Blind Search Research Articles

Assessing protein homology models with docking reproducibility

Results of the recent Critical Assessment of Protein Structure (CASP) competitions demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able to produce structures that were similar enough to experimental structures that many described the problem of protein prediction solved. However, for such structures to be used for drug docking studies requires precision in the placement of side chain atoms as well. Here we built a library of 1334 small molecules and examined how reproducibly they bound to the same site on a protein using QuickVina-W, a branch of the program Autodock that is optimized for blind searches. We discovered that the higher the backbone quality of the homology model the greater the similarity between the small molecule docking to the experimental and modeled structures. Furthermore, we found that specific subsets of this library were particularly useful for identifying small differences between the best of the best modeled structures. Specifically, when the number of rotatable bonds in the small molecule increased, differences in binding sites became more apparent.

Kepler K2Campaign 9 – II. First space-based discovery of an exoplanet using microlensing

ABSTRACTWe present K2-2016-BLG-0005Lb, a densely sampled, planetary binary caustic-crossing microlensing event found from a blind search of data gathered from Campaign 9 of the Kepler K2 mission (K2C9). K2-2016-BLG-0005Lb is the first bound microlensing exoplanet discovered from space-based data. The event has caustic entry and exit points that are resolved in the K2C9 data, enabling the lens-source relative proper motion to be measured. We have fitted a binary microlens model to the Kepler data and to simultaneous observations from multiple ground-based surveys. Whilst the ground-based data only sparsely sample the binary caustic, they provide a clear detection of parallax that allows us to break completely the microlensing mass-position-velocity degeneracy and measure the planet’s mass directly. We find a host mass of 0.58 ± 0.04 M⊙ and a planetary mass of 1.1 ± 0.1 MJ. The system lies at a distance of 5.2 ± 0.2 kpc from Earth towards the Galactic bulge, more than twice the distance of the previous most distant planet found by Kepler. The sky-projected separation of the planet from its host is found to be 4.2 ± 0.3 au which, for circular orbits, deprojects to a host separation $a = 4.4^{+1.9}_{-0.4}$ au and orbital period $P = 13^{+9}_{-2}$ yr. This makes K2-2016-BLG-0005Lb a close Jupiter analogue orbiting a low-mass host star. According to current planet formation models, this system is very close to the host mass threshold below which Jupiters are not expected to form. Upcoming space-based exoplanet microlensing surveys by NASA’s Nancy Grace Roman Space Telescope and, possibly, ESA’s Euclid mission, will provide demanding tests of current planet formation models.

Gaussian blur aided blind phase search algorithm in low SNR QAM transmission system

Probabilistic constellation shaping (PCS) reduces the required SNR compared with the uniform distribution system to achieve the same mutual information (MI). However, severe amplified spontaneous emission (ASE) noise degenerates the performance of the conventional blind phase search (BPS) algorithm, showing an unpleasant MI penalty and reducing the shaping gain. In this paper, we reveal that the MI impairment comes from the misjudgment of phase noise estimation by the conventional BPS algorithm interfered by severe ASE noise. To cope with this problem, we propose a Gaussian blur-aided BPS (GBA-BPS) algorithm by introducing an unequal weight filter with an efficient solution of variance configuration into the conventional BPS. Details about why the GBA-BPS algorithm outperforms the conventional BPS algorithm are elaborated based on the spectrum analysis of the phase noise estimated by both schemes. Evaluated on a 50-GBaud PCS-64QAM system, the proposed GBA-BPS algorithm with a 31-tap filter effectively mitigates the misjudgment of phase noise estimation, achieving a maximum MI gain of 0.5 and 0.25 bits/symbol compared with conventional BPS when the SNR is 16 dB and 18 dB respectively. The proposed GBA-BPS is a significant improvement over conventional BPS and it is more suitable for carrier phase recovery in low SNR systems.

Ultra-High Capacity Optical Satellite Communication System Using PDM-256-QAM and Optical Angular Momentum Beams.

