Effective Non-Hermitian Hamiltonians for Studying Resonance Statistics in Open Disordered Systems

We briefly discuss construction of energy-dependent effective non-hermitian hamiltonians for studying resonances in open disordered systemsComment: Latex, 20 pages, 1 fig. Expanded version of a talk at the Workshop on Pseudo-Hermitian Hamiltonians in Quantum Physics IX, June 21-24 2010, Zhejiang University, Hangzhou, China. Accepted for publication in the Internationa Journal of Theoretical Physics (Springer Verlag

Is the Atmosphere of the Ultra-hot Jupiter WASP-121 b Variable?

We present a comprehensive analysis of the Hubble Space Telescope observations of the atmosphere of WASP121 b, an ultra-hot Jupiter. After reducing the transit, eclipse, and phase-curve observations with a uniform methodology and addressing the biases from instrument systematics, sophisticated atmospheric retrievals are used to extract robust constraints on the thermal structure, chemistry, and cloud properties of the atmosphere. Our analysis shows that the observations are consistent with a strong thermal inversion beginning at ∼104 Pa on the dayside, solar to subsolar metallicity Z (i.e., -0.77 log 0.05 < < ( ) Z ), and supersolar C/O ratio (i.e., 0.59 < C/O < 0.87). More importantly, utilizing the high signal-to-noise ratio and repeated observations of the planet, we identify the following unambiguous time-varying signals in the data: (i) a shift of the putative hotspot offset between the two phase curves and (ii) varying spectral signatures in the transits and eclipses. By simulating the global dynamics of WASP-121 b's atmosphere at high resolution, we show that the identified signals are consistent with quasiperiodic weather patterns, hence atmospheric variability, with signatures at the level probed by the observations (∼5% to ∼10%) that change on a timescale of ∼5 planet days; in the simulations, the weather patterns arise from the formation and movement of storms and fronts, causing hot (as well as cold) patches of atmosphere to deform, separate, and mix in time

"Hey Model!" -- Natural User Interactions and Agency in Accessible Interactive 3D Models

While developments in 3D printing have opened up opportunities for improved access to graphical information for people who are blind or have low vision (BLV), they can provide only limited detailed and contextual information. Interactive 3D printed models (I3Ms) that provide audio labels and/or a conversational agent interface potentially overcome this limitation. We conducted a Wizard-of-Oz exploratory study to uncover the multi-modal interaction techniques that BLV people would like to use when exploring I3Ms, and investigated their attitudes towards different levels of model agency. These findings informed the creation of an I3M prototype of the solar system. A second user study with this model revealed a hierarchy of interaction, with BLV users preferring tactile exploration, followed by touch gestures to trigger audio labels, and then natural language to fill in knowledge gaps and confirm understanding.Comment: Paper presented at ACM CHI 2020: Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems, ACM, New York, April 2020; Replacement: typos correcte

The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures

We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent Ni and Ni+1 protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the Ni+1 N-terminus and Ni-1 C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

Gene disruption by structural mutations drives selection in US rice breeding over the last century.

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection

Two mini-Neptunes Transiting the Adolescent K-star HIP 113103 Confirmed with TESS and CHEOPS

We report the discovery of two mini-Neptunes in near 2:1 resonance orbits ($P=7.610303$ d for HIP 113103 b and $P=14.245651$ d for HIP 113103 c) around the adolescent K-star HIP 113103 (TIC 121490076). The planet system was first identified from the TESS mission, and was confirmed via additional photometric and spectroscopic observations, including a $\sim$17.5 hour observation for the transits of both planets using ESA CHEOPS. We place $\leq4.5$ min and $\leq2.5$ min limits on the absence of transit timing variations over the three year photometric baseline, allowing further constraints on the orbital eccentricities of the system beyond that available from the photometric transit duration alone. With a planetary radius of $R_{p}=1.829^{+0.096}_{-0.067}\,R_{\oplus}$, HIP 113103 b resides within the radius gap, and this might provide invaluable information on the formation disparities between super-Earths and mini-Neptunes. Given the larger radius $R_{p}=2.40^{+0.10}_{-0.08}\,R_{\oplus}$ for HIP 113103 c, and close proximity of both planets to HIP 113103, it is likely that HIP 113103 b might have lost (or is still losing) its primordial atmosphere. We therefore present simulated atmospheric transmission spectra of both planets using JWST, HST, and Twinkle. It demonstrates a potential metallicity difference (due to differences in their evolution) would be a challenge to detect if the atmospheres are in chemical equilibrium. As one of the brightest multi sub-Neptune planet systems suitable for atmosphere follow up, HIP 113103 b and HIP 113103 c could provide insight on planetary evolution for the sub-Neptune K-star population.Comment: 18 pages, 12 figures, accepted for publication in the Monthly Notices of the Royal Astronomical Societ