Self-Supplying Guide RNA-Mediated CRISPR/Cas12a Fluorescence System for Sensitive Detection of T4 PNKP.

Sensitive detection methods for T4 polynucleotide kinase/phosphatase (T4 PNKPP) are urgently required to obtain information on malignancy and thereby to provide better guidance in PNKP-related diagnostics and drug screening. Although the CRISPR/Cas12a system shows great promise in DNA-based signal amplification protocols, its guide RNAs with small molecular weight often suffer nuclease degradation during storage and utilization, resulting in reduced activation efficiency. Herein, we proposed a self-supplying guide RNA-mediated CRISPR/Cas12a system for the sensitive detection of T4 PNKP in cancer cells, in which multiple copies of guide RNA were generated by in situ transcription. In this assay, T4 PNKP was chosen as a model, and a dsDNA probe with T7 promoter region and the transcription region of guide RNA were involved. Under the action of T4 PNKP, the 5'-hydroxyl group of the dsDNA probe was converted to a phosphate group, which can be recognized and digested by Lambda Exo, resulting in dsDNA hydrolysis. The transcription template was destroyed, which resulted in the failure to generate guide RNA by the transcription pathway. Therefore, the CRISPR/Cas12a system could not be activated to effectively cleavage the F-Q-reporter, and the fluorescence signal was turned off. In the absence of T4 PNKP, the 5'-hydroxyl group of the substrate DNA cannot be digested by Lambda Exo. The intact dsDNA acts as the transcription template to generate a large amount of guide RNA. Finally, the formed Cas12a/gRNA complex triggered the reverse cleavage of Cas12a on the F-Q-reporter, resulting in a "turn-on" fluorescence signal. This strategy displayed sharp sensitivity of T4 PNKP with the limit of detection (LOD) down to 0.0017 mU/mL, which was mainly due to the multiple regulation effect of transcription amplification. In our system, the dsDNA simultaneously serves as the T4 PNKP substrate, transcription template, and Lambda Exo substrate, avoiding the need for multiple probe designs and saving costs. By integrating the target recognition, Lambda Exo activity, and trans-cleavage activity of Cas12a, CRISPR/Cas12a catalyzed the cleavage of fluorescent-labeled short-stranded DNA probes and enabled synergetic signal amplification for sensitive T4 PNKP detection. Furthermore, the T4 PNKP in cancer cells has been evaluated as a powerful tool for biomedical research and clinical diagnosis, proving a good practical application capacity.

Single-shot wavefront sensing with deep neural networks for free-space optical communications.

Applying deep neural networks in image-based wavefront sensing allows for the non-iterative regression of the aberrated phase in real time. In view of the nonlinear mapping from phase to intensity, it is common to utilize two focal plane images in the manner of phase diversity, while algorithms based on only one focal plane image generally yield less accurate estimations. In this paper, we demonstrate that by exploiting a single image of the pupil plane intensity pattern, it is possible to retrieve the wavefront with high accuracy. In the context of free-space optical communications (FSOC), a compact dataset, in which considerable low-order aberrations exist, is generated to train the EfficientNet which learns to regress the Zernike polynomial coefficients from the intensity frame. The performance of ResNet-50 and Inception-V3 are also tested in the same task, which ended up outperformed by EfficientNet by a large margin. To validate the proposed method, the models are fine-tuned and tested with experimental data collected in an adaptive optics platform.

Centroid drift of laser beam propagation through a water surface with wave turbulence.

For underwater optical wireless communication (UOWC), the influence of waves close to the water's surface cannot be ignored. We build an experimental system of UOWC in a laboratory environment, where two fans are employed to produce water waves to simulate the turbulent water surface. The propagation and scattering of the input light are experimentally investigated, which shows that the scattering depends on the intensity of the water surface wave as well as the depth of its turbulence. Although at the receiver the laser spots are random and chaotic, their centroid drifts present spatial dependence, which is then investigated from the statistical point of view. Such characteristics may provide guidance to the optimization of receiving, tracking, and aiming devices.

Numerical research on partially coherent flat-topped beam propagation through atmospheric turbulence along a slant path.

In this paper, we investigate the propagation of partially coherent flat-topped (PCFT) beams through atmospheric turbulence along a slant path. Using wave optics simulation (WOS), we calculated the on-axis intensity of PCFT beams in both vacuum and turbulence links, finding that PCFT beams will self-focus during propagation and that the beam coherence length has a significant impact on this focusing phenomenon. The effects of the zenith angle and the source coherence length on the scintillation index and mean signal-to-noise ratio (SNR) are analyzed. Furthermore, taking into consideration the limitation of available devices, we examined the impacts of source coherence time and detector integration time on the performance of PCFT beams in slant links. WOS results indicate as much as an extra 2 dB SNR gain from PCFT beams in short links in comparison with Gaussian Schell-model beams.

