Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames.

Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used to predict ORFs. The ribosome-protected footprints (RPFs) feature a significant 3-nt periodicity on mRNAs and are powerful in predicting translating ORFs, including small ORFs (sORFs), but the application of RPFs is limited because they are too short to be accurately mapped in complex genomes. In this study, we found a significant 3-nt periodicity in the datasets of populational genomic variants in coding sequences, in which the nucleotide diversity increases every three nucleotides. We suggest that this feature can be used to predict ORFs and develop the Python package 'OrfPP', which recovers ~83% of the annotated ORFs in the tested genomes on average, independent of the population sizes and the complexity of the genomes. The novel ORFs, including sORFs, identified from single-nucleotide polymorphisms are supported by protein mass spectrometry evidence comparable to that of the annotated ORFs. The application of OrfPP to tetraploid cotton and hexaploid wheat genomes successfully identified 76.17% and 87.43% of the annotated ORFs in the genomes, respectively, as well as 4704 sORFs, including 1182 upstream and 2110 downstream ORFs in cotton and 5025 sORFs, including 232 upstream and 234 downstream ORFs in wheat. Overall, we propose an alternative and supplementary approach for ORF prediction that can extend the studies of sORFs to more complex genomes.

Transition from anisotropic to isotropic optical absorption in core-shell square nanowires tuned by anti-crossing engineering.

The transition from anisotropic to isotropic optical properties in nanostructures plays an important role in developing next-generation intelligent photonic devices. Currently, core-shell nanostructures, frequently accompanied by different growth rates, are typically characterized by anisotropic optical properties at mid-infrared wavelengths. This inherent anisotropy, however, poses formidable challenges in achieving optical isotropy. In this work, an electric field is employed to transform the optical anisotropy of the off-centered core-shell square nanowires into optical isotropy. Based on the finite difference method, the results show that by tuning the electric field reasonably, the anti-crossing behavior of energy levels can be induced to align the energy structures in both eccentric and concentric nanowires. Although the optical anisotropy is strongly dependent on the distance and direction of the core shift, we marks, to the best of our knowledge, the first demonstration that the restored electronic states can effectively neutralize the polarization sensitivity, achieving isotropic optical absorption with wavelengths longer than 10 µm. Our finding indicates that the anti-crossing behavior of energy levels can serve as a viable mechanism to achieve switchable optical isotropy.

Resolution improvement in aerial imaging by a retroreflector using micro aperture arrays.

For a floating display system using a prism- or bead-type retroreflector, non-retroreflected light is the key cause of the deterioration in image resolution. In the present study, a micro aperture array was used to enhance the image resolution of aerial imaging displays based on prism and bead retroreflectors. The effects of different micro aperture parameters on the divergence angle of the retroreflector were experimentally studied, and the modulation of the point spread function of different retroreflectors was also explored in detail. The experimental results showed that by properly arranging the micro aperture array, the divergence angle of the retroreflective light could be effectively reduced. Moreover, the full width at half maximum of the point spread function of the retroreflector was effectively narrowed. Finally, after the modulation of the micro aperture array, the imaging resolution was increased by 115%-150% compared to the original resolution. The proposed micro array is low cost, easy to process, and flexible and can be applied to a retroreflector-based aerial imaging system to provide high image quality.

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence.

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. RESULTS: In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. CONCLUSIONS: The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.

Semidiscrete optical vortex droplets in quasi-phase-matched photonic crystals.

What we believe is a new scheme for producing semidiscrete self-trapped vortices ("swirling photon droplets") in photonic crystals with competing quadratic (χ(2)) and self-defocusing cubic (χ(3)) nonlinearities is proposed. The photonic crystal is designed with a striped structure, in the form of spatially periodic modulation of the χ(2) susceptibility, which is imposed by the quasi-phase-matching technique. Unlike previous realizations of semidiscrete optical modes in composite media, built as combinations of continuous and arrayed discrete waveguides, the semidiscrete vortex "droplets" are produced here in the fully continuous medium. This work reveals that the system supports two types of semidiscrete vortex droplets, viz., onsite- and intersite-centered ones, which feature, respectively, odd and even numbers of stripes, N. Stability areas for the states with different values of N are identified in the system's parameter space. Some stability areas overlap with each other, giving rise to the multistability of states with different N. The coexisting states are mutually degenerate, featuring equal values of the Hamiltonian and propagation constant. An experimental scheme to realize the droplets is outlined, suggesting new possibilities for the long-distance transmission of nontrivial vortex beams in nonlinear media.

Vortex Solitons in Quasi-Phase-Matched Photonic Crystals.

