Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.

Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol.

Augmenting Transcriptome Annotations through the Lens of Splicing Evolution.

Alternative splicing (AS) is a ubiquitous mechanism in eukaryotes. It is estimated that 90% of human genes are alternatively spliced. Despite enormous efforts, transcriptome annotations remain, nevertheless, incomplete.

Facile fabrication of THz metasurfaces by a spatially shaped femtosecond laser printing system.

Terahertz (THz) metasurfaces provide unprecedented abilities to realize versatile THz wavefronts manipulations. Nevertheless, these high degree of freedom, non-periodic, densely arranged subwavelength unit cells pose numerous extreme parameter requirements for the fabrication of metasurfaces, presenting significant challenges to their practical application. Herein, a spatial shaping femtosecond laser printing system, based on spatial light modulation (SLM), is proposed for the creation of THz metasurfaces.

Accurate assembly of circular RNAs with TERRACE.

Circular RNA (circRNA) is a class of RNA molecules that forms a closed loop with their 5' and 3' ends covalently bonded. CircRNAs are known to be more stable than linear RNAs, have distinct properties and functions, and are promising biomarkers. Existing methods for assembling circRNAs heavily rely on the annotated transcriptomes, hence exhibiting unsatisfactory accuracy without a high-quality transcriptome.

Terahertz metalens for generating multi-polarized focal points and images with uniform intensity distributions.

Metasurfaces have provided a flexible platform for designing ultracompact metalenses with unusual functionalities. However, traditional multi-foci metalenses are limited to generating circularly polarized (CP) or linearly polarized (LP) focal points, and the intensity distributions are always inhomogeneous/chaotical between the multiple focal points. Here, an inverse design approach is proposed to optimize the in-plane orientation of each meta-atom in a terahertz (THz) multi-foci metalens that can generate multi-polarized focal points with nearly uniform intensity distributions.

Mode-order conversion in a Mach-Zehnder interferometer based on Chern insulators.

Mode-order conversion devices can provide a flexible platform to achieve mode coupling and optimizing in mode division multiplex (MDM) that can eliminate the restrain of capacity and density in photonic integration and communication. However, mode-order converters based on traditional photonic crystal (PC) waveguides are susceptible to defects, which always render device incapacitation in mode-order conversion. Herein, a mode converter designed by the Mach-Zehnder interferometer (MZI) structure is proposed to manipulate the conversion of topological edge states (TESs) based on Chern insulators consisting of gyromagnetic PCs.

Spin-decoupled excitation and wavefront shaping of structured surface waves on-chip terahertz metasurfaces.

Surface waves (SWs) are of great importance in terahertz (THz) photonics applications due to their subwavelength properties. Hence, it is crucial to develop surface wavefront shaping techniques, which is urgent in modern information technologies. In this paper, a new scheme is proposed to realize SW excitation and spin-decoupled wavefront shaping with an ultracompact planar meta-device working in the THz range.

Manipulating electromagnetic waves in a cavity-waveguide system with nontrivial and trivial modes.

The coupled cavity-waveguide approach provides a flexible platform to design integrated photonic devices that are widely applied in optical communications and information processing. Topological photonic crystals that can excite the nontrivial edge state (ES) and corner state (CS) have an unprecedented capability to manipulate electromagnetic (EM) waves, leading to a variety of unusual functionalities that are impossible to achieve with conventional cavity-waveguide systems. In this Letter, two-dimensional photonic crystals consisting of an ES waveguide, a CS cavity, and a trivial cavity are proposed as a means to robustly control the transmission characteristics of electromagnetic waves.

Tunable Transmissive Terahertz Linear Polarizer for Arbitrary Linear Incidence Based on Low-Dimensional Metamaterials.

In this work, we propose a structure consisting of three metamaterial layers and a metallic grating layer to rotate the polarization of arbitrary linearly polarized incidence to the y-direction with high transmissivity by electrically tuning these metamaterials. The transfer matrix method together with a harmonic oscillator model is adopted to theoretically study the proposed structure. Numerical simulation based on the finite difference time-domain method is performed assuming that the metamaterial layers are constituted by graphene ribbon arrays.

A Review on Terahertz Technologies Accelerated by Silicon Photonics.

In the last couple of decades, terahertz (THz) technologies, which lie in the frequency gap between the infrared and microwaves, have been greatly enhanced and investigated due to possible opportunities in a plethora of THz applications, such as imaging, security, and wireless communications. Photonics has led the way to the generation, modulation, and detection of THz waves such as the photomixing technique. In tandem with these investigations, researchers have been exploring ways to use silicon photonics technologies for THz applications to leverage the cost-effective large-scale fabrication and integration opportunities that it would enable.

Terahertz Broadband Polarization Conversion for Transmitted Waves Based on Graphene Plasmon Resonances.

We applied the harmonic oscillator model combined with the transfer matrix method to study the polarization conversion for transmitted waves in metallic grating/plasmon-excitation layer/metallic grating structure in the terahertz (THz) region. By comparing the calculated spectra and the simulated (by the finite-difference-time-domain method) ones, we found that they correspond well with each other. Both methods show that the Drude background absorption and the excited plasmon resonances are responsible for polarization conversion.