Propagation of partially coherent beams with convex-shaped spatial coherence modulation in vertical turbulent links.

The convex partially coherent beam (CPCB) is a special type of nonuniformly correlated beam with a convex-shaped complex degree of coherence (DoC) distributions. Previously our research has illustrated the potential of CPCBs with super-Gaussian DoCs in free-space optical communications (FSOC), mainly manifested as self-focusing which can be transferred into extra scintillation reduction and SNR gain. In this study, the effects of the DoC transition slopes are analyzed and more details about the turbulence propagation of CPCBs with super-Gaussian shaped DoC are revealed. By means of wave optics simulation, the longitudinal intensity evolution of the CPCB is explored, showing that the DoC slope has a profound influence on the self-focusing features such as the focusing plane and the peak intensity. Aperture scintillation and mean SNR at the receiver end of some short-range vertical turbulent links are numerically computed. The obtained results show that, with CPCBs, an ~2 dB SNR gain can be achieved as compared to conventional Gaussian Schell-modal (GSM) beams. However, CPCBs are preferred only in shorter links, which is found to be relevant to the power-in-the-bucket of the receiving aperture. Furthermore, the impacts of the ratio of the source coherence time to the detector integration time are investigated, implying that the CPCB is less susceptible than the GSM. We have also examined the off-axis scintillation of the CPCB. Due to its convex-shaped DoC, the CPCB has significantly reduced off-axis scintillation, which can be beneficial in the presence of pointing errors.

Potentials of radial partially coherent beams in free-space optical communication: a numerical investigation.

Nonuniformly correlated partially coherent beams (PCBs) have extraordinary propagation properties, making it possible to further improve the performance of free-space optical communications. In this paper, a series of PCBs with varying degrees of coherence in the radial direction, academically called radial partially coherent beams (RPCBs), are considered. RPCBs with arbitrary coherence distributions can be created by adjusting the amplitude profile of a spatial modulation function imposed on a uniformly correlated phase screen. Since RPCBs cannot be well characterized by the coherence length, a modulation depth factor is introduced as an indicator of the overall distribution of coherence. By wave optics simulation, free-space and atmospheric propagation properties of RPCBs with (inverse) Gaussian and super-Gaussian coherence distributions are examined in comparison with conventional Gaussian Schell-model beams. Furthermore, the impacts of varying central coherent areas are studied. Simulation results reveal that under comparable overall coherence, beams with a highly coherent core and a less coherent margin exhibit a smaller beam spread and greater on-axis intensity, which is mainly due to the self-focusing phenomenon right after the beam exits the transmitter. Particularly, those RPCBs with super-Gaussian coherence distributions will repeatedly focus during propagation, resulting in even greater intensities. Additionally, RPCBs also have a considerable ability to reduce scintillation. And it is demonstrated that those properties have made RPCBs very effective in improving the mean signal-to-noise ratio of small optical receivers, especially in relatively short, weakly fluctuating links.

Research on partially coherent flat-topped vortex hollow beam propagation in turbulent atmosphere.

In this paper, the aperture averaged scintillation, mean signal-to-noise ratio (SNR), and average bit error rate (BER) for the partially coherent flat-topped vortex hollow beams propagating in turbulent atmosphere are evaluated. The variation of the aperture averaged scintillation against the coherence length of the beams and size of the receiver aperture is studied. It is also found that the aperture averaged scintillation increases with the topological charge of the partially coherent flat-topped vortex hollow beams. The partially coherent flat-topped vortex hollow beam with the smaller beam order has advantage to resist the effect of the turbulence. We also investigated the variation of the mean SNR and average BER against the coherence length.

Free-form surface generation in a double pole coordinate system for off-axis illumination application.

We apply the previously proposed double pole ray mapping technique to design a non-symmetrical optical surface for generating an off-axis rectangular illumination pattern, which is aimed for road luminaire. This paper explores the methods to determine the edges of an unsymmetrical collection solid angle in the source space for different target requirements as well as the mechanical structures of optical surfaces. By sampling source grids within the defined region in a double pole coordinate system, we achieve nearly perfect mapping between source and target with a high uniformity for the off-axis rectangular illumination pattern. The testing result of the prototyped free-form lens also shows good illumination performance, which is consistent with our simulation result. Besides, the tolerance analysis of the luminaire system is performed to understand the sensitivity of the LED's position on illumination performance.

Numerical investigation of flat-topped vortex hollow beams and Bessel beams propagating in a turbulent atmosphere.

In this paper, the aperture averaged scintillation, mean signal-to-noise ratio (SNR), and average bit error rate (BER) for both flat-topped vortex hollow beams and Bessel beams propagating in a turbulent atmosphere are evaluated. Investigations are also made illustrating the variation of aperture averaged scintillation, mean SNR, and average BER against the beam type, propagation distance, and size of the receiver aperture. Compared with the flat-topped vortex hollow beams, the Bessel beams have a smaller aperture averaged scintillation, higher mean SNR, and lower average BER when the receiver aperture is relatively small under the same conditions.