We report solutions for stable compound solitons in a three-dimensional quasi-phase-matched photonic crystal with the quadratic (χ^{(2)}) nonlinearity. The photonic crystal is introduced with a checkerboard structure, which can be realized by means of the available technology. The solitons are built as four-peak vortex modes of two types, rhombuses and squares (intersite- and onsite-centered self-trapped states, respectively). Their stability areas are identified in the system's parametric space (rhombuses occupy an essentially broader stability domain), while all bright vortex solitons are subject to strong azimuthal instability in uniform χ^{(2)} media. Possibilities for experimental realization of the solitons are outlined.

Fano effect induced giant and robust enhancement of photon correlations in cavity QED systems.

The Fano effect arising from the interference between two dissipation channels of the radiation continuum enables tuning of the photon statistics. Understanding the role of the Fano effect and exploiting it to achieve strong photon correlations are of both fundamental and applied significance. We present an analytical description of Fano-enhanced photon correlations based on cavity quantum electrodynamics to show that the Fano effect in atom-cavity systems can improve the degree of antibunching by over four orders of magnitude. The enhancement factors and the optimal conditions are explicitly given, and found to relate to the Fano parameter q. Remarkably, the Fano enhancement manifests robustness against the decoherence processes and can survive in the weak coupling regime. We expect our work to provide insight to tuning the photon statistics through the Fano effect, which offers a new, to the best of our knowledge, route to enhance the photon correlations, as well as the possibility of generating nonclassical light in a wider diversity of systems without the need of a strong light-matter interaction.

Geometric representation and the adiabatic geometric phase in four-wave mixing processes.

The application of the adiabatic geometric phase (AGP) to nonlinear frequency conversion may help to develop new types of all-optical devices, which leads to all-optical modulation of the phase front of one wave by the intensity of other waves. In this paper, we develop the canonical Hamilton equation and a corresponding geometric representation for two schemes of four-wave mixing (FWM) processes (ω1 + ω2 = ω3 + ω4 and ω1 + ω2 + ω3 = ω4), which can precisely describe and calculate the AGP controlled by the quasi-phase matching technique. The AGPs of the idler (ω1) and signal (ω4) waves for these two schemes of FWM are studied systematically when the two pump waves (ω2 and ω3) are in either the undepleted or in the depleted pump cases, respectively. The analysis reveals that the proposed methods for calculating the AGP are universal in both cases. We expect that the analysis of AGP in FWM processes can be applied to all-optically shaping or encoding of ultrafast light pulse.

Geometric phase with full-wedge and half-wedge rotation in nonlinear frequency conversion.

When the quasi-phase matching (QPM) parameters of the χ(2) nonlinear crystal rotate along a closed path, geometric phase will be generated in the signal and idler waves that participate in the nonlinear frequency conversion. In this paper, we study two rotation schemes, full-wedge rotation and half-wedge rotation, of the QPM parameters in the process of fully nonlinear three-wave mixing. These two schemes can effectively suppress the uncertainty in creating the geometric phase in the nonlinear frequency conversion process when the intensity of the pump is depleted. The finding of this paper provides an avenue toward constant control of the geometric phase in nonlinear optics applications and quantum information processing.

Freeform construction method for illumination design by using two orthogonal tangent vectors based on ray mapping.

An illumination design problem can be transformed into an optimal mass transport problem based on ray mapping. To construct a freeform surface that best fits the normal field, an efficient numerical method is put forward in this paper. In this method, the normal vectors are constructed by two adjacent orthogonal tangent vectors at each point, and then the normal vectors are substituted into Snell's law to obtain nonlinear equations describing the surface coordinates. Finally, the continuous and accurate freeform surface can be obtained by solving these nonlinear equations. The simulation results show that the proposed method not only provides lower relative standard deviation, but also significantly reduces the normal deviation more than the traditional one. It can be seen from the comparison results that different numerical integrations of a non-integrable normal field calculated by optimal mass transport can lead to different results, and the proposed method is more feasible than the traditional one, especially in the off-axis case. The simulation results of the illumination effect of some complex patterns also show that the freeform surface constructed by this method can restore the target pattern efficiently and control the normal vector error in a low range.

A Lightweight Localization Strategy for LiDAR-Guided Autonomous Robots with Artificial Landmarks.

