Improvement of photon transport model by including coupled photon-electron transport and kernel refinement

The first part of this work deals with the inverse problem solution in the X-ray spectroscopy field. An original strategy to solve the inverse problem by using the maximum entropy principle is illustrated. It is built the code UMESTRAT, to apply the described strategy in a semiautomatic way. The application of UMESTRAT is shown with a computational example. The second part of this work deals with the improvement of the X-ray Boltzmann model, by studying two radiative interactions neglected in the current photon models. Firstly it is studied the characteristic line emission due to Compton ionization. It is developed a strategy that allows the evaluation of this contribution for the shells K, L and M of all elements with Z from 11 to 92. It is evaluated the single shell Compton/photoelectric ratio as a function of the primary photon energy. It is derived the energy values at which the Compton interaction becomes the prevailing process to produce ionization for the considered shells. Finally it is introduced a new kernel for the XRF from Compton ionization. In a second place it is characterized the bremsstrahlung radiative contribution due the secondary electrons. The bremsstrahlung radiation is characterized in terms of space, angle and energy, for all elements whit Z=1-92 in the energy range 1–150 keV by using the Monte Carlo code PENELOPE. It is demonstrated that bremsstrahlung radiative contribution can be well approximated with an isotropic point photon source. It is created a data library comprising the energetic distributions of bremsstrahlung. It is developed a new bremsstrahlung kernel which allows the introduction of this contribution in the modified Boltzmann equation. An example of application to the simulation of a synchrotron experiment is shown.

Transport model of the human Na+-coupled L-ascorbic acid (vitamin C) transporter SVCT1

Vitamin C (L-ascorbic acid) is an essential micronutrient that serves as an antioxidant and as a cofactor in many enzymatic reactions. Intestinal absorption and renal reabsorption of the vitamin is mediated by the epithelial apical L-ascorbic acid cotransporter SVCT1 (SLC23A1). We explored the molecular mechanisms of SVCT1-mediated L-ascorbic acid transport using radiotracer and voltage-clamp techniques in RNA-injected Xenopus oocytes. L-ascorbic acid transport was saturable (K(0.5) approximately 70 microM), temperature dependent (Q(10) approximately 5), and energized by the Na(+) electrochemical potential gradient. We obtained a Na(+)-L-ascorbic acid coupling ratio of 2:1 from simultaneous measurement of currents and fluxes. L-ascorbic acid and Na(+) saturation kinetics as a function of cosubstrate concentrations revealed a simultaneous transport mechanism in which binding is ordered Na(+), L-ascorbic acid, Na(+). In the absence of L-ascorbic acid, SVCT1 mediated pre-steady-state currents that decayed with time constants 3-15 ms. Transients were described by single Boltzmann distributions. At 100 mM Na(+), maximal charge translocation (Q(max)) was approximately 25 nC, around a midpoint (V(0.5)) at -9 mV, and with apparent valence approximately -1. Q(max) was conserved upon progressive removal of Na(+), whereas V(0.5) shifted to more hyperpolarized potentials. Model simulation predicted that the pre-steady-state current predominantly results from an ion-well effect on binding of the first Na(+) partway within the membrane electric field. We present a transport model for SVCT1 that will provide a framework for investigating the impact of specific mutations and polymorphisms in SLC23A1 and help us better understand the contribution of SVCT1 to vitamin C metabolism in health and disease.

Imminent ocean acidification in the Arctic projected with the NCAR global coupled carbon cycle-climate model

Ocean acidification from the uptake of anthropogenic carbon is simulated for the industrial period and IPCC SRES emission scenarios A2 and B1 with a global coupled carbon cycle-climate model. Earlier studies identified seawater saturation state with respect to aragonite, a mineral phase of calcium carbonate, as a key variable governing impacts on corals and other shell-forming organisms. Globally in the A2 scenario, water saturated by more than 300%, considered suitable for coral growth, vanishes by 2070 AD (CO2≈630 ppm), and the ocean volume fraction occupied by saturated water decreases from 42% to 25% over this century. The largest simulated pH changes worldwide occur in Arctic surface waters, where hydrogen ion concentration increases by up to 185% (ΔpH=−0.45). Projected climate change amplifies the decrease in Arctic surface mean saturation and pH by more than 20%, mainly due to freshening and increased carbon uptake in response to sea ice retreat. Modeled saturation compares well with observation-based estimates along an Arctic transect and simulated changes have been corrected for remaining model-data differences in this region. Aragonite undersaturation in Arctic surface waters is projected to occur locally within a decade and to become more widespread as atmospheric CO2 continues to grow. The results imply that surface waters in the Arctic Ocean will become corrosive to aragonite, with potentially large implications for the marine ecosystem, if anthropogenic carbon emissions are not reduced and atmospheric CO2 not kept below 450 ppm.