Polarization-insensitive resonances with high quality-factors in meta-molecule metamaterials.

Achieving narrow resonance is an area of interest within the field of metamaterials. However, only a few studies have investigated the polarization-insensitive resonances. A general principle for improving quality Q-factor of a sharp resonance is still unclear. In this work, we proposed a kind of planar meta-molecule metamaterials, which can exhibit polarization-insensitive resonance with high Q-factor. The proposed structures have a unit cell consisting of four arrayed ring resonant elements with two different sizes. Moreover, the investigation on surface current and two referential simulated structures confirm a principle for improving Q-factor.

Range accuracy of photon heterodyne detection with laser pulse based on Geiger-mode APD.

In this paper, we propose a combined system of heterodyne detection with laser pulse and photon counting based on Geiger-mode avalanche photodiode (GM-APD) that is designed to achieve the range of remote non-cooperative target. Based on the heterodyne principle and assuming that the creation of primary electrons in GM-APD is Poisson-distributed, the range accuracy model is established. The factors that influence the range accuracy, namely pulse width, echo intensity, local oscillator (LO) intensity, noise, echo position, and beat frequency, are discussed. The results show that these six factors have significant influence on the range accuracy when the echo intensity is extremely weak. In case that the primary electrons of the echo signal are beyond 4, the pulse width and echo intensity are the main influence factors. It is also shown that the stronger echo intensity, narrower pulse width, low noise, large echo position, and small beat frequency produce higher range accuracy in a pulsed photon heterodyne detection system based on GM-APD.

Capacity of MIMO free space optical communications using multiple partially coherent beams propagation through non-Kolmogorov strong turbulence.

We study the average capacity performance for multiple-input multiple-output (MIMO) free-space optical (FSO) communication systems using multiple partially coherent beams propagating through non-Kolmogorov strong turbulence, assuming equal gain combining diversity configuration and the sum of multiple gamma-gamma random variables for multiple independent partially coherent beams. The closed-form expressions of scintillation and average capacity are derived and then used to analyze the dependence on the number of independent diversity branches, power law α, refractive-index structure parameter, propagation distance and spatial coherence length of source beams. Obtained results show that, the average capacity increases more significantly with the increase in the rank of MIMO channel matrix compared with the diversity order. The effect of the diversity order on the average capacity is independent of the power law, turbulence strength parameter and spatial coherence length, whereas these effects on average capacity are gradually mitigated as the diversity order increases. The average capacity increases and saturates with the decreasing spatial coherence length, at rates depending on the diversity order, power law and turbulence strength. There exist optimal values of the spatial coherence length and diversity configuration for maximizing the average capacity of MIMO FSO links over a variety of atmospheric turbulence conditions.

Electromagnetic manifestation of chirality in layer-by-layer chiral metamaterials.

The three-dimensional (3D) and two-dimensional (2D) chiral metamaterials (CMMs) have been proved to exhibit circular dichroism and circular conversion dichroism, respectively. The layer-by-layer chiral metamaterials, as a category of 3D CMMs, are expected to show the same properties as bulk 3D structures (e.g. helices). However, in this paper, we demonstrated that the layer-by-layer CMMs exhibit circular dichroism and circular conversion dichroism simultaneously by using both theoretical and experimental methods. This work showed that asymmetric transmissions of circular polarizations can also be observed in layer-by-layer CMMs. Moreover, we provided some necessary requirements for the existing of asymmetric transmissions in layer-by-layer CMMs.

Method for estimating the axial intensity derivative in the TIE with higher order intensity derivatives and noise suppression.

It is an effective scheme to the phase retrieval for axial intensity derivative computing. In this paper, we demonstrate a method for estimating the axial intensity derivative and improving the calculation accuracy in the transport of intensity equation (TIE) from multiple intensity measurements. The method takes both the higher-order intensity derivatives and the noise into account, and minimizes the impact of detecting noise. The simulation results demonstrate that the proposed method can effectively reduce the error of intensity derivative computing.

What makes single-helical metamaterials generate "pure" circularly polarized light?