Twisted light beams such as optical angular momentum (OAM) with numerous possible orthogonal states have drawn the prodigious contemplation of researchers. OAM multiplexing is a futuristic multi-access technique that has not been scrutinized for optical satellite communication (OSC) systems thus far, and it opens up a new window for ultra-high-capacity systems. This paper presents the 4.8 Tbps (5 wavelengths × 3 OAM beams × 320 Gbps) ultra-high capacity OSC system by incorporating polarization division multiplexed (PDM) 256-Quadrature amplitude modulation (256-QAM) and OAM beams. To realize OAM multiplexing, Laguerre Gaussian (LG) transverse mode profiles such as LG00, LG140, and LG400 were used in the proposed study. The effects of the receiver's digital signal processing (DSP) module were also investigated, and performance improvement was observed using DSP for its potential to compensate for the effects of dispersion, phase errors, and nonlinear effects using the blind phase search (BPS), Viterbi phase estimation (VPE), and the constant modulus algorithm (CMA). The results revealed that the proposed OAM-OSC system successfully covered the 22,000 km OSC link distance and, out of three OAM beams, fundamental mode LG00 offered excellent performance. Further, a detailed comparison of the proposed system and reported state-of-the-art schemes was performed.

QUIJOTE scientific results – IX. Radio sources in the QUIJOTE-MFI wide survey maps

ABSTRACT We present the catalogue of Q-U-I JOint TEnerife (QUIJOTE) Wide Survey radio sources extracted from the maps of the Multi-Frequency Instrument compiled between 2012 and 2018. The catalogue contains 786 sources observed in intensity and polarization, and is divided into two separate sub-catalogues: one containing 47 bright sources previously studied by the Planck collaboration and an extended catalogue of 739 sources either selected from the Planck Second Catalogue of Compact Sources or found through a blind search carried out with a Mexican Hat 2 wavelet. A significant fraction of the sources in our catalogue (38.7 per cent) are within the |b| ≤ 20° region of the Galactic plane. We determine statistical properties for those sources that are likely to be extragalactic. We find that these statistical properties are compatible with currently available models, with a ∼1.8 Jy completeness limit at 11 GHz. We provide the polarimetric properties of (38, 33, 31, 23) sources with P detected above the $99.99{{\ \rm per\, cent}}$ significance level at (11, 13, 17, 19) GHz respectively. Median polarization fractions are in the 2.8–4.7 per cent range in the 11–19 GHz frequency interval. We do not distinguish between Galactic and extragalactic sources here. The results presented here are consistent with those reported in the literature for flat- and steep-spectrum radio sources.

Blind phase search algorithm based on threshold simplification

A simplified scheme for the blind phase search (BPS) algorithm is proposed. By comparing the loss function with a threshold value, the number of test phases is reduced. Simulation and experimental results show that compared with the traditional BPS algorithm, this algorithm only needs half of the test phases under the same performance.

Analytical Study and Noise Mitigation for Complex-Valued Optical DSB Transmission With Carrier-Assisted Differential Detection Receiver

A thorough analysis of the system model for complex-valued optical double-sideband (DSB) transmission with carrier-assisted differential detection (CADD) receiver under the influence of laser phase noise and fiber chromatic dispersion (CD) is presented. It is shown that the interaction of laser phase noise and CD leads to the phenomenon of phase-to-amplitude (P2A) noise and equalization-enhanced phase noise (EEPN). The achievable performance of the complex-valued optical DSB transmission with CADD receiver under the influence of EEPN and P2A noise is estimated by a closed-form expression, and it is verified by simulation that the results show an inaccuracy of less than 1 dB for a wide range of system parameters. In addition, in order to mitigate the EEPN and P2A noise, we propose a pre-decision aid-based simplified blind phase search (BPS) algorithm, commonly referred to as PDA-BPS algorithm. The PDA-BPS algorithm allows for reduced complexity by decreasing the number of symbols entering the BPS algorithm. Theoretical derivation and simulation verification illustrate that the PDA-BPS algorithm can achieve similar mitigation performance to the BPS algorithm with lower complexity. Specifically, under the condition that classification decision threshold R is equal to 0.25, the complexity can be reduced by 40%/16.6% with 1 MHz/7 MHz linewidth for 16-QAM and 29%/10.9% with 0.5 MHz/3 MHz linewidth for 64-QAM.

Intelligent Warehouse Robot Path Planning Based on Improved Ant Colony Algorithm

To improve the safety and accuracy of path planning of intelligent warehouse robots, this paper establishes a storage shelf model, incorporates Poisson Distribution to simulate the influence of unknown factors, and establishes a three-color raster map. The pheromone update mechanism is optimized by considering the path safety, path length, and turning elements under the influence of unknown factors. The two models based on the three-dimensional shelves are simulated separately, and the planned paths are de-pointed and smoothed. The simulation results show that the improved algorithm can design the optimal route safely and effectively in the storage environment under the influence of unknown factors. The proposed algorithm not only solves the blind search and deadlock problems, but also has better performances than other algorithms, i.e., 4 iterations compared to 22 and 30 iterations, 3 turns compared to 9 and 7 turns, 8.468s running time compared to 16.974s and 13.754s.