Spin-independent metalens for helicity-multiplexing of converged vortices and cylindrical vector beams.

The converged vortex beam with a well-defined focal plane is an essential ingredient for trapping and rotating microparticles. Metasurfaces, two-dimensional metamaterials, provide an ultra-compact and flexible platform for designing a converged vortex by integrating the functions of a lens and vortex plate. A spin-defocused metasurface can further boost information capacity such as the multiplexing of helicity-dependent functionalities.

Geometry phase for generating multiple focal points with different polarization states.

Conventional lenses are always large and bulky to achieve desired wave-manipulating functions, hindering the development of integrated and miniaturized optical systems. Metasurfaces, two-dimensional counterparts of metamaterials, can accurately tailor the wavefront of electromagnetic waves at subwavelength scale, providing a flexible platform for designing ultra-compact and ultra-flat lenses, namely as metalenses. However, the previous geometry-phase-based metalenses usually generate focal point(s) with only one special polarization state, i.

Critical Factors for In Vivo Measurements of Human Skin by Terahertz Attenuated Total Reflection Spectroscopy.

Attenuated total reflection (ATR) geometry is a suitable choice for in vivo measurements of human skin due to the deep penetration of the field into the sample and since it makes it easy to measure the reference spectrum. On the other hand, there are several critical factors that may affect the terahertz (THz) response in these kinds of experiments. Here, we analyse in detail the influence of the following factors: the contact positions between the thumb and the prism, the contact pressure, the contact duration, and the materials of the prism.

Terahertz-frequency temporal differentiator enabled by a high-Q resonator.

Terahertz (THz) fundamental "building blocks" equivalent to those used in multi-functional electronic circuits are very helpful for actual applications in THz data-processing technology and communication. Here, we theoretically and experimentally demonstrate a THz temporal differentiator based on an on-chip high-quality (Q) factor resonator. The resonator is made of low-loss high-resistivity silicon material in a monolithic, integrated platform, which is carefully designed to operate near the critical coupling region.

Flexibly designed spoof surface plasmon waveguide array for topological zero-mode realization.

We propose a flexibly designed photonic system based on ultrathin corrugated metallic "H-bar" waveguide that supports spoof surface plasmon polariton (SPP) at microwave frequencies. Five designs were presented, in order to demonstrate flexibility according to varying height, period, core width, rotation, and shifting on the "H-bar" unit of the waveguide. The propagation constant between two hybrid designs of period and height structure was then shown in order to study the coupling effect.

Polarization Encoded Color Image Embedded in a Dielectric Metasurface.

Optical metasurfaces have shown unprecedented capabilities in the local manipulation of the light's phase, intensity, and polarization profiles, and represent a new viable technology for applications such as high-density optical storage, holography and display. Here, a novel metasurface platform is demonstrated for simultaneously encoding color and intensity information into the wavelength-dependent polarization profile of a light beam. Unlike typical metasurface devices in which images are encoded by phase or amplitude modulation, the color image here is multiplexed into several sets of polarization profiles, each corresponding to a distinct color, which further allows polarization modulation-induced additive color mixing.

High-resolution grayscale image hidden in a laser beam.

Images perceived by human eyes or recorded by cameras are usually optical patterns with spatially varying intensity or color profiles. In addition to the intensity and color, the information of an image can be encoded in a spatially varying distribution of phase or polarization state. Interestingly, such images might not be able to be directly viewed by human eyes or cameras because they may exhibit highly uniform intensity profiles.

Geometric Phase Generated Optical Illusion.

An optical illusion, such as "Rubin's vase", is caused by the information gathered by the eye, which is processed in the brain to give a perception that does not tally with a physical measurement of the stimulus source. Metasurfaces are metamaterials of reduced dimensionality which have opened up new avenues for flat optics. The recent advancement in spin-controlled metasurface holograms has attracted considerate attention, providing a new method to realize optical illusions.

High extinction ratio electromagnetically induced transparency analogue based on the radiation suppression of dark modes.

A high extinction ratio (ER) electromagnetically induced transparency (EIT) analogue based on single-layer metamaterial is designed and experimentally demonstrated in this paper. This design involves four mirror-like symmetrically coupled split ring resonators (SRRs) that exhibit a bright-dark-dark-bright mode configuration. The EIT-like effect is realized by coupling between the bright resonators and dark resonators.

Broadband unidirectional behavior of electromagnetic waves based on transformation optics.

High directive antennas are fundamental elements for microwave communication and information processing. Here, inspired by the method of transformation optics, we propose and demonstrate a transformation medium to control the transmission path of a point source, resulting in the unidirectional behavior of electromagnetic waves (directional emitter) without any reflectors. The network of inductor-capacitor transmission lines is designed to experimentally realize the transformation medium.

0.1-20 THz ultra-broadband perfect absorber via a flat multi-layer structure.

An ultra-broadband perfect absorber based on graded-index mechanism is designed and fabricated. The perfect absorber is comprised of a heavily-doped silicon absorption substrate and a flat six-layer antireflective structure. The refractive index of each layer was widely tuned by hollow polystyrene microsphere and TiO nanoparticle dopants, which can offer a gradually changed refractive index profile from 1.