Circular polarizers with left-handed helical metamaterials can transmit right-handed circularly polarized (RCP) light with few losses. But a certain amount of left-handed circularly polarized (LCP) light will occur in the transmitted light, which is the noise of the circular polarizer. Therefore, we defined the ratio of the RCP light intensity to the LCP light intensity as the signal-to-noise (S/N) ratio. In our previous work, it's found that circular polarizers with multi-helical metamaterials have two orders higher S/N ratios than that of single-helical metamaterials. However, it has been a great challenge to fabricate such multi-helical structures with micron or sub-micron feature sizes. Is it possible for the single-helical metamaterials to obtain equally high S/N ratios as the multi-helical ones? To answer this question, we systematically investigated the influences of structure parameters of single-helical metamaterials on the S/N ratios using the finite-different time-domain (FDTD) method. It was found that the single-helical metamaterials can also reach about 30dB S/N ratios, which are equal to the multi-helical ones. Furthermore, we explained the phenomenon by the antenna theory and optimized the performances of the single-helical circular polarizers.

Lapping Quality Prediction of Ceramic Fiber Brush Based on Gaussian-Restricted Boltzmann Machine.

Although ceramic fiber brushes have been widely used for deburring and surface finishing, the associated relationship between process parameters and lapping quality is still unclear. In order to optimize the lapping process of ceramic fiber brushes, this paper proposes a multi-layer neural network based on the Gaussian-restricted Boltzmann machine (GRBM), and verified its prediction effectiveness. Compared with a traditional back-propagation neural network, its prediction error was reduced from 7.6% to 4.5%, and the determination coefficient was increased from 0.96 to 0.98, respectively. The comparison results showed that the proposed model can better grasp the relationship between process parameters and machining quality, which can be used as a decision-making foundation for lapping-process optimization.

Application of phase-conjugate beams in beam correction and underwater optical wireless communication subject to surface wave turbulence.

Water surface wave turbulence is one of the factors affecting the performances of underwater optical wireless communication (UOWC) systems. In our research, a phase-conjugate beam was used to correct the beam distortion and enhance the communication performances when a system is subject to surface wave turbulence. The phase-conjugate beam was generated by a phase-conjugate mirror (PCM), and a turbulence generator was used to generate surface wave turbulence in the experiment. We calculated the beam centroid distribution and the results showed that the phase-conjugate beam had a better propagation performance than the distorted beam at the different water depths. The root mean square (RMS) of the beam centroid for the phase-conjugate beam was 11 times less than that for the distorted beam, which meant that the phase-conjugate beam could effectively correct the beam drift. We further investigated the scintillation index and the signal-to-noise ratio (SNR); the results showed that the phase-conjugate beam was able to reduce the scintillation and an obvious improvement in SNR could be obtained. This research has the potential to be applied in UWC.

Polarization characteristics of the metallic structure with elliptically helical metamaterials.

In the last few years, there has been growing interest in the research of the polarizing optics consisting of sub-wavelength metamaterials due to the advantages of broad wavelength ranges, high temperature durability, and compact structures. So far, the metallic structure with the sub-wavelength metamaterials has been proved to achieve the linearly and the circularly polarized light. Therefore, there should be one question raised easily: Is it possible for the metallic structure with sub-wavelength metamaterials to generate the elliptically polarized light? To answer this question, we proposed a metallic structure with elliptically helical nanowires, and analyzed the polarization states of the transmitted light using FDTD method. It is confirmed that this metallic structure does have a giant elliptical dichroism. Furthermore, we also compared the distinct optical performances of elliptical single-, double-, three-, and four-helixes, and made a qualitative explanation for them.

InGaAs-InP avalanche photodiodes with dark current limited by generation-recombination.

Separate absorption grading charge multiplication avalanche photodiodes (SAGCM APDs) are widely accepted in photon starved optical communication systems due to the presence of large photocurrent gain. In this work, we present a detailed analysis of dark currents of planar-type SAGCM InGaAs-InP APDs with different thicknesses of multiplication layer. The effect of the diffusion process, the generation-recombination process, the tunneling process and the multiplication process on the total leakage current is discussed. A new empirical formula has been established to predict the optimal multiplication layer thickness of SAGCM APDs with dark current limited by generation-recombination at multiplication gain of 8.

Numerical and Experimental Research on the Brushing Aluminium Alloy Mechanism Using an Abrasive Filament Brush.

Abrasive filament brushes have been widely used in surface processes for a wide range of applications, including blending, edge-radiusing, and polishing. However, the associated brush mechanics of material removal is still not clear. In order to analyze the brush grinding of aluminium alloy, this paper constructed a kinematic model of a single filament, simulated the scratch process of a single abrasive grain, and investigated the brush force and material removal based on the finite element approach. The simulated result shows that the brush grinding can be changed from elastic-plastic deformation to chip formation when increasing the brush speed to 1000 r/min. The normal and tangential forces increase linearly and quadratically with the increase in the rotation speed (500-5000 r/min), respectively, and increase linearly with the increase in the penetration depth (0.1-1 mm), which is consistent with the experiment results. In addition, the amount of material removal initially increases with the increase in penetration depth, and then decreases. This paper provides a new approach to understanding the process of material removal and is helpful for the selection of reasonable brush parameters in the intelligent grinding control application.