The coupled atmosphere–chemistry–ocean model SOCOL-MPIOM

The newly developed atmosphere–ocean-chemistry-climate model SOCOL-MPIOM is presented by demonstrating the influence of the interactive chemistry module on the climate state and the variability. Therefore, we compare pre-industrial control simulations with (CHEM) and without (NOCHEM) interactive chemistry. In general, the influence of the chemistry on the mean state and the variability is small and mainly restricted to the stratosphere and mesosphere. The largest differences are found for the atmospheric dynamics in the polar regions, with slightly stronger northern and southern winter polar vortices in CHEM. The strengthening of the vortex is related to larger stratospheric temperature gradients, which are attributed to a parametrization of the absorption of ozone and oxygen in the Lyman-alpha, Schumann–Runge, Hartley, and Higgins bands. This effect is parametrized in the version with interactive chemistry only. A second reason for the temperature differences between CHEM and NOCHEM is related to diurnal variations in the ozone concentrations in the higher atmosphere, which are missing in NOCHEM. Furthermore, stratospheric water vapour concentrations differ substantially between the two experiments, but their effect on the temperatures is small. In both setups, the simulated intensity and variability of the northern polar vortex is inside the range of present day observations. Sudden stratospheric warming events are well reproduced in terms of their frequency, but the distribution amongst the winter months is too uniform. Additionally, the performance of SOCOL-MPIOM under changing external forcings is assessed for the period 1600–2000 using an ensemble of simulations driven by a spectral solar forcing reconstruction. The amplitude of the reconstruction is large in comparison to other state-of-the-art reconstructions, providing an upper limit for the importance of the solar signal. In the pre-industrial period (1600–1850) the simulated surface temperature trends are in reasonable agreement with temperature reconstructions, although the multi-decadal variability is more pronounced. This enhanced variability can be attributed to the variability in the solar forcing. The simulated temperature reductions during the Maunder Minimum are in the lowest probability range of the proxy records. During the Dalton Minimum, when also volcanic forcing is an important driver of temperature variations, the agreement is better. In the industrial period from 1850 onward SOCOL-MPIOM overestimates the temperature increase in comparison to observational data sets. Sensitivity simulations show that this overestimation can be attributed to the increasing trend in the solar forcing reconstruction that is used in this study and an additional warming induced by the simulated ozone changes.

Three time-slice simulations of the Eemian (eem), the mid-Holocene (hol), and a pre-industrial (pri) control run with the coupled atmosphere-ocean-model ECHAM5/MPI-OM

Orbital forcing does not only exert direct insolation effects, but also alters climate indirectly through feedback mechanisms that modify atmosphere and ocean dynamics and meridional heat and moisture transfers. We investigate the regional effects of these changes by detailed analysis of atmosphere and ocean circulation and heat transports in a coupled atmosphere-ocean-sea ice-biosphere general circulation model (ECHAM5/JSBACH/MPI-OM). We perform long term quasi equilibrium simulations under pre-industrial, mid-Holocene (6000 years before present - yBP), and Eemian (125 000 yBP) orbital boundary conditions. Compared to pre-industrial climate, Eemian and Holocene temperatures show generally warmer conditions at higher and cooler conditions at lower latitudes. Changes in sea-ice cover, ocean heat transports, and atmospheric circulation patterns lead to pronounced regional heterogeneity. Over Europe, the warming is most pronounced over the north-eastern part in accordance with recent reconstructions for the Holocene. We attribute this warming to enhanced ocean circulation in the Nordic Seas and enhanced ocean-atmosphere heat flux over the Barents Shelf in conduction with retreat of sea ice and intensified winter storm tracks over northern Europe.

A coupled elastoplastic-damage constitutive model with Lode angle dependent failure criterion

A coupled elastoplastic-damage constitutive model with Lode angle dependent failure criterion for high strain and ballistic applications is presented. A Lode angle dependent function is added to the equivalent plastic strain to failure definition of the Johnson–Cook failure criterion. The weakening in the elastic law and in the Johnson–Cook-like constitutive relation implicitly introduces the Lode angle dependency in the elastoplastic behaviour. The material model is calibrated for precipitation hardened Inconel 718 nickel-base superalloy. The combination of a Lode angle dependent failure criterion with weakened constitutive equations is proven to predict fracture patterns of the mechanical tests performed and provide reliable results. Additionally, the mesh size dependency on the prediction of the fracture patterns was studied, showing that was crucial to predict such patterns

