection (TIR) in a highindex material (core) surrounded by a low-indexmaterial (cladding); the TIR mechanism can strongly confine light in the high-index material. In recent years a number of structures have been proposed to guide or enhance light in low-index materials, 6–1 1 relying on external ref lections provided by interference effects. Unlike TIR, the external ref lection cannot be perfectly unity; therefore the modes in these structures are inherently leaky modes. In addition, since interference is involved, these structures are strongly wavelength dependent. Here we show that the optical field can be enhanced and conf ined in the low-index material even when light is guided by TIR. For a high-index-contrast interface, Maxwell’s equations state that, to satisfy the continuity of the normal component of electric f lux density D, the corresponding electric field (E-field) must undergo a large discontinuity with much higher amplitude in the low-index side. We show that this discontinuity can be used to strongly enhance and confine light in a nanometer-wide region of low-index material. The proposed structure presents an eigenmode, and it is compatible with highly integrated photonics technology. The principle of operation of the novel structure can be illustrated by analysis of the slab-based structure shown in Fig. 1(a), where a low-index slot is embedded between two high-index slabs (shaded regions). The novel structure is hereafter referred to as a slot waveguide. The slot waveguide eigenmode can be seen as being formed by the interaction between the fundamental eigenmodes of the individual slab waveguides. Rigorously, the analytical solution for the transverse E-field profile Ex of the fundamental TM eigenmode of the slab-based slot waveguide is

/pdf/guiding-and-confining-light-in-void-nanostructure-2oa0yk6hqm.pdf

Guiding and confining light in void nanostructure.

We present a construction approach to long-lasting rubidium (Rb) atomic vapor cells compatible with integrated photonic platforms. Indium solder seals did not exhibit any decrease in optical atomic density after being held at 95 °C for thirty days.

High longevity rubidium packaging method suitable for integrated optics

Scanning electrical impedance imaging (SII) has been developed and implemented as a novel high resolution imaging modality with the potential of imaging the electrical properties of biological tissues. In this paper, a fast linear model is derived and applied to the impedance image re- construction of scanning impedance imaging. With the help of both the deblurring concept and the reciprocity principle, this new approach leads to a calibrated approximation of the exact impedance distribution rather than a relative one from the original simplified linear method. Additionally, the method shows much less computational cost than the more straightforward nonlinear inverse method based on the forward model. The kernel function of this new approach is described and compared to the kernel of the simplified linear method. Two-dimensional impedance images of a flower petal and cancer cells are reconstructed using this method. The images reveal details not present in the measured images. I. INTRODUCTION

A Fast Linear Reconstruction Method for Scanning Impedance Imaging

Silica waveguides are often etched by reactive ion etch (RIE) processes. These processes can leave residual topography that can increase optical loss. We investigated the relation between optical loss and various RIE etch. A wet etch step meant to remove microstructures was also considered and compared. Ridge waveguides were fabricated in plasma enhanced chemical vapor deposited films by three different RIE processes, each with a different gas composition, pressure setting, and applied power setting. Half of each set of waveguides were also subjected to a hydrofluoric acid (HF) solution. The waveguides were tested for optical transmission via the cutback method. The transmission vs waveguide length measurements were plotted to fit an exponential curve and the optical loss and measurement uncertainty for each waveguide set was calculated. Clear distinctions in optical loss were found between the different RIE processes. The HF treatment also has an effect, significantly reducing optical loss for two processes and increasing it for the third. Of the tested RIE processes, one can be suggested for silica waveguides. It results in the lowest optical loss and coincidently has the fastest etch rate.

Effects of Post-Etch Microstructures on the Optical Transmittance of Silica Ridge Waveguides

Planar Resistive Electrode Ion Traps: A New Tool for Planetary Atmosphere Analysis

Multiplexed detection of biomarkers in real-time is crucial for sensitive and accurate diagnosis at the point of use. This scenario poses tremendous challenges for detection and identification of signals of varying shape and quality at the edge of the signal-to-noise limit. Here, we demonstrate a robust target identification scheme that utilizes a Deep Neural Network (DNN) for multiplex detection of single particles and molecular biomarkers. The model combines fast wavelet particle detection with Short-Time Fourier Transform analysis, followed by DNN identification on an AI-specific edge device (Google Coral Dev board). The approach is validated using multi-spot optical excitation of Klebsiella Pneumoniae bacterial nucleic acids flowing through an optofluidic waveguide chip that produces fluorescence signals of varying amplitude, duration, and quality. Amplification-free 3× multiplexing in real-time is demonstrated with excellent specificity, sensitivity, and a classification accuracy of 99.8%. These results show that a minimalistic DNN design optimized for mobile devices provides a robust framework for accurate pathogen detection using compact, low-cost diagnostic devices. 

/pdf/machine-learning-at-the-edge-for-ai-enabled-multiplexed-39r85m50.pdf

Aaron R. Hawkins

Papers

High longevity rubidium packaging method suitable for integrated optics

A Fast Linear Reconstruction Method for Scanning Impedance Imaging

Effects of Post-Etch Microstructures on the Optical Transmittance of Silica Ridge Waveguides

Planar Resistive Electrode Ion Traps: A New Tool for Planetary Atmosphere Analysis

Machine learning at the edge for AI-enabled multiplexed pathogen detection