COSMIC-LAB: Unexpected Results from High-resolution Spectra of AGB Stars in Globular Clusters

We have used high-resolution spectra, acquired with UVES@ESO-VLT, to determine the chemical abundances of different samples of AGB and RGB stars in 4 Galactic globular clusters, namely 47Tuc, NGC3201, M22 and M62. For almost all the analyzed AGB stars we found a clear discrepancy between the iron abundance measured from neutral lines and that obtained from single ionized lines, while this discrepancy is not obtained for the RGB samples observed in the same clusters and analyzed with the same procedure. Such a behavior exactly corresponds to what expected in the case of Non-Local Thermodynamical Equilibrium (NLTE) in the star atmosphere. These results have a huge impact on the proper determination of GC chemistry. In fact, one of the most intriguing consequences is that, at odds with previous claims, no iron spread is found in NGC3201 and M22 if the iron abundance is obtained from ionized lines only.

Vibrational Relaxation of O3(nu2) by O((3)P)

Laboratory measurements of the rate coefficient for quenching of O3(nu2) by ground-state atomic oxygen, kO(nu2), at room temperature are presented. kO(nu2) is currently not well known and is necessary for appropriate nonlocal thermodynamic equilibrium modeling of the upper mesosphere and lower thermosphere. In this work, a 266 nm laser pulse photolyzes a small amount of O3 in a slow-flowing gas mixture of O3, Xe, and Ar. This process simultaneously produces atomic oxygen and increases the temperature of the gas mixture slightly, thereby increasing the population in the O3(nu2) state. Transient diode laser absorption spectroscopy is used to monitor the populations of the O3(nu2) and ground vibrational states as the system re-equilibrates. Relaxation rates are measured over a range of quencher concentrations to extract the rate coefficient of interest. The value of kO(nu2) was determined to be (2.2 0.5) * 10(-12) cm(3) s(-1).

Relating in situ gas measurements to the surface outgassing properties of cometary nuclei

The sensitivity of the gas flow field to changes in different initial conditions has been studied for the case of a highly simplified cometary nucleus model. The nucleus model simulated a homogeneously outgassing sphere with a more active ring around an axis of symmetry. The varied initial conditions were the number density of the homogeneous region, the surface temperature, and the composition of the flow (varying amounts of H2O and CO2) from the active ring. The sensitivity analysis was performed using the Polynomial Chaos Expansion (PCE) method. Direct Simulation Monte Carlo (DSMC) was used for the flow, thereby allowing strong deviations from local thermal equilibrium. The PCE approach can be used to produce a sensitivity analysis with only four runs per modified input parameter and allows one to study and quantify non-linear responses of measurable parameters to linear changes in the input over a wide range. Hence the PCE allows one to obtain a functional relationship between the flow field properties at every point in the inner coma and the input conditions. It is for example shown that the velocity and the temperature of the background gas are not simply linear functions of the initial number density at the source. As probably expected, the main influence on the resulting flow field parameter is the corresponding initial parameter (i.e. the initial number density determines the background number density, the temperature of the surface determines the flow field temperature, etc.). However, the velocity of the flow field is also influenced by the surface temperature while the number density is not sensitive to the surface temperature at all in our model set-up. Another example is the change in the composition of the flow over the active area. Such changes can be seen in the velocity but again not in the number density. Although this study uses only a simple test case, we suggest that the approach, when applied to a real case in 3D, should assist in identifying the sensitivity of gas parameters measured in situ by, for example, the Rosetta spacecraft to the surface boundary conditions and vice versa.

Sulphur and iron species in Dvurechenskii mud volcano sediments

The deep Black Sea is known to be depleted in electron-acceptors for sulphide oxidation. This study on depth distributions of sulphur species (S(II), S(0),S(n)**2-,S2O3**2-,SO3**2-,SO4**2-) in the Dvurechenskii mud volcano, a cold seep situated in the permanently anoxic eastern Black Sea basin (Sorokin Trough, 2060 m water depth), showed remarkable concentrations of sulphide oxidation products. Sulphite concentrations of up to 11 µmol L**1-, thiosulphate concentrations of up to 22 µmol L**1-, zero-valent sulphur concentrations of up to 150 µmol L**1- and up to five polysulphide species were measured in the upper 20 cm of the sediment. Electron-acceptors found to be available in the Dvurechenskii mud volcano (DMV) for the oxidation of hydrogen sulphide to sulphide oxidation intermediates are iron-minerals, and probably also reactive manganese phases. Up to 60 µmol g**1- of reactive iron-minerals and up to 170 µmol L**1- dissolved iron was present in the central summit with the highest fluid upflow and fresh mud outflow. Thus, the source for the oxidative power in the DMV are reactive iron phases extruded with the mud from an ancient source in the deeply buried sediments, leading to the formation of various sulphur intermediates in comparably high concentrations. Another possible source of sulphide oxidation intermediates in DMV sediments could be the formation of zero-valent sulphur by sulphate dependent anaerobic microbial oxidation of methane followed by disproportionation of zero-valent sulphur. Sulphide oxidation intermediates, which are produced by these processes, do not reach thermodynamic equilibrium with rhombic sulphur, especially close to the active center of the DMV due to a short equilibration time. Thus, mud volcano sediments, such as in the DMV, can provide oxidizing niches even in a highly reduced environment like the abyssal part of the Black Sea.

