Distances and classification of amino acids for different protein secondary structures

Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of amino acids and secondary structure conformations. Distance matrices of amino acid pairs at different conformations are obtained, which display a non-negligible dependence of amino acid similarity on conformations. Based on the conformation specific distances clustering analysis for amino acids is conducted.Comment: 15 pages, 8 figure

Global properties of Stochastic Loewner evolution driven by Levy processes

Standard Schramm-Loewner evolution (SLE) is driven by a continuous Brownian motion which then produces a trace, a continuous fractal curve connecting the singular points of the motion. If jumps are added to the driving function, the trace branches. In a recent publication [1] we introduced a generalized SLE driven by a superposition of a Brownian motion and a fractal set of jumps (technically a stable L\'evy process). We then discussed the small-scale properties of the resulting L\'evy-SLE growth process. Here we discuss the same model, but focus on the global scaling behavior which ensues as time goes to infinity. This limiting behavior is independent of the Brownian forcing and depends upon only a single parameter, $\alpha$, which defines the shape of the stable L\'evy distribution. We learn about this behavior by studying a Fokker-Planck equation which gives the probability distribution for endpoints of the trace as a function of time. As in the short-time case previously studied, we observe that the properties of this growth process change qualitatively and singularly at $\alpha =1$. We show both analytically and numerically that the growth continues indefinitely in the vertical direction for $\alpha > 1$, goes as $\log t$ for $\alpha = 1$, and saturates for $\alpha< 1$. The probability density has two different scales corresponding to directions along and perpendicular to the boundary. In the former case, the characteristic scale is $X(t) \sim t^{1/\alpha}$. In the latter case the scale is $Y(t) \sim A + B t^{1-1/\alpha}$ for $\alpha \neq 1$, and $Y(t) \sim \ln t$ for $\alpha = 1$. Scaling functions for the probability density are given for various limiting cases.Comment: Published versio

Jordan-Wigner fermionization for the one-dimensional Bariev model of three coupled XY chains

The Jordan-Wigner fermionization for the one-dimensional Bariev model of three coupled XY chains is formulated. The Lax operator in terms of fermion operators and the quantum R-matrix are presented explicitly. Furthermore, the graded reflection equations and their solutions are discussed.Comment: 10 pages, no figur

Evidence for the super Tonks-Girardeau gas

We provide evidence in support of a recent proposal by Astrakharchik at al. for the existence of a super Tonks-Girardeau gas-like state in the attractive interaction regime of quasi-one-dimensional Bose gases. We show that the super Tonks-Giradeau gas-like state corresponds to a highly-excited Bethe state in the integrable interacting Bose gas for which the bosons acquire hard-core behaviour. The gas-like state properties vary smoothly throughout a wide range from strong repulsion to strong attraction. There is an additional stable gas-like phase in this regime in which the bosons form two-body bound states behaving like hard-core bosons.Comment: 10 pages, 1 figure, 2 tables, additional text on the stability of the super T-G gas-like stat

Liquid Chromatography Electron Capture Dissociation Tandem Mass Spectrometry (LC-ECD-MS/MS) versus Liquid Chromatography Collision-induced Dissociation Tandem Mass Spectrometry (LC-CID-MS/MS) for the Identification of Proteins

Electron capture dissociation (ECD) offers many advantages over the more traditional fragmentation techniques for the analysis of peptides and proteins, although the question remains: How suitable is ECD for incorporation within proteomic strategies for the identification of proteins? Here, we compare LC-ECD-MS/MS and LC-CID-MS/MS as techniques for the identification of proteins.Experiments were performed on a hybrid linear ion trap–Fourier transform ion cyclotron resonance mass spectrometer. Replicate analyses of a six-protein (bovine serum albumin, apo-transferrin,lysozyme, cytochrome c, alcohol dehydrogenase, and β-galactosidase) tryptic digest were performed and the results analyzed on the basis of overall protein sequence coverage and sequence tag lengths within individual peptides. The results show that although protein coverage was lower for LC-ECDMS/MS than for LC-CID-MS/MS, LC-ECD-MS/MS resulted in longer peptide sequence tags,providing greater confidence in protein assignment