Multi-Level Phase Noise Model for CO-OFDM Spatial-Division Multiplexed Transmission

Spatial division multiplexed (SDM) transmission systems with coherence communication technology have become an important issue in meeting the demands for the capacity of fiber. However, research on the phase noise from lasers is mainly focused on single-channel systems or single-carrier SDM systems. In this paper, a phase noise model comprising common laser phase noise, in addition to the core phase drifts induced by the SDM, is introduced and analyzed for a coherence orthogonal frequency-division multiplexing (CO-OFDM) spatial-division multiplexed transmission (SDM) system. Based on the phase noise model, the applicability of the blind phase search algorithm and the pilot-aided phase estimation algorithm is discussed and demonstrated via simulation. The results show that these two algorithms can work well when considering combined laser linewidths with core phase drifts for CO-OFDM 7-core multi-core fiber (MCF). The results mean that with the SDM phase noise model, phase noise estimation in other cores can be transferred from one core to lower the complexity with the help of the model. This research provides a proper application of the phase noise analysis of large-capacity optical communication based on a weak-coupled MCF.

Robot Path Planning of Improved Adaptive Ant Colony System Algorithm Based on Dijkstra

Path planning is one of the key technologies of robot. Aiming at the problems of slow convergence speed and inefficient search of traditional Ant Colony System Algorithm, an adaptive Ant Colony System Algorithm based on Dijkstra is proposed in the paper. Firstly, Dijkstra algorithm is applied to searching the initial path in the grid environment, constructing the initial path, optimizing the initial pheromone in the region, therefore, the Ant Colony System Algorithm avoid falling into blind search in the initial stage; In the transition probability, the disguised angle probability function and parameter adaptive pseudo-random proportion rule are introduced to improve the search efficiency and convergence speed of the algorithm, and eliminate the inferior ant path; Finally, B-spline interpolation curve is used to smooth the path. Compared with the traditional Ant Colony System Algorithm, the simulation results in the grid environment demonstrating its effectiveness to improve convergence speed and to enhance search efficiency are provided. The characteristics of the improved Ant Colony System Algorithm are faster convergence speed and better planning.

Application of hybrid artificial bee colony algorithm based on load balancing in aerospace composite material manufacturing

The manufacturing of composite materials for the aerospace industry represents a cornerstone of future development in this advanced field. In this study, a mathematical model of flexible job-shop scheduling problem (FJSP) was established by extracting the key manufacturing information from an aerospace composite manufacturing workshop. Intelligent algorithms can effectively solve FJSP. However, when applied to a multi-objective FJSP (MOFJSP), they suffer from drawbacks such as blind search and low efficiency. Therefore, this study proposes a new artificial bee colony algorithm and implements it as part of a hybrid method (referred to as the HMABC) to solve MOFJSP. The method involves three steps: (1) A multiple-rule initial population is constructed to minimize randomness and improve quality. (2) A greedy decoding method is used to decode each individual to further narrow the search range to replace the conventional decoding method. (3) By considering the machine load index (which has often been neglected), the concept of machine load rate is proposed, and three heuristic strategies are designed (with the influences ranging from small to high) to diverge the solution in all directions instead of just a direction. The performance of the proposed method is compared with those of existing algorithms using a classical FJSP test example, and the effectiveness and efficiency of HMABC is verified. Finally, the method is applied to an actual aerospace composite manufacturing system to realize the scheduling of actual production activities.

Brighter and More Massive Galaxies in the Vicinity of Lyα Nebulae

It has been well established in the local universe that galaxy properties differ based on the large-scale environment in which they reside. As luminous Lyα nebulae have been shown to trace overdense environments at z ∼ 2–3, comparing the properties of galaxies within Lyα nebulae systems to those in the field can provide insight into how and when locally observed trends between galaxy properties and environment emerged. Six Lyα nebulae were discovered at z ∼ 2.3 in a blind search of the GOODS-S extragalactic field, a region also covered by the 3D-HST spectroscopic survey. Utilizing 3D-HST data, we identified 86 galaxies in the vicinity of these nebulae and used statistical tests to compare their physical properties to galaxies elsewhere in the field. Galaxies lying within 320 proper kpc of a Lyα nebula are roughly half a magnitude brighter than those in the field, with higher stellar masses, higher star formation rates, and larger effective radii. Even when considering the effects of sample incompleteness, our study suggests that galaxies in overdensities at z ∼ 2.3 traced by Lyα nebulae are being influenced by their environment. Furthermore, Lyα-nebula-associated galaxies lie on the same main sequence of star formation as field galaxies but have a larger proportion of high-mass galaxies, consistent with the idea that galaxy evolution is accelerated in rich environments. Expanded surveys for Lyα nebulae in other deep extragalactic fields and galaxy spectroscopic follow-up with the James Webb Space Telescope (JWST) will better constrain the demographics of Lyα-nebula-associated galaxies.

DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space.

We present Deep learning for Collective Variables (DeepCV), a computer code that provides an efficient and customizable implementation of the deep autoencoder neural network (DAENN) algorithm that has been developed in our group for computing collective variables (CVs) and can be used with enhanced sampling methods to reconstruct free energy surfaces of chemical reactions. DeepCV can be used to conveniently calculate molecular features, train models, generate CVs, validate rare events from sampling, and analyze a trajectory for chemical reactions of interest. We use DeepCV in an example study of the conformational transition of cyclohexene, where metadynamics simulations are performed using DAENN-generated CVs. The results show that the adopted CVs give free energies in line with those obtained by previously developed CVs and experimental results. DeepCV is open-source software written in Python/C++ object-oriented languages, based on the TensorFlow framework and distributed free of charge for noncommercial purposes, which can be incorporated into general molecular dynamics software. DeepCV also comes with several additional tools, i.e., an application program interface (API), documentation, and tutorials.

The Gaia-ESO Survey: Chemical tagging in the thin disk

Context. The chemical makeup of a star provides the fossil information of the environment where it formed. Under this premise, it should be possible to use chemical abundances to tag stars that formed within the same stellar association. This idea – known as chemical tagging – has not produced the expected results, especially within the thin disk where open stellar clusters have chemical patterns that are difficult to disentangle. Aims. The ultimate goal of this study is to probe the feasibility of chemical tagging within the thin disk population using high-quality data from a controlled sample of stars. We also aim at improving the existing techniques of chemical tagging and giving some kind of guidance on different strategies of clustering analysis in the elemental abundance space. Methods. Here we develop the first blind search of open clusters’ members through clustering analysis in the elemental abundance space using the OPTICS algorithm applied to data from the Gaia-ESO survey. First, we evaluate different strategies of analysis (e.g., choice of the algorithm, data preprocessing techniques, metric, space of data clustering), determining which ones are more performing. Second, we apply these methods to a data set including both field stars and open clusters attempting a blind recover of as many open clusters as possible. Results. We show how specific strategies of data analysis can improve the final results. Specifically, we demonstrate that open clusters can be more efficaciously recovered with the Manhattan metric and on a space whose dimensions are carefully selected. Using these (and other) prescriptions we are able to recover open clusters hidden in our data set and find new members of these stellar associations (i.e., escapers, binaries). Conclusions. Our results indicate that there are chances of recovering open clusters’ members via clustering analysis in the elemental abundance space, albeit in a data set that has a very high fraction of cluster members compared to an average field star sample. Presumably, the performances of chemical tagging will further increase with higher quality data and more sophisticated clustering algorithms, which will likely became available in the near future.

Optimal Option of n-Level Polybinary Transformation in Faster than Nyquist System According to the Time-Packing Factor

According to an in-depth analysis of the relationship among n-level polybinary transformation, the time-packing factor and the performance of the decoding algorithm, we find that the appropriate n-level polybinary transformation can improve the performance of the decoding algorithm within a certain range of the time-packing factor in the Faster than Nyquist (FTN) system. In this paper, we explain the reason that this phenomenon occurs. Based on the above analysis, we propose a modified blind phase search (BPS) algorithm to compensate for phase noise (PN) in the FTN system with an extremely small time-packing factor. As a result, the modified-BPS algorithm can cope with the PN with the linewidth × symbol rate at 1.07 × 10−5, 1.79 × 10−5, 2.86 × 10−5 and 3.57 × 10−5 under a time-packing factor of 0.55, 0.50 and 0.45, respectively. At the same time, the spectrum efficiency (SE) is improved to 3.27 bit/s/Hz, 4 bit/s/Hz and 4.88 bit/s/Hz.

