How can the Fourier Transform be Used in Radio Astronomy to Perform Spectral Analysis of Pulsars

The analysis of pulsars is a complicated procedure due to the influence of background radio waves. Special radio telescopes designed to detect pulsar signals have to employ many techniques to reconstruct interstellar signals and determine if they originated from a pulsating radio source. The Discrete Fourier Transform on its own has allowed astronomers to perform basic spectral analysis of potential pulsar signals. However, Radio Frequency Interference (RFI) makes the process of detecting and analyzing pulsars extremely difficult. This has forced astronomers to be creative in identifying and determining the specific characteristics of these unique rotating neutron stars. Astrophysicists have utilized algorithms such as the Fast Fourier Transform (FFT) to predict the spin period and harmonic frequencies of pulsars. However, FFT-based searches cannot be utilized alone because low-frequency pulsar signals go undetected in the presence of background radio noise. Astrophysicists must stack up pulses using the Fast Folding Algorithm (FFA) and utilize the coherent dedispersion technique to improve FFT sensitivity. The following research paper will discuss how the Discrete Fourier Transform is a useful technique for detecting radio signals and determining the pulsar frequency. It will also discuss how dedispersion and the pulsar frequency are critical for predicting multiple characteristics of pulsars and correcting the influence of the Interstellar Medium (ISM).

Distance-guided protein folding based on generalized descent direction

Advances in the prediction of the inter-residue distance for a protein sequence have increased the accuracy to predict the correct folds of proteins with distance information. Here, we propose a distance-guided protein folding algorithm based on generalized descent direction, named GDDfold, which achieves effective structural perturbation and potential minimization in two stages. In the global stage, random-based direction is designed using evolutionary knowledge, which guides conformation population to cross potential barriers and explore conformational space rapidly in a large range. In the local stage, locally rugged potential landscape can be explored with the aid of conjugate-based direction integrated into a specific search strategy, which can improve exploitation ability. GDDfold is tested on 347 proteins of a benchmark set, 24 FM targets of CASP13 and 20 FM targets of CASP14. Results show that GDDfold correctly folds (TM-score ≥ 0.5) 316 out of 347 proteins, where 65 proteins have TM-scores that are greater than 0.8, and significantly outperforms Rosetta-dist (distance-assisted fragment assembly method) and L-BFGSfold (distance geometry optimization method). On CASP FM targets, GDDfold is comparable with five state-of-the-art full-version methods, namely, Quark, RaptorX, Rosetta, MULTICOM and trRosetta in the CASP 13 and 14 server groups.

Computational analysis of vertebrate myoglobins reveals aggregation resistance in aquatic birds and higher surface hydrophobicity in fish

Myoglobin is the major oxygen carrying protein in vertebrate muscle. Previous studies identified in secondarily aquatic mammalian lineages high myoglobin net charge, which serves to prevent aggregation at the extremely high intracellular myoglobin concentrations found in these species. However, it is unknown how aquatic birds that dive for extended durations prevent myoglobin aggregation at their high intracellular myoglobin concentrations. It is also unknown whether secondarily aquatic lineages reduced the surface hydrophobicity of their myoglobins to prevent aggregation. Here, we used a deep learning-predicted distance-based protein folding algorithm to model the tertiary structures of 302 vertebrate myoglobin orthologs and performed a comparative analysis of their predicted net charge and surface hydrophobicities. The results suggest that aquatic avian divers, such as penguins and diving ducks, evolved highly charged myoglobins to reduce aggregation propensity and allow greater storage of oxygen for extended underwater foraging. High myoglobin net charge was also identified in golden eagles, a species that routinely suffers high-altitude hypoxia. Although no general association was found between myoglobin surface hydrophobicity and intracellular concentration, comparison of predicted net charge and surface hydrophobicities revealed significant differences between major vertebrate classes; bird myoglobins are the most positively charge, reptile myoglobins are the most negatively charged, and the myoglobins of ray-finned fish (Actinopterygii) have higher surface hydrophobicity than those of lobe-finned fish (Sarcopterygii). Our findings indicate the convergent evolution of high myoglobin net charge in aquatic birds and mammals, and offer novel insights into the diversification of myoglobin among vertebrate clades.