This paper proposes and implements a lightweight, "real-time" localization system (SORLA) with artificial landmarks (reflectors), which only uses LiDAR data for the laser odometer compensation in the case of high-speed or sharp-turning. Theoretically, due to the feature-matching mechanism of the LiDAR, locations of multiple reflectors and the reflector layout are not limited by geometrical relation. A series of algorithms is implemented to find and track the features of the environment, such as the reflector localization method, the motion compensation technique, and the reflector matching optimization algorithm. The reflector extraction algorithm is used to identify the reflector candidates and estimates the precise center locations of the reflectors from 2D LiDAR data. The motion compensation algorithm predicts the potential velocity, location, and angle of the robot without odometer errors. Finally, the matching optimization algorithm searches the reflector combinations for the best matching score, which ensures that the correct reflector combination could be found during the high-speed movement and fast turning. All those mechanisms guarantee the algorithm's precision and robustness in the high speed and noisy background. Our experimental results show that the SORLA algorithm has an average localization error of 6.45 mm at a speed of 0.4 m/s, and 9.87 mm at 4.2 m/s, and still works well with the angular velocity of 1.4 rad/s at a sharp turn. The recovery mechanism in the algorithm could handle the failure cases of reflector occlusion, and the long-term stability test of 72 h firmly proves the algorithm's robustness. This work shows that the strategy used in the SORLA algorithm is feasible for industry-level navigation with high precision and a promising alternative solution for SLAM.

Talbot effect in waveforms containing subwavelength multilobe superoscillations.

The self-imaging of periodic light patterns, also known as the Talbot effect, is usually limited to periods that are larger than the wavelength. Here we present, theoretically and experimentally, a method to overcome this limitation by using superoscillating light patterns. The input intensity distribution is a periodic band-limited function with relatively large periods, but it contains regions of multilobe periodic oscillations with periods that are smaller than half of the wavelength. We observe the revival of the input pattern, including the subwavelength superoscillating regions, at large distances of more than 40 times the optical wavelength. Moreover, at fractional Talbot distances, we observe even faster local oscillations, with periods of approximately one-third of the optical wavelength.

Spin-Orbit Optical Hall Effect.

The optical Hall effect manifests itself as angular momentum separation induced by the photonic spin-orbit interaction. Such a celebrated Hall effect, at the mercy of the angular momentum conservation law, has attracted tremendous interest owing to its science and potential applications in precision measurements, material characterizations, and photonic devices, as well as quantum optics. However, to date, the Hall effect only expresses angular momentum separation of the spin term (spin-spin separation) or the orbital term (orbit-orbit separation), whereas the spin-orbit angular momentum separation, named as the spin-orbit Hall effect, remains unexplored. Here we demonstrate for the first time that this spin-orbit effect could appear when the polarization state of the light beam evolves adiabatically from the equator toward the poles of the higher-order Poincaré sphere, rather than the conventional Poincaré sphere. In this scenario, the intrinsic spin and orbital components of the light beam become separated, leading to equal nonzero spin and orbital angular momenta in magnitude but with the opposite sign. We further show that the spin-orbit Hall effect can be controlled via crystal birefringence and hence holds promise for applications; e.g., it is shown that the separated orbital angular momentum could be utilized in particle manipulations.

Semidiscrete Quantum Droplets and Vortices.

We consider a binary bosonic condensate with weak mean-field (MF) residual repulsion, loaded in an array of nearly one-dimensional traps coupled by transverse hopping. With the MF force balanced by the effectively one-dimensional attraction, induced in each trap by the Lee-Hung-Yang correction (produced by quantum fluctuations around the MF state), stable on-site- and intersite-centered semidiscrete quantum droplets (QDs) emerge in the array, as fundamental ones and self-trapped vortices, with winding numbers, at least, up to five, in both tightly bound and quasicontinuum forms. The application of a relatively strong trapping potential leads to squeezing transitions, which increase the number of sites in fundamental QDs and eventually replace vortex modes by fundamental or dipole ones. The results provide the first realization of stable semidiscrete vortex QDs, including ones with multiple vorticity.

𝒫𝒯-symmetric and antisymmetric nonlinear states in a split potential box.

We introduce a one-dimensional [Formula: see text]-symmetric system, which includes the cubic self-focusing, a double-well potential in the form of an infinitely deep potential box split in the middle by a delta-functional barrier of an effective height ε, and constant linear gain and loss, γ, in each half-box. The system may be readily realized in microwave photonics. Using numerical methods, we construct [Formula: see text]-symmetric and antisymmetric modes, which represent, respectively, the system's ground state and first excited state, and identify their stability. Their instability mainly leads to blowup, except for the case of ε=0, when an unstable symmetric mode transforms into a weakly oscillating breather, and an unstable antisymmetric mode relaxes into a stable symmetric one. At ε>0, the stability area is much larger for the [Formula: see text]-antisymmetric state than for its symmetric counterpart. The stability areas shrink with increase of the total power, P In the linear limit, which corresponds to [Formula: see text], the stability boundary is found in an analytical form. The stability area of the antisymmetric state originally expands with the growth of γ, and then disappears at a critical value of γThis article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.

