Relaxation of Chemical Reactions to Stationary States in the Chemical Affinities Space

Using the mass balance equations for chemical reactions, we show how the system relaxes towards a steady state in and out of the Onsager region. In the chemical affinities space, after fast transients, the relaxation process is a straight line when operating in the Onsager region, while out of this regime, the evolution of the system is such that the projections of the evolution equations for the forces and the shortest path on the flows coincide. For spatially-extended systems, similar results are valid for the evolution of the thermodynamic mode (i.e., the mode with wave-number k = 0). These results allow us to obtain the expression for the affine connection of the space covered by the thermodynamic forces, close to the steady states. Through the affine connection, the nonlinear closure equations are derived.Comment: 23 pages

Assessment of Lactobacillus crispatus´ role in vaginal infections: friend or foe?

Lactobacillus spp. are the most prevalent microorganisms in the vaginal milleu. Several probiotic mechanisms have been associated with Lactobacillus, but the most relevant one is lactate production – resulting in a low pH value, typical of the healthy vagina. However, its pathogenic state is still unknown. We aim to elucidate the role of a commensal vaginal microorganism, Lactobacillus crispatus, in vaginal infections. Twenty-four vaginal washes have been collected from women attending a gynaecology consultation of a private clinic. The samples were categorized according with clinical diagnosis at the time of sampling. The distribution of bacterial species, and their prevalence was assessed by Next-Generation Sequencing of the 16S rRNA V4 region. In addition, L- and D-lactate concentration, and LDH enzymatic activity was quantified in all washes by a commercial kit. Detection of Candida spp. was performed by PCR. L. crispatus was dominant (>70%) in 11 out of 24 samples – diagnosed for vaginal atrophy (VA, 3), cytolytic vaginosis (CV, 2) and lactobacillosis (LB, 2). Lactate was increased in CV, LB and VA cases only. The remaining samples, diagnosed for vulvovaginal candidosis in its majority, had lower prevalence of L. crispatus; and lower to moderate lactate metabolite. There was not a direct relationship between LDH enzymatic activity and clinical diagnosis. L. crispatus dominance, associated with increased lactate production, was observed in CV, LB and VA cases. These results indicate that this microorganism might have a role in dysbiosis of the vagina associated with these specific pathologies.info:eu-repo/semantics/publishedVersio

Role of Lactobacillus crispatus in vaginal infections: insights from metagenomics and metabolomics studies

Objective: Lactobacillus spp. constitute the most prevalent bacterial microorganism in the vaginal milleu. Several probiotic mechanisms have been associated with Lactobacillus, but the most relevant one is lactate production – resulting in a low pH value, typical of the healthy vagina. We aim to elucidate the role of a native vaginal microorganism, Lactobacillus crispatus, in vaginal infections. Methods: Twenty-four vaginal washes have been collected from women (mean 38±14 years of age) attending a gynecology consultation of a private clinic. The samples were categorized according with clinical diagnosis at the time of sampling. The distribution of bacterial species, and their prevalence was assessed by next-generation sequencing of the 16S V4 region. In addition, lactate was quantified in all washes by a commercial kit. Results: L. crispatus was dominant (>70%) in 11 out of 24 samples – diagnosed for vaginal atrophy (VA, 3), cytolytic vaginosis (CV, 2), lactobacillosis (LB, 2) and vulvovaginal candidosis (VVC, 1). For three samples, diagnostic was inconclusive. Lactate was increased in CV, LB and VA cases only. One sample, diagnosed with VVC had 23% dominance of L. crispatus; and lower lactate metabolite. L. crispatus was not detected in the remaining 12 cases (6 VVC, 4 VA, 1 healthy and 1 inconclusive). Of these, only 5 samples had moderate lactate metabolite. Conclusions: L. crispatus dominance, associated with increased lactate production, was observed in CV, LB and VA cases. These results indicate that this microorganism might have a role in dysbiosis of the vagina associated with these specific pathologies.info:eu-repo/semantics/publishedVersio

The detection of ultra-relativistic electrons in low Earth orbit

Aims. To better understand the radiation environment in low Earth orbit (LEO), the analysis of in-situ observations of a variety of particles, at different atmospheric heights, and in a wide range of energies, is needed. Methods. We present an analysis of energetic particles, indirectly detected by the Large Yield RAdiometer (LYRA) instrument on board ESA's Project for On-board Autonomy 2 (PROBA2) satellite as background signal. Combining Energetic Particle Telescope (EPT) observations with LYRA data for an overlapping period of time, we identified these particles as electrons with an energy range of 2 to 8 MeV. Results. The observed events are strongly correlated to geo-magnetic activity and appear even during modest disturbances. They are also well confined geographically within the L=4-6 McIlwain zone, which makes it possible to identify their source. Conclusions. Although highly energetic particles are commonly perturbing data acquisition of space instruments, we show in this work that ultra-relativistic electrons with energies in the range of 2-8 MeV are detected only at high latitudes, while not present in the South Atlantic Anomaly region.Comment: Topical Issue: Flares, CMEs and SEPs and their space weather impacts; 20 pages; 7 figures; Presented during 13th European Space Weather Week, 201

Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws

In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated to nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation $a + b = s^Y$ between the number of fundamental affinities $a$, that of broken conservation laws $b$ and the number of chemostats $s^Y$. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction and of thermodynamic constraints for network reconstruction.Comment: 18 page

A Simple Family of Analytical Trumpet Slices of the Schwarzschild Spacetime

We describe a simple family of analytical coordinate systems for the Schwarzschild spacetime. The coordinates penetrate the horizon smoothly and are spatially isotropic. Spatial slices of constant coordinate time $t$ feature a trumpet geometry with an asymptotically cylindrical end inside the horizon at a prescribed areal radius $R_0$ (with $0<R_{0}\leq M$) that serves as the free parameter for the family. The slices also have an asymptotically flat end at spatial infinity. In the limit $R_{0}=0$ the spatial slices lose their trumpet geometry and become flat -- in this limit, our coordinates reduce to Painlev\'e-Gullstrand coordinates.Comment: 7 pages, 3 figure

Search for an Near-IR Counterpart to the Cas A X-ray Point Source

We report deep near-infrared and optical observations of the X-ray point source in the Cassiopeia A supernova remnant, CXO J232327.9+584842. We have identified a J=21.4 +/- 0.3 mag and Ks=20.5 +/- 0.3 mag source within the 1-sigma error circle, but we believe this source is a foreground Pop II star with Teff=2600-2800 K at a distance of ~2 kpc, which could not be the X-ray point source. We do not detect any sources in this direction at the distance of Cas A, and therefore place 3-sigma limits of R >~ 25 mag, F675W >~ 27.3 mag, J >~ 22.5 mag and Ks >~ 21.2 mag (and roughly H >~ 20 mag) on emission from the X-ray point source, corresponding to M_{R} >~ 8.2 mag, M_{F675W} >~ 10.7 mag, M_{J} >~ 8.5 mag, M_{H} >~ 6.5 mag, and M_{Ks} >~ 8.0 mag, assuming a distance of 3.4 kpc and an extinction A_{V}=5 mag.Comment: 14 pages, 7 figures. Accepted by Ap

Random paths and current fluctuations in nonequilibrium statistical mechanics

An overview is given of recent advances in nonequilibrium statistical mechanics about the statistics of random paths and current fluctuations. Although statistics is carried out in space for equilibrium statistical mechanics, statistics is considered in time or spacetime for nonequilibrium systems. In this approach, relationships have been established between nonequilibrium properties such as the transport coefficients, the thermodynamic entropy production, or the affinities, and quantities characterizing the microscopic Hamiltonian dynamics and the chaos or fluctuations it may generate. This overview presents results for classical systems in the escape-rate formalism, stochastic processes, and open quantum systems

Non-equilibrium Thermodynamics: Structural Relaxation, Fictive temperature and Tool-Narayanaswamy phenomenology in Glasses

Starting from the second law of thermodynamics applied to an isolated system consisting of the system surrounded by an extremely large medium, we formulate a general non-equilibrium thermodynamic description of the system when it is out of equilibrium. We then apply it to study the structural relaxation in glasses and establish the phenomenology behind the concept of the fictive temperature and of the empirical Tool-Narayanaswamy equation on firmer theoretical foundation.Comment: 20 pages, 1 figur

Testing numerical relativity with the shifted gauge wave

Computational methods are essential to provide waveforms from coalescing black holes, which are expected to produce strong signals for the gravitational wave observatories being developed. Although partial simulations of the coalescence have been reported, scientifically useful waveforms have so far not been delivered. The goal of the AppleswithApples (AwA) Alliance is to design, coordinate and document standardized code tests for comparing numerical relativity codes. The first round of AwA tests have now being completed and the results are being analyzed. These initial tests are based upon periodic boundary conditions designed to isolate performance of the main evolution code. Here we describe and carry out an additional test with periodic boundary conditions which deals with an essential feature of the black hole excision problem, namely a non-vanishing shift. The test is a shifted version of the existing AwA gauge wave test. We show how a shift introduces an exponentially growing instability which violates the constraints of a standard harmonic formulation of Einstein's equations. We analyze the Cauchy problem in a harmonic gauge and discuss particular options for suppressing instabilities in the gauge wave tests. We implement these techniques in a finite difference evolution algorithm and present test results. Although our application here is limited to a model problem, the techniques should benefit the simulation of black holes using harmonic evolution codes.Comment: Submitted to special numerical relativity issue of Classical and Quantum Gravit