Macroscopic motion and gravitation in thermodynamics

A series of examples rarely presented to students is discussed to illustrate a property of thermodynamic equilibrium: small parts of a fully isolated system move as if points of a rigid body, so as to minimize the macroscopic (kinetic) energy EM. Most examples lie in the fields of astronomy and astrophysics, EM then including the gravitational energy. The paradoxical behaviour of gravitation, in particular in the extreme case of black holes,is discussed.

Métodos computacionales para visco-hiperelasticidad anisótropa en grandes deformaciones

El comportamiento mecánico de muchos materiales biológicos y poliméricos en grandes deformaciones se puede describir adecuadamente mediante formulaciones isocóricas hiperelásticas y viscoelásticas. Las ecuaciones de comportamiento elástico y viscoelástico y las formulaciones computacionales para materiales incompresibles isótropos en deformaciones finitas están ampliamente desarrolladas en la actualidad. Sin embargo, el desarrollo de modelos anisótropos no lineales y de sus correspondientes formulaciones computacionales sigue siendo un tema de investigación de gran interés. Cuando se consideran grandes deformaciones, existen muchas medidas de deformación disponibles con las que poder formular las ecuaciones de comportamiento. Los modelos en deformaciones cuadráticas facilitan la implementación en códigos de elementos finitos, ya que estas medidas surgen de forma natural en la formulación. No obstante, pueden dificultar la interpretación de los modelos y llevar a resultados pocos realistas. El uso de deformaciones logarítmicas permite el desarrollo de modelos más simples e intuitivos, aunque su formulación computacional debe ser adaptada a las exigencias del programa. Como punto de partida, en esta tesis se demuestra que las deformaciones logarítmicas representan la extensión natural de las deformaciones infinitesimales, tanto axiales como angulares, al campo de las grandes deformaciones. Este hecho permite explicar la simplicidad de las ecuaciones resultantes. Los modelos hiperelásticos predominantes en la actualidad están formulados en invariantes de deformaciones cuadráticas. Estos modelos, ya sean continuos o microestructurales, se caracterizan por tener una forma analítica predefinida. Su expresión definitiva se calcula mediante un ajuste de curvas a datos experimentales. Un modelo que no sigue esta metodología fue desarrollado por Sussman y Bathe. El modelo es sólo válido para isotropía y queda definido por una función de energía interpolada con splines, la cual reproduce los datos experimentales de forma exacta. En esta tesis se presenta su extensión a materiales transversalmente isótropos y ortótropos utilizando deformaciones logarítmicas. Asimismo, se define una nueva propiedad que las funciones de energía anisótropas deben satisfacer para que su convergencia al caso isótropo sea correcta. En visco-hiperelasticidad, aparte de las distintas funciones de energía disponibles, hay dos aproximaciones computational típicas basadas en variables internas. El modelo original de Simó está formulado en tensiones y es válido para materiales anisótropos, aunque sólo es adecuado para pequeñas desviaciones con respecto al equilibrio termodinámico. En cambio, el modelo basado en deformaciones de Reese y Govindjee permite grandes deformaciones no equilibradas pero es, en esencia, isótropo. Las formulaciones anisótropas en este último contexto son microestructurales y emplean el modelo isótropo para cada uno de los constituyentes. En esta tesis se presentan dos formulaciones fenomenológicas viscoelásticas definidas mediante funciones hiperelásticas anisótropas y válidas para grandes desviaciones con respecto al equilibrio termodinámico. El primero de los modelos está basado en la descomposición multiplicativa de Sidoroff y requiere un comportamiento viscoso isótropo. La formulación converge al modelo de Reese y Govindjee en el caso especial de isotropía elástica. El segundo modelo se define a partir de una descomposición multiplicativa inversa. Esta formulación está basada en una descripción co-rotacional del problema, es sustancialmente más compleja y puede dar lugar a tensores constitutivos ligeramente no simétricos. Sin embargo, su rango de aplicación es mucho mayor ya que permite un comportamiento anisótropo tanto elástico como viscoso. Varias simulaciones de elementos finitos muestran la gran versatilidad de estos modelos cuando se combinan con funciones hiperelásticas formadas por splines. ABSTRACT The mechanical behavior of many polymeric and biological materials may be properly modelled be means of isochoric hyperelastic and viscoelastic formulations. These materials may sustain large strains. The viscoelastic computational formulations for isotropic incompressible materials at large strains may be considered well established; for example Ogden’s hyperelastic function and the visco-hyperelastic model of Reese and Govindjee are well known models for isotropy. However, anisotropic models and computational procedures both for hyperelasticity and viscohyperelasticity are still under substantial research. Anisotropic hyperelastic models are typically based on structural invariants obtained from quadratic strain measures. These models may be microstructurallybased or phenomenological continuum formulations, and are characterized by a predefined analytical shape of the stored energy. The actual final expression of the stored energy depends on some material parameters which are obtained from an optimization algorithm, typically the Levenberg-Marquardt algorithm. We present in this work anisotropic spline-based hyperelastic stored energies in which the shape of the stored energy is obtained as part of the procedure and which (exactly in practice) replicates the experimental data. These stored energies are based on invariants obtained from logarithmic strain measures. These strain measures preserve the metric and the physical meaning of the trace and deviator operators and, hence, are interesting and meaningful for anisotropic formulations. Furthermore, the proposed stored energies may be formulated in order to have material-symmetries congruency both from a theoretical and from a numerical point of view, which are new properties that we define in this work. On the other hand, visco-hyperelastic formulations for anisotropic materials are typically based on internal stress-like variables following a procedure used by Sim´o. However, it can be shown that this procedure is not adequate for large deviations from thermodynamic equilibrium. In contrast, a formulation given by Reese and Govindjee is valid for arbitrarily large deviations from thermodynamic equilibrium but not for anisotropic stored energy functions. In this work we present two formulations for visco-hyperelasticity valid for anisotropic stored energies and large deviations from thermodynamic equilibrium. One of the formulations is based on the Sidoroff multiplicative decomposition and converges to the Reese and Govindjee formulation for the case of isotropy. However, the formulation is restricted to isotropy for the viscous component. The second formulation is based on a reversed multiplicative decomposition. This last formulation is substantially more complex and based on a corotational description of the problem. It can also result in a slightly nonsymmetric tangent. However, the formulation allows for anisotropy not only in the equilibrated and non-equilibrated stored energies, but also in the viscous behavior. Some examples show finite element implementation, versatility and interesting characteristics of the models.

