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.

Photonics has long been used to study non-solid materials such as liquids, gases and plasmas, but these fluidic media have traditionally not comprised a functional part of the photonic device or system. The emerging field of optofluidics seeks to create new ways of uniting solid and non-solid materials in a single photonic system whose optical properties are typically defined by the fluidic component. This Review summarizes the current state of optofluidics from a photonics perspective. First, we describe a new class of photonic elements based on the combination of fluidic media and integrated optical structures. We then discuss the applications of optofluidic principles to particle sensing and manipulation in fluids, and finally assess current challenges and potential directions for future developments.

The photonic integration of non-solid media using optofluidics

Guiding light through hollow optical waveguides has opened the field of photonics to the investigation of non-solid materials that have all the convenience of integrated optics. Of particular interest is the confinement of atomic vapours, such as rubidium, because of its wide range of applications, including slow and stopped light1, single-photon nonlinear optics2, quantum information processing3, precision spectroscopy4 and frequency stabilization5. Here, we present the first monolithically integrated rubidium vapour cell using hollow-core antiresonant reflecting optical waveguides (ARROWs) on a silicon chip. The cells have a footprint of less than 1 cm2, fully planar fibre-optical access, and a cell volume more than 7 orders of magnitude less than conventional bulk cells. The micrometre-sized mode areas enable high beam intensities over near centimetre lengths. We demonstrate optical densities in excess of 2, and saturation absorption spectroscopy on a chip. These results allow the study of atoms and molecules on a platform that combines the advantages of photonic-crystal-like structures with integrated optics.

Atomic spectroscopy on a chip

We review recent developments and current status of liquid-core optical waveguides in optofluidics with emphasis on suitability for creating fully planar optofluidic labs-on-a-chip. In this first of two contributions, we give an overview of the different waveguide types that are being considered for effectively combining micro and nanofluidics with integrated optics. The large number of approaches is separated into conventional index-guided waveguides and more recent implementations using wave interference. The underlying principle for waveguiding and the current status are described for each type. We then focus on reviewing recent work on microfabricated liquid-core antiresonant reflecting optical (ARROW) waveguides, including the development of intersecting 2D waveguide networks and optical fluorescence and Raman detection with planar beam geometry. Single molecule detection capability and addition of electrical control for electrokinetic manipulation and analysis of single bioparticles are demonstrated. The demonstrated performance of liquid-core ARROWs is representative of the potential of integrated waveguides for on-chip detection with ultrahigh sensitivity, and points the way towards the next generation of high-performance, low-cost and portable biomedical instruments.

Optofluidic waveguides: I. Concepts and implementations

We report the design, fabrication, and demonstration of antiresonant reflecting optical (ARROW) waveguides with hollow cores. We describe the design principles to achieve low waveguide loss in both transverse and lateral directions. A novel fabrication process using silicon dioxide and silicon nitride layers as well as sacrificial polyimide core layers was developed. Optical characterization of 3.5µm thick waveguides with air cores was carried out. We demonstrate single-mode propagation through these hollow ARROW waveguides with propagation loss as low as 6.5cm-1 and mode cross sections down to 6.7µm2. Applications of these waveguides to sensing and quantum communication are discussed.

Integrated ARROW waveguides with hollow cores.

A large number of novel devices have been recently demonstrated using wafer fusion to integrate materials with different lattice constants. In many cases, devices created using this technique have shown dramatic improvements over those which maintain a single lattice constant. We present device results and characterizations of the fused interface between several groups of materials.

Aaron R. Hawkins

Papers

The photonic integration of non-solid media using optofluidics

Atomic spectroscopy on a chip

Optofluidic waveguides: I. Concepts and implementations

Integrated ARROW waveguides with hollow cores.

Wafer fusion: materials issues and device results