A Cloudiness Index for Transiting Exoplanets Based on the Sodium and Potassium Lines: Tentative Evidence for Hotter Atmospheres Being Less Cloudy at Visible Wavelengths

We present a dimensionless index that quantifies the degree of cloudiness of the atmosphere of a transiting exoplanet. Our cloudiness index is based on measuring the transit radii associated with the line center and wing of the sodium or potassium line. In deriving this index, we revisited the algebraic formulae for inferring the isothermal pressure scale height from transit measurements. We demonstrate that the formulae of Lecavelier et al. and Benneke & Seager are identical: the former is inferring the temperature while assuming a value for the mean molecular mass and the latter is inferring the mean molecular mass while assuming a value for the temperature. More importantly, these formulae cannot be used to distinguish between cloudy and cloudfree atmospheres. We derive values of our cloudiness index for a small sample of 7 hot Saturns/Jupiters taken from Sing et al. We show that WASP-17b, WASP-31b and HAT-P-1b are nearly cloudfree at visible wavelengths. We find the tentative trend that more irradiated atmospheres tend to have less clouds consisting of sub-micron-sized particles. We also derive absolute sodium and/or potassium abundances $\sim 10^2$ cm$^{-3}$ for WASP-17b, WASP-31b and HAT-P-1b (and upper limits for the other objects). Higher-resolution measurements of both the sodium and potassium lines, for a larger sample of exoplanetary atmospheres, are needed to confirm or refute this trend.Comment: Accepted by ApJL. 6 pages, 1 figure, 2 table

Distinguishability and indistinguishability by LOCC

We show that a set of linearly independent quantum states $\{(U_{m,n}\otimes I)\rho ^{AB}(U_{m,n}^{\dagger}\otimes I)\}_{m,n=0}^{d-1}$, where $U_{m,n}$ are generalized Pauli matrices, cannot be discriminated deterministically or probabilistically by local operations and classical communications (LOCC). On the other hand, any $l$ maximally entangled states from this set are locally distinguishable if $l(l-1)\le 2d$. The explicit projecting measurements are obtained to locally discriminate these states. As an example, we show that four Werner states are locally indistinguishable.Comment: 5 page

Fast construction of FM-index for long sequence reads

Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: [email protected]: 2 page

Minimap2: pairwise alignment for nucleotide sequences

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Results: Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of $\ge$100bp in length, $\ge$1kb genomic reads at error rate $\sim$15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times faster than mainstream short-read mappers at comparable accuracy and $\ge$30 times faster at higher accuracy for both genomic and mRNA reads, surpassing most aligners specialized in one type of alignment. Availability and implementation: https://github.com/lh3/minimap2 Contact: [email protected]: The final submitted versio