Time-multiscale methods for the simulation of slow transport problems in atomistic systems

En esta tesis presentamos una teoría adaptada a la simulación de fenómenos lentos de transporte en sistemas atomísticos. En primer lugar, desarrollamos el marco teórico para modelizar colectividades estadísticas de equilibrio. A continuación, lo adaptamos para construir modelos de colectividades estadísticas fuera de equilibrio. Esta teoría reposa sobre los principios de la mecánica estadística, en particular el principio de máxima entropía de Jaynes, utilizado tanto para sistemas en equilibrio como fuera de equilibrio, y la teoría de las aproximaciones del campo medio. Expresamos matemáticamente el problema como un principio variacional en el que maximizamos una entropía libre, en lugar de una energía libre. La formulación propuesta permite definir equivalentes atomísticos de variables macroscópicas como la temperatura y la fracción molar. De esta forma podemos considerar campos macroscópicos no uniformes. Completamos el marco teórico con reglas de cuadratura de Monte Carlo, gracias a las cuales obtenemos modelos computables. A continuación, desarrollamos el conjunto completo de ecuaciones que gobiernan procesos de transporte. Deducimos la desigualdad de disipación entrópica a partir de fuerzas y flujos termodinámicos discretos. Esta desigualdad nos permite identificar la estructura que deben cumplir los potenciales cinéticos discretos. Dichos potenciales acoplan las tasas de variación en el tiempo de las variables microscópicas con las fuerzas correspondientes. Estos potenciales cinéticos deben ser completados con una relación fenomenológica, del tipo definido por la teoría de Onsanger. Por último, aportamos validaciones numéricas. Con ellas ilustramos la capacidad de la teoría presentada para simular propiedades de equilibrio y segregación superficial en aleaciones metálicas. Primero, simulamos propiedades termodinámicas de equilibrio en el sistema atomístico. A continuación evaluamos la habilidad del modelo para reproducir procesos de transporte en sistemas complejos que duran tiempos largos con respecto a los tiempos característicos a escala atómica. ABSTRACT In this work, we formulate a theory to address simulations of slow time transport effects in atomic systems. We first develop this theoretical framework in the context of equilibrium of atomic ensembles, based on statistical mechanics. We then adapt it to model ensembles away from equilibrium. The theory stands on Jaynes' maximum entropy principle, valid for the treatment of both, systems in equilibrium and away from equilibrium and on meanfield approximation theory. It is expressed in the entropy formulation as a variational principle. We interpret atomistic equivalents of macroscopic variables such as the temperature and the molar fractions, wich are not required to be uniform, but can vary from particle to particle. We complement this theory with Monte Carlo summation rules for further approximation. In addition, we provide a framework for studying transport processes with the full set of equations driving the evolution of the system. We first derive a dissipation inequality for the entropic production involving discrete thermodynamic forces and fluxes. This discrete dissipation inequality identifies the adequate structure for discrete kinetic potentials which couple the microscopic field rates to the corresponding driving forces. Those kinetic potentials must finally be expressed as a phenomenological rule of the Onsanger Type. We present several validation cases, illustrating equilibrium properties and surface segregation of metallic alloys. We first assess the ability of a simple meanfield model to reproduce thermodynamic equilibrium properties in systems with atomic resolution. Then, we evaluate the ability of the model to reproduce a long-term transport process in complex systems.

