VEGA: visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019)

In the field of evolutionary genome analysis, biologists seek to identify important genes or chromosome regions by comparing phylogenetic trees and analyzing the mutation at which locus might affect phenotypic traits. Unfortunately, the tree comparison and accompanying analysis are often performed manually. In this paper, we characterize the workflow of evolutionary genome analysis and present a task analysis for the fundamental questions asked by biologists during the analysis procedure. We propose two algorithms to enable quantitative tree comparison. One is to measure the differences between corresponding leaf nodes on two trees, and the other is to compute the classification inconsistency of each leaf node by comparing tree structure with a given biological classification. Configuring with the obtained difference and inconsistency, we present a visual analysis system, visual comparison of phylogenetic trees for evolutionary genome analysis, which not only enables biologists to intuitively explore trees but also identify locus which affects their traits by comparing SNP variants of selected leaf nodes. We conclude with case studies from two biologists who used our system to augment their previous manual analysis workflow and demonstrate that our system can reveal more insight.     

Plasma Photocathodes

Plasma wakefield accelerators offer accelerating and focusing electric fields three to four orders of magnitude larger than state-of-the-art radiofrequency cavity-based accelerators. Plasma photocathodes can release ultracold electron populations within such plasma waves and thus open a path toward tunable production of well-defined, compact electron beams with normalized emittance and brightness many orders of magnitude better than state-of-the-art. Such beams will have far-reaching impact for applications such as light sources, but also open up new vistas on high energy and high field physics. This paper reviews the innovation of plasma photocathodes, and reports on the experimental progress, challenges, and future prospects of the approach. Details of the proof-of-concept demonstration of a plasma photocathode in 90° geometry at SLAC FACET within the E-210: Trojan Horse program are described. Using this experience, alongside theoretical and simulation-supported advances, an outlook is given on future realizations of plasma photocathodes such as the upcoming E-310: Trojan Horse-II program at FACET-II with prospects toward excellent witness beam parameter quality, tunability, and stability. Future installations of plasma photocathodes also at compact, hybrid plasma wakefield accelerators, will then boost capacities and open up novel capabilities for experiments at the forefront of interaction of high brightness electron and photon beams.     

Constraints on an asymptotic safety scenario for the Wess–Zumino model

Using the nonrenormalization theorem and Pohlmeyer's theorem, it is proven that there cannot be an asymptotic safety scenario for the Wess–Zumino model unless there exists a non-trivial fixed point with (i) a negative anomalous dimension (ii) a relevant direction belonging to the Kähler potential.     

The Mode Solution of the Wave Equation in Kasner Spacetimes and Redshift

We study the mode solution to the Cauchy problem of the scalar wave equation □φ = 0 in Kasner spacetimes. As a first result, we give the explicit mode solution in axisymmetric Kasner spacetimes, of which flat Kasner spacetimes are special cases. Furthermore, we give the small and large time asymptotics of the modes in general Kasner spacetimes. Generically, the modes in non-flat Kasner spacetimes grow logarithmically for small times, while the modes in flat Kasner spacetimes stay bounded for small times. For large times, however, the modes in general Kasner spacetimes oscillate with a polynomially decreasing amplitude. This gives a notion of large time frequency of the modes, which we use to model the wavelength of light rays in Kasner spacetimes. We show that the redshift one obtains in this way actually coincides with the usual cosmological redshift.     

Curve encirclement and protein structure

A method of measuring the extent to which space curves encircle one another is introduced. The method provides a family of sets which characterize encircling curves, allowing curve pairs that engage (and also single curves that self-engage) to be distinguished. The method is applied to the backbone chains of protein molecules.     

Near-Enantiopure Trimerization of 9-Ethynylphenanthrene on a Chiral Metal Surface

Enantioselectivity in heterogeneous catalysis strongly depends on the chirality transfer between catalyst surface and all reactants, intermediates, and the product along the reaction pathway. Herein we report the first enantioselective on-surface synthesis of molecular structures from an initial racemic mixture and without the need of enantiopure modifier molecules. The reaction consists of a trimerization via an unidentified bonding motif of prochiral 9-ethynylphenanthrene (9-EP) upon annealing to 500 K on the chiral Pd₃-terminated PdGa{111} surfaces into essentially enantiopure, homochiral 9-EP propellers. The observed behavior strongly contrasts the reaction of 9-EP on the chiral Pd₁-terminated PdGa{111} surfaces, where 9-EP monomers that are in nearly enantiopure configuration, dimerize without enantiomeric excess. Our findings demonstrate strong chiral recognition and a significant ensemble effect in the PdGa system, hence highlighting the huge potential of chiral intermetallic compounds for enantioselective synthesis and underlining the importance to control the catalytically active sites at the atomic level.     

Tin-rich Phases RE2Au3Sn6 with RE = La,Ce, Pr,Nd, Sm – Synthesis,Structure, Magnetic Properties,and 119Sn Mössbauer Spectra

The stannides RE₂Au₃Sn₆ (RE = La, Ce, Pr, Nd, Sm) were synthesized from the elements by arc-melting. Small single crystals were grown by annealing samples in sealed tantalum tubes in an induction furnace with a special annealing sequence. The polycrystalline phases were characterized through their X-ray powder diffraction pattern. The structures of Ce₂Au₃Sn₆, Pr₂Au₃Sn₆, and Nd₂Au₃Sn₆ were refined from single-crystal X-ray diffractometer data. The RE₂Au₃Sn₆ stannides crystallize with the orthorhombic La₂Zn₃Ge₆ type, space group Cmcm. The basic structural building units are Au1@Sn₄ tetrahedra and Au2@Sn₅ square pyramids. These units are condensed to layers and the structure can be described by a simple stacking of tetrahedral and pyramidal layers with the rare earth cations in between. Temperature dependent susceptibility studies indicate that all rare earth atoms are in the trivalent oxidation state, as their effective magnetic moments match the expected values of the free RE³⁺ ions. Pr₂Au₃Sn₆ and Nd₂Au₃Sn₆ exhibit antiferromagnetic ordering at T_N = 6.3(1) and 6.7(1) K. Investigations of the electrical resistivity of La₂Au₃Sn₆ and Ce₂Au₃Sn₆ confirmed that these compounds are metallic, for La₂Au₃Sn₆ a lower resistivity was observed, in line with the absence of screening unpaired electrons. ¹¹⁹Sn Mössbauer spectra for La₂Au₃Sn₆, Ce₂Au₃Sn₆, Pr₂Au₃Sn₆ and Nd₂Au₃Sn₆ show a complex superposition of three sub-spectra which can be differentiated through their distinctly different quadrupole splitting parameters. The isomer shifts (1.87 to 2.22 mm · s^–1) indicate significant s electron density at the tin nuclei.     

Organophotocatalytic N-Demethylation of Oxycodone Using Molecular Oxygen

N-Demethylation of oxycodone is one of the key steps in the synthesis of important opioid antagonists like naloxone or analgesics like nalbuphine. The reaction is typically carried out using stoichiometric amounts of toxic and corrosive reagents. Herein, we present a green and scalable organophotocatalytic procedure that accomplishes the N-demethylation step using molecular oxygen as the terminal oxidant and an organic dye (rose bengal) as an effective photocatalyst. Optimization of the reaction conditions under continuous flow conditions using visible-light irradiation led to an efficient, reliable, and scalable process, producing noroxycodone hydrochloride in high isolated yield and purity after a simple workup.     

Probing molecular free energy landscapes by periodic loading

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular, for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's relation for obtaining equilibrium quantities from nonequilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.