Abstract: A novel real-time Fourier and inverse Fourier transforming (RTFaIFT) system realizing both positive and inverse transformations is designed and verified, using non-uniform coupled-line phaser. Two kinds of Fourier transformations are integrated within one system for the first time. This system can map the spectrum of the input signal into a waveform in time domain whose amplitude mimics the spectrum magnitude, owing to the frequency-varying group delay (GD) response of the phaser. Furthermore, the correspondence between the output waveform and the spectrum of the input signal is given for accurate analysis of the spectrum. This configuration possesses the characteristic of compact structure, simple design procedure, and perfect performance, consisting of a mixer, a phaser with linear group delay, a diode, and a LPF. For experimental demonstration, a RTFaIFT system operating at 6 GHz is designed and fabricated, the bandwidth of which is 4 GHz with −0.5 ns/GHz GD slope. Both single- and double-pulse signals have been chosen as the test signals to verify the performance of the RTFaIFT system, respectively. The experimental results agree well with simulation and theoretical results.

Abstract: An active phaser based on co-directional couplers is proposed for achieving a flat magnitude transmission while preserving its strong dispersive delay response. The phasers are realized using Half-Mode Substrate Integrated Waveguide (HMSIW) structures, and are successfully demonstrated using full-wave simulations. Due to the non-TEM nature of the device, the proposed phasers are ideally suitable for mm-wave real-time analog signal processing systems.

Abstract: An active microwave C-section phaser is proposed which provides a flat magnitude transmission in a wide frequency band along with a frequency-dependent group delay response considering practical dissipation losses. The key lies in integrating a constant gain amplifier inside a microwave C-section, which perfectly compensates the distributed conductor and dielectric losses of the coupler, while preserving the intrinsic dispersion of the C-section. The operation of the proposed device is confirmed using numerical analysis and full-wave simulations.

Abstract: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.

Abstract: The production of large quantities of diploid genotype data has created a need for computational methods for large-scale inference of haplotypes from genotypes. One promising approach to the problem has been to infer possible phylogenies explaining the observed genotypes in terms of putative descendants of some common ancestral haplotype. The first attempts at this problem proceeded on the restrictive assumption that observed sequences could be explained by a perfect phylogeny, in which each variant locus is presumed to have mutated exactly once over the sampled population’s history. Recently, the perfect phylogeny model was relaxed and the problem of reconstructing an imperfect phylogeny (IPPH) from genotype data was considered. A polynomial time algorithm was developed for the case when a single site is allowed to mutate twice, but the general problem remained open. In this work, we solve the general IPPH problem and show for the first time that it is possible to infer optimal q-near-perfect phylogenies from diploid genotype data in polynomial time for any constant q, where q is the number of “extra” mutations required in the phylogeny beyond what would be present in a perfect phylogeny. This work has application to the haplotype phasing problem as well as to various related problems in phylogenetic inference, analysis of sequence variability in populations, and association study design. Empirical studies on human data of known phase show this method to be competitive with the leading phasing methods and provide strong support for the value of continued research into algorithms for general phylogeny construction from diploid data.

Abstract: The high-intensity version of multiwavelength anomalous diffraction (MAD) has a potential for solving the phase problem in femtosecond crystallography with x-ray free-electron lasers (XFELs). For MAD phasing, it is required to calculate or measure the MAD coefficients involved in the key equation, which depend on XFEL pulse parameters. In this work, we revisit the generalized Karle–Hendrickson equation to clarify the importance of configurational fluctuations of heavy atoms induced by intense x-ray pulses, and investigate the high-intensity cases of transmission and fluorescence measurements of samples containing heavy atoms. Based on transmission/fluorescence and diffraction experiments with crystalline samples of known structures, we propose an experimental procedure to determine all MAD coefficients at high x-ray intensity, which can be used in ab initio phasing for unknown structures.

Abstract: Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r.m.s.d. of below 2 A to the target position, which is 10% higher than was obtained by Phaser. However, cases studies show that many of the models for which Phaser failed and MR-REX succeeded can be solved by Phaser by pruning them and using nondefault parameters. The factors effecting success and the parts of the methodology which lead to success are studied. The results demonstrate a new avenue for molecular replacement which outperforms (and has results that are complementary to) the state-of-the-art MR methods, in particular for distantly homologous proteins.

Abstract: The production of large quantities of diploid genotype data has created a need for computational methods for large-scale inference of haplotypes from genotypes. One promising approach to the problem has been to infer possible phylogenies explaining the observed genotypes in terms of putative descendants of some common ancestral haplotype. The first attempts at this problem proceeded on the restrictive assumption that observed sequences could be explained by a perfect phylogeny, in which each variant locus is presumed to have mutated exactly once over the sampled population’s history. Recently, the perfect phylogeny model was relaxed and the problem of reconstructing an imperfect phylogeny (IPPH) from genotype data was considered. A polynomial time algorithm was developed for the case when a single site is allowed to mutate twice, but the general problem remained open. In this work, we solve the general IPPH problem and show for the first time that it is possible to infer optimal q-near-perfect phylogenies from diploid genotype data in polynomial time for any constant q, where q is the number of “extra” mutations required in the phylogeny beyond what would be present in a perfect phylogeny. This work has application to the haplotype phasing problem as well as to various related problems in phylogenetic inference, analysis of sequence variability in populations, and association study design. Empirical studies on human data of known phase show this method to be competitive with the leading phasing methods and provide strong support for the value of continued research into algorithms for general phylogeny construction from diploid data.

Abstract: Specific radiation damage can be used to determine phases de novo from macromolecular crystals. This method is known as radiation-damage-induced phasing (RIP). One limitation of the method is that the dose of individual data sets must be minimized, which in turn leads to data sets with low multiplicity. A solution to this problem is to use data from multiple crystals. However, the resulting signal can be degraded by a lack of isomorphism between crystals. Here, it is shown that serial synchrotron crystallography in combination with selective merging of data sets can be used to determine high-quality phases for insulin and thaumatin, and that the increased multiplicity can greatly enhance the success rate of the experiment.

Abstract: This article presents a novel, compact reflectar-ray antenna operating at 5 GHz. The array consists of two types of phasing element - square ring and complementary square ring. The complementary square ring is used for the phase values that are not covered by the single ring element. The grid size of the array is 0.28 lambda x 0.28 lambda at operating frequency 5 GHz that is much smaller than the conventional periodicity 0.5 lambda x 0.5 lambda. The aim of unit cell de sign is to have a slower slope of the reflection phase graph without sacrificing the phase range of 360 degrees where in general there is a trade-off between these two goals. The maximum slope in reflection phase graph obtained here is 34 degrees/mm. The proposed array is fabricated on a low loss PTFE substrate of thickness 3.175 mm (0.053 lambda at 5 GHz) and illuminated by a horn antenna. Radiation pattern results show a very precise far-field beam with 3-dB beam-width of 7 degrees and 7.3 degrees for two principal planes respectively. The gain of the antenna is 26 dBi at 5 GHz.