Building intuition of iron evolution during solar cell processing through analysis of different process models

An important aspect of Process Simulators for photovoltaics is prediction of defect evolution during device fabrication. Over the last twenty years, these tools have accelerated process optimization, and several Process Simulators for iron, a ubiquitous and deleterious impurity in silicon, have been developed. The diversity of these tools can make it difficult to build intuition about the physics governing iron behavior during processing. Thus, in one unified software environment and using self-consistent terminology, we combine and describe three of these Simulators. We vary structural defect distribution and iron precipitation equations to create eight distinct Models, which we then use to simulate different stages of processing. We find that the structural defect distribution influences the final interstitial iron concentration ([Fe-i]) more strongly than the iron precipitation equations. We identify two regimes of iron behavior: (1) diffusivity-limited, in which iron evolution is kinetically limited and bulk [Fe-i] predictions can vary by an order of magnitude or more, and (2) solubility-limited, in which iron evolution is near thermodynamic equilibrium and the Models yield similar results. This rigorous analysis provides new intuition that can inform Process Simulation, material, and process development, and it enables scientists and engineers to choose an appropriate level of Model complexity based on wafer type and quality, processing conditions, and available computation time.

Mechanism of topology simplification by type II DNA topoisomerases

Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.

Mapping the intrinsic curvature and flexibility along the DNA chain

The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a “natural” DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.

We propose a general mean field model of ligand-protein interactions to determine the thermodynamic equilibrium of a system at finite temperature. The method is employed in structural assessments of two human immuno-deficiency virus type 1 protease complexes where the gross effects of protein flexibility are incorporated by utilizing a data base of crystal structures. Analysis of the energy spectra for these complexes has revealed that structural and thermo-dynamic aspects of molecular recognition can be rationalized on the basis of the extent of frustration in the binding energy landscape. In particular, the relationship between receptor-specific binding of these ligands to human immunodeficiency virus type 1 protease and a minimal frustration principle is analyzed.

O conceito de equilíbrio hidráulico e termodinâmico da água no solo aplicado ao estudo da curva de retenção e murchamento de plantas