Coupled Nonlinear Ginzburg-Landau and Mechanics Model for Martensitic Transformations in Polycrystals

Las transformaciones martensíticas (MT) se definen como un cambio en la estructura del cristal para formar una fase coherente o estructuras de dominio multivariante, a partir de la fase inicial con la misma composición, debido a pequeños intercambios o movimientos atómicos cooperativos. En el siglo pasado se han descubierto MT en diferentes materiales partiendo desde los aceros hasta las aleaciones con memoria de forma, materiales cerámicos y materiales inteligentes. Todos muestran propiedades destacables como alta resistencia mecánica, memoria de forma, efectos de superelasticidad o funcionalidades ferroicas como la piezoelectricidad, electro y magneto-estricción etc. Varios modelos/teorías se han desarrollado en sinergia con el desarrollo de la física del estado sólido para entender por qué las MT generan microstructuras muy variadas y ricas que muestran propiedades muy interesantes. Entre las teorías mejor aceptadas se encuentra la Teoría Fenomenológica de la Cristalografía Martensítica (PTMC, por sus siglas en inglés) que predice el plano de hábito y las relaciones de orientación entre la austenita y la martensita. La reinterpretación de la teoría PTMC en un entorno de mecánica del continuo (CM-PTMC) explica la formación de los dominios de estructuras multivariantes, mientras que la teoría de Landau con dinámica de inercia desentraña los mecanismos físicos de los precursores y otros comportamientos dinámicos. La dinámica de red cristalina desvela la reducción de la dureza acústica de las ondas de tensión de red que da lugar a transformaciones débiles de primer orden en el desplazamiento. A pesar de las diferencias entre las teorías estáticas y dinámicas dado su origen en diversas ramas de la física (por ejemplo mecánica continua o dinámica de la red cristalina), estas teorías deben estar inherentemente conectadas entre sí y mostrar ciertos elementos en común en una perspectiva unificada de la física. No obstante las conexiones físicas y diferencias entre las teorías/modelos no se han tratado hasta la fecha, aun siendo de importancia crítica para la mejora de modelos de MT y para el desarrollo integrado de modelos de transformaciones acopladas de desplazamiento-difusión. Por lo tanto, esta tesis comenzó con dos objetivos claros. El primero fue encontrar las conexiones físicas y las diferencias entre los modelos de MT mediante un análisis teórico detallado y simulaciones numéricas. El segundo objetivo fue expandir el modelo de Landau para ser capaz de estudiar MT en policristales, en el caso de transformaciones acopladas de desplazamiento-difusión, y en presencia de dislocaciones. Comenzando con un resumen de los antecedente, en este trabajo se presentan las bases físicas de los modelos actuales de MT. Su capacidad para predecir MT se clarifica mediante el ansis teórico y las simulaciones de la evolución microstructural de MT de cúbicoatetragonal y cúbicoatrigonal en 3D. Este análisis revela que el modelo de Landau con representación irreducible de la deformación transformada es equivalente a la teoría CM-PTMC y al modelo de microelasticidad para predecir los rasgos estáticos durante la MT, pero proporciona una mejor interpretación de los comportamientos dinámicos. Sin embargo, las aplicaciones del modelo de Landau en materiales estructurales están limitadas por su complejidad. Por tanto, el primer resultado de esta tesis es el desarrollo del modelo de Landau nolineal con representación irreducible de deformaciones y de la dinámica de inercia para policristales. La simulación demuestra que el modelo propuesto es consistente fcamente con el CM-PTMC en la descripción estática, y también permite una predicción del diagrama de fases con la clásica forma ’en C’ de los modos de nucleación martensítica activados por la combinación de temperaturas de enfriamiento y las condiciones de tensión aplicada correlacionadas con la transformación de energía de Landau. Posteriomente, el modelo de Landau de MT es integrado con un modelo de transformación de difusión cuantitativa para elucidar la relajación atómica y la difusión de corto alcance de los elementos durante la MT en acero. El modelo de transformaciones de desplazamiento y difusión incluye los efectos de la relajación en borde de grano para la nucleación heterogenea y la evolución espacio-temporal de potenciales de difusión y movilidades químicas mediante el acoplamiento de herramientas de cálculo y bases de datos termo-cinéticos de tipo CALPHAD. El modelo se aplica para estudiar la evolución microstructural de aceros al carbono policristalinos procesados por enfriamiento y partición (Q&P) en 2D. La microstructura y la composición obtenida mediante la simulación se comparan con los datos experimentales disponibles. Los resultados muestran el importante papel jugado por las diferencias en movilidad de difusión