The ionized and hot gas in M17 SW: SOFIA/GREAT THz observations of [C II] and 12CO J=13-12

With new THz maps that cover an area of ~3.3x2.1 pc^2 we probe the spatial distribution and association of the ionized, neutral and molecular gas components in the M17 SW nebula. We used the dual band receiver GREAT on board the SOFIA airborne telescope to obtain a 5'.7x3'.7 map of the 12CO J=13-12 transition and the [C II] 158 um fine-structure line in M17 SW and compare the spectroscopically resolved maps with corresponding ground-based data for low- and mid-J CO and [C I] emission. For the first time SOFIA/GREAT allow us to compare velocity-resolved [C II] emission maps with molecular tracers. We see a large part of the [C II] emission, both spatially and in velocity, that is completely non-associated with the other tracers of photon-dominated regions (PDR). Only particular narrow channel maps of the velocity-resolved [C II] spectra show a correlation between the different gas components, which is not seen at all in the integrated intensity maps. These show different morphology in all lines but give hardly any information on the origin of the emission. The [C II] 158 um emission extends for more than 2 pc into the M17 SW molecular cloud and its line profile covers a broader velocity range than the 12CO J=13-12 and [C I] emissions, which we interpret as several clumps and layers of ionized carbon gas within the telescope beam. The high-J CO emission emerges from a dense region between the ionized and neutral carbon emissions, indicating the presence of high-density clumps that allow the fast formation of hot CO in the irradiated complex structure of M17 SW. The [C II] observations in the southern PDR cannot be explained with stratified nor clumpy PDR models.Comment: 4 pages, 4 figures, letter accepted for the SOFIA/GREAT A&A 2012 special issu

Do Not Mask What You Do Not Need to Mask: a Parser-Free Virtual Try-On

The 2D virtual try-on task has recently attracted a great interest from the research community, for its direct potential applications in online shopping as well as for its inherent and non-addressed scientific challenges. This task requires fitting an in-shop cloth image on the image of a person, which is highly challenging because it involves cloth warping, image compositing, and synthesizing. Casting virtual try-on into a supervised task faces a difficulty: available datasets are composed of pairs of pictures (cloth, person wearing the cloth). Thus, we have no access to ground-truth when the cloth on the person changes. State-of-the-art models solve this by masking the cloth information on the person with both a human parser and a pose estimator. Then, image synthesis modules are trained to reconstruct the person image from the masked person image and the cloth image. This procedure has several caveats: firstly, human parsers are prone to errors; secondly, it is a costly pre-processing step, which also has to be applied at inference time; finally, it makes the task harder than it is since the mask covers information that should be kept such as hands or accessories. In this paper, we propose a novel student-teacher paradigm where the teacher is trained in the standard way (reconstruction) before guiding the student to focus on the initial task (changing the cloth). The student additionally learns from an adversarial loss, which pushes it to follow the distribution of the real images. Consequently, the student exploits information that is masked to the teacher. A student trained without the adversarial loss would not use this information. Also, getting rid of both human parser and pose estimator at inference time allows obtaining a real-time virtual try-on.Comment: Accepted at ECCV 2020. arXiv admin note: text overlap with arXiv:1906.0134

A Schwarz lemma for K\"ahler affine metrics and the canonical potential of a proper convex cone

This is an account of some aspects of the geometry of K\"ahler affine metrics based on considering them as smooth metric measure spaces and applying the comparison geometry of Bakry-Emery Ricci tensors. Such techniques yield a version for K\"ahler affine metrics of Yau's Schwarz lemma for volume forms. By a theorem of Cheng and Yau there is a canonical K\"ahler affine Einstein metric on a proper convex domain, and the Schwarz lemma gives a direct proof of its uniqueness up to homothety. The potential for this metric is a function canonically associated to the cone, characterized by the property that its level sets are hyperbolic affine spheres foliating the cone. It is shown that for an $n$-dimensional cone a rescaling of the canonical potential is an $n$-normal barrier function in the sense of interior point methods for conic programming. It is explained also how to construct from the canonical potential Monge-Amp\`ere metrics of both Riemannian and Lorentzian signatures, and a mean curvature zero conical Lagrangian submanifold of the flat para-K\"ahler space.Comment: Minor corrections. References adde