Commodity Search Based on the Hybrid Breadth-Depth Algorithm in the Crowd Intelligence Based Transaction Network

Crowd intelligence based transaction network (CIbTN) is a new generation of e-commerce. In a CIbTN, buyers, sellers, and other institutions are all independent and intelligent agents. Each agent stores the commodity information in a local node. The agents interconnect through a circle of friends and construct an unstructured network. To conduct the commodity search task in a network more efficiently and in an energy-saving manner when a buyer presents a commodity demand, a hybrid breadth-depth search algorithm (HBDA) is proposed, which combines the search logic of the breadth-first search algorithm and the depth-first search algorithm. We defined the correlation degree of nodes in a network, optimized the rules of search and forwarding paths using the correlation degree between a node and its neighboring nodes in the circle of friends, and realized the HBDA based on the PeerSim simulation tool and Java. Experimental results show that, in general, the proposed HBDA has a better search success rate, search time, commodity matching degree, and search network consumption over the two blind search algorithms. The HBDA also has good expansibility, thus allowing it to be used for commodity search efficiently with a high success rate in large-scale networks.

Pushchino multibeam pulsar search – I. Targeted search of weak pulsars

ABSTRACT The search for pulsars in a sample of pulsar candidates found based on a multi-year survey conducted with low (six channels; sampling 0.1s) time-frequency resolution on declinations −9° < δ < +42° was carried out with the Large Phased Array of the Lebedev Physical Institute (LPA LPI). LPA is a transit telescope operating at 111 MHz with a bandwidth of 2.5 MHz. Search, analysis and evidence of pulsar detection were carried out using a visualization programme of summed up power spectra obtained from the survey data with high (32 channels; sampling 12.5 ms) time-frequency resolution. 11 new pulsars with periods P0 = 0.41–3.75 s and dispersion measure DM = 15–154 pc cm−3 have been discovered. In total, in the survey with a low-time-frequency resolution for the period 2016–2021 in a blind search 203 pulsars were found, among them 42 new and 161 known pulsars. It is shown that in the search on the data with high-time-frequency resolution accumulated over a time interval of seven years, pulsars with a flux density of 0.1–0.2 mJy at the frequency of 111 MHz can be detected. When searching for pulsars with regular (periodic) emission at declinations +21° < δ < +42o, all pulsars located outside the galactic plane having P0 ≥ 0.5 s, DM ≤ 100 pc cm−3, and the flux density S ≥ 0.5 mJy can be detected.

Breakthrough Listen Search for the WOW! Signal* *Dedicated to the memory of Bart S. Wlodarczyk-Sroka.

Caballero identified the star 2MASS 19281982-2640123 as a potential Sun-like star from which the WOW! signal could have originated. We conducted a search for artificial narrowband (2.79 Hz/1.91 Hz), drifting (±4 Hz s−1) technosignatures from this source using the turboSETI pipeline, from 1–2 GHz, using simultaneous multi-telescope observations with both the Robert C. Byrd Green Bank Telescope and the newly refurbished Allen Telescope Array on 2022 May 21. Both telescope observations had an overlap of 580 s. While blind searches using radio telescopes have been conducted in the general field of view in which the WOW! signal was first detected, this is the first time a targeted search has been done. No technosignature candidates were detected.

A Blind All-sky Search for Star Clusters in Gaia EDR3: 886 Clusters within 1.2 kpc of the Sun

Although previous searches for star clusters have been very successful, many clusters are likely still omitted, especially at high-Galactic-latitude regions. In this work, based on the astrometry of Gaia EDR3, we searched nearby (ϖ > 0.8 mas) all-sky regions, obtaining 886 star clusters, of which 270 candidates have not been cataloged before. At the same time, we have presented the physical parameters of the clusters by fitting theoretical isochrones to their optical magnitudes. More halo members and expanding structures in many star clusters were also found. Most of the new objects are young clusters that are less than 100 million years old. Our work greatly increased the sample size and physical parameters of star clusters in the solar neighborhood, in particular, 46 clusters are newly found with ∣b∣ > 20°, which represents a nearly threefold increase in the number of clusters at high-Galactic-latitude regions.

Construction of Higher Education Management and Student Achievement Evaluation Mechanism Based on Apriori Algorithm

The Apriori algorithm and DM technology are introduced, examined, and a relationship between bettering teachers’ classroom teaching quality, methods, and means is discussed. An evaluation system for student achievement in higher education is proposed and built on the basis of the Apriori algorithm. The Apriori algorithm is also improved in order to further avoid blind search during mining and increase the effectiveness of frequent itemsets. This paper avoids repeatedly scanning the database and instead reads the entire database into a two-dimensional array, which increases program performance. The algorithm is used to extract useful data from the database using data association mining in the higher education management system. According to the experimental findings, the improved Apriori algorithm’s accuracy can reach 94.81%, which is 10.31% higher than the accuracy of the original Apriori algorithm. The outcomes demonstrate the applicability and reliability of the algorithm model developed in this paper. For managers in teaching and management, it can be a useful reference.