Estimativas sobre alterações climáticas globais têm aumentando a demanda por estudos sobre propriedades dos solos relativamente secos e limitações impostas à absorção de água pelas plantas em condições de escassez hídrica. Neste estudo, fatores que influenciam a retenção da água no solo e o murchamento de plantas foram avaliados com base no conceito de equilíbrio da água no solo. Objetivou-se com este estudo: (i) avaliar a confiabilidade de medições do conteúdo de água no solo sob altas sucções matriciais em câmaras de pressão, usando como referência a técnica de ponto de orvalho (ii) avaliar as interações entre espécies de plantas e solos com diferentes classes texturais no ponto de murcha permanente (iii) investigar as relações entre equilíbrio hidráulico da água no solo e murchamento de plantas a partir do conceito de corte hidráulico. Para tanto, um experimento para avaliar a influência dos tipos de solos e espécies de plantas, no ponto de murcha permanente foi conduzido em casa de vegetação da Escola Superior de Agricultura \"Luiz de Queiroz\" da Universidade de São Paulo, Piracicaba, São Paulo. Avaliou-se o murchamento de plantas de girassol (Helianthus annuus L.), milho (Zea mays L.) e soja (Glycine max L.). Os solos utilizados no estudo foram coletados na camada superficial (0-10 cm) em quatro áreas, selecionadas com o objetivo de obter classes texturais contrastantes, localizadas no município de Piracicaba, São Paulo, Brasil. Sub-amostras foram utilizadas para determinação da distribuição do tamanho de partículas e atributos químicos. Amostras indeformadas foram coletadas para a determinação da curva de retenção da água no solo pela técnica de câmaras de pressão. Adicionalmente, amostras deformadas foram utilizadas para determinação das características de retenção da água no solo pela técnica do ponto de orvalho em altos valores de sucções matriciais. Os dados de retenção de água no solo foram ajustados a modelos empíricos para estimativas da sucção matricial e conteúdo de água relacionada à água em equilíbrio hidráulico (água residual). Foram observadas similaridades nas determinações das características de retenção da água no solo entre as técnicas de câmaras de pressão e ponto de orvalho, sugerindo a boa drenagem das amostras de solo em câmaras de pressão. Interações significativas foram observadas entre os tipos de solos e espécies de plantas no ponto de murcha permanente, indicando que o movimento de água no contínuo solo-planta-atmosfera foi dependente de resistências relacionadas tanto ao solo quanto às plantas. Ou seja, tanto à capacidade do solo em transportar água até raízes, quanto à habilidade das plantas em absorver a água transportada, assim como, aos processos de regulação de água que ocorrem nas plantas. A abordagem baseada no conteúdo de água residual para o intervalo de sucções matriciais de 0 a 15.000 hPa não foi adequada para ilustrar a condição de equilíbrio hidráulico da água no solo, definidos pelo corte hidráulico, e relações com as sucções matriciais em ocorre o murchamento de plantas.

Modeling collisional processes in plasmas using discontinuous numerical methods

Thesis (Ph.D.)--University of Washington, 2016-06

Performance of hydrophobic and hydrophilic silica membrane reactors for the water gas shift reaction

In this study, a novel molecular sieve silica (MSS) membrane packed bed reactor (PBR) using a Cu/ZnO/Al2O3 catalyst was applied to the low-temperature water gas shift reaction (WGS). Best permeation results were H-2 permeances of 1.5 x 10(-6) mol(.)s(-1) m(-2) Pa-1, H-2/CO2 selectivities of 8 and H-2/N-2 selectivities of 18. It was shown that an operation with a sweep gas flow of 80 cm 3 min(-1), a feed flow rate of 50 cm(3) min(-1) and a H2O/CO molar ratio of one at 280 degreesC reached a 99% CO conversion. This is well above the thermodynamic equilibrium and achievable PBR conversion. Hydrophilic membranes underwent pore widening during the reaction while hydrophobic membranes indicated no such behaviour and also showed increased H-2 permeation with temperature, a characteristic of activated transport. (C) 2003 Elsevier Science B.V. All rights reserved.

The effects of energy sites on adsorption of Lennard–Jones fluids and phase transition in carbon slit pore of finite length a computer simulation study

A Monte Carlo simulation method is Used 10 study the effects of adsorption strength and topology of sites on adsorption of simple Lennard-Jones fluids in a carbon slit pore of finite length. Argon is used as a model adsorbate, while the adsorbent is modeled as a finite carbon slit pore whose two walls composed of three graphene layers with carbon atoms arranged in a hexagonal pattern. Impurities having well depth of interaction greater than that of carbon atom are assumed to be grafted onto the surface. Different topologies of the impurities; corner, centre, shelf and random topologies are studied. Adsorption isotherms of argon at 87.3 K are obtained for pore having widths of 1, 1.5 and 3 11111 using a Grand Canonical Monte Carlo simulation (GCMC). These results are compared with isotherms obtained for infinite pores. It is shown that the Surface heterogeneity affects significantly the overall adsorption isotherm, particularly the phase transition. Basically it shifts the onset of adsorption to lower pressure and the adsorption isotherms for these four impurity models are generally greater than that for finite pore. The positions of impurities on solid Surface also affect the shape of the adsorption isotherm and the phase transition. We have found that the impurities allocated at the centre of pore walls provide the greatest isotherm at low pressures. However when the pressure increases the impurities allocated along the edges of the graphene layers show the most significant effect on the adsorption isotherm. We have investigated the effect of surface heterogeneity on adsorption hysteresis loops of three models of impurity topology, it shows that the adsorption branches of these isotherms are different, while the desorption branches are quite close to each other. This suggests that the desorption branch is either the thermodynamic equilibrium branch or closer to it than the adsorption branch. (c) 2005 Elsevier Inc. All rights reserved.