RNA structure prediction using positive and negative evolutionary information

Knowing the structure of conserved structural RNAs is important to elucidate their function and mechanism of action. However, predicting a conserved RNA structure remains unreliable, even when using a combination of thermodynamic stability and evolutionary covariation information. Here we present a method to predict a conserved RNA structure that combines the following three features. First, it uses significant covariation due to RNA structure and removes spurious covariation due to phylogeny. Second, it uses negative evolutionary information: basepairs that have variation but no significant covariation are prevented from occurring. Lastly, it uses a battery of probabilistic folding algorithms that incorporate all positive covariation into one structure. The method, named CaCoFold (Cascade variation/covariation Constrained Folding algorithm), predicts a nested structure guided by a maximal subset of positive basepairs, and recursively incorporates all remaining positive basepairs into alternative helices. The alternative helices can be compatible with the nested structure such as pseudoknots, or overlapping such as competing structures, base triplets, or other 3D non-antiparallel interactions. We present evidence that CaCoFold predictions are consistent with structures modeled from crystallography.

Optimal periodicity searching: revisiting the fast folding algorithm for large-scale pulsar surveys

ABSTRACT The fast folding algorithm (FFA) is a phase-coherent search technique for periodic signals. It has rarely been used in radio pulsar searches, having been historically supplanted by the less computationally expensive fast fourier transform (FFT) with incoherent harmonic summing (IHS). Here, we derive from first principles that an FFA search closely approaches the theoretical optimum sensitivity to all periodic signals; it is analytically shown to be significantly more sensitive than the standard FFT+IHS method, regardless of pulse period and duty cycle. A portion of the pulsar phase space has thus been systematically underexplored for decades; pulsar surveys aiming to fully sample the pulsar population should include an FFA search as part of their data analysis. We have developed an FFA software package, riptide, fast enough to process radio observations on a large scale; riptide has already discovered sources undetectable using existing FFT+IHS implementations. Our sensitivity comparison between search techniques also shows that a more realistic radiometer equation is needed, which includes an additional term: the search efficiency. We derive the theoretical efficiencies of both the FFA and the FFT+IHS methods and discuss how excluding this term has consequences for pulsar population synthesis studies.

The SUrvey for pulsars and extragalactic radio bursts V: recent discoveries and full timing solutions

ABSTRACT The SUrvey for Pulsars and Extragalactic Radio Bursts ran from 2014 April to 2019 August, covering a large fraction of the Southern hemisphere at mid- to high-galactic latitudes and consisting of 9-min pointings taken with the 20-cm multibeam receiver on the Parkes Radio Telescope. Data up to 2017 September 21 have been searched using standard Fourier techniques, single-pulse searches, and Fast Folding Algorithm searches. We present 19 new discoveries, bringing the total to 27 discoveries in the programme, and we report the results of follow-up timing observations at Parkes for 26 of these pulsars, including the millisecond pulsar PSR J1421−4409; the faint, highly modulated, slow pulsar PSR J1646−1910; and the nulling pulsar PSR J1337−4441. We present new timing solutions for 23 pulsars, and we report flux densities, modulation indices, and polarization properties.

Noise reduction for digital communications – A modified Costas loop

An efficient way of noise reduction has been presented: A modified Costas loop called as Masterpiece. The basic version of the Costas loop has been developed for SSB SC demodulation, but the same circuit can be applied for QAM demodulation as well. Noise sensitivity of the basic version has been decreased. One trick is the transformation of the real channel input into complex signal, the other one is the application of our folding algorithm. The result is that the Masterpiece provides a 4QAM symbol error rate (SER) of 6*10-4 for input signal to noise ratio (SNR) of -1 dB. In this paper, an improved version of the original Masterpiece is introduced. The complex channel input signal is normalized, and rotational average is applied. The 4QAM result is SER of 3*10-4 for SNR of -1 dB. At SNR of 0 dB, the improved version produces 100 times better SER than that the original Costas loop does.