Directional release of the stored ultrashort light pulses from a tunable Bragg-grating microcavity.

We demonstrate numerically the ability for directionally releasing the stored ultrashort light pulse from a microcavity by means of two-pulse nonlinear interaction in a cascading Bragg grating structure. The setting is built by a chirped grating segment which is linked through a uniform segment, including a tunable microcavity located at the junction between the two components. Our simulations show that stable trapping of an ultrashort light pulse can be achieved in the setting. The stored light pulse in a microcavity can be possibly released, by nonlinearly interacting with the lateral incident control pulse. Importantly, by breaking the symmetry of potential cavity, the stably trapped light pulse can be successfully released from the microcavity to the expected direction. Owing to the induced optical nonlinearity, the released ultrashort light pulses could preserve their shapes, propagating in a form of Bragg grating solitons through the uniform component, which is in contrast to the extensively studied light pulse trappings in photonic crystal cavities which operate at the linear regime.

Dispersion Management of Propagating Waveguide Modes on the Water Surface.

We report on the theoretical and experimental study of the generation of propagating waveguide modes on the water surface. These propagating modes are modulated in the transverse direction in a manner that satisfies boundary conditions on the walls of the water tank. It is shown that the propagating modes possess both anomalous and normal dispersion regimes, in contrast to the extensively studied zero mode that, in the case of deep water, only has normal dispersion with a fixed frequency independent dispersion coefficient. Importantly, by using a carrier frequency at which the group velocity dispersion crosses zero, a linear nonspreading and shape-preserving wave packet is observed. By increasing the wave steepness, nonlinear effects become pronounced, thereby enabling the first observation of linearly chirped parabolic water wave pulses in the anomalous dispersion regime. This parabolic wave maintains its linear frequency chirp and does not experience wave breaking during propagation.

Anderson localization in metallic nanoparticle arrays.

Anderson localization has been observed in various types of waves, such as matter waves, optical waves and acoustic waves. Here we reveal that the effect of Anderson localization can be also induced in metallic nonlinear nanoparticle arrays excited by a random electrically driving field. We find that the dipole-induced nonlinearity results in ballistic expansion of dipole intensity during evolution; while the randomness of the external driving field can suppress such an expansion. Increasing the strength of randomness above the threshold value, a localized pattern of dipole intensity can be generated in the metallic nanoparticle arrays. By means of statistics, the mean intensity distribution of the dipoles reveals the formation of Anderson localization. We further show that the generated Anderson localization is highly confined, with its size down to the scale of incident wavelength. The reported results might facilitate the manipulations of electromagnetic fields in the scale of wavelength.

Slow-light all-optical soliton diode based on tailored Bragg-grating structure.

All-optical soliton diode (AOSD) is proposed based on a sandwich nonlinear Bragg-grating structure: a linearly chirped Bragg-grating linked to a uniform Bragg-grating and again to a chirped Bragg-grating. The nonreciprocity is achieved by introducing two spatially asymmetric chirped Bragg-gratings with optical nonlinearity. High transmission ratio up to 150 is obtained when launching a picosecond Gaussian pulse into the setting. We find that such pulses in a form of solitons propagate at a rather small velocity (<0.03c) when pulse wavelength is selected in the vicinity of photonic bandgap.

Discrete solitons and vortices on two-dimensional lattices of PT-symmetric couplers.

We introduce a 2D network built of PT-symmetric dimers with on-site cubic nonlinearity, the gain and loss elements of the dimers being linked by parallel square-shaped lattices. The system may be realized as a set of PT-symmetric dual-core waveguides embedded into a photonic crystal. The system supports PT-symmetric and antisymmetric fundamental solitons (FSs) and on-site-centered solitary vortices (OnVs). Stability of these discrete solitons is the central topic of the consideration. Their stability regions in the underlying parameter space are identified through the computation of stability eigenvalues, and verified by direct simulations. Symmetric FSs represent the system's ground state, being stable at lowest values of the power, while anti-symmetric FSs and OnVs are stable at higher powers. Symmetric OnVs, which are also stable at lower powers, are remarkably robust modes: on the contrary to other PT-symmetric states, unstable OnVs do not blow up, but spontaneously rebuild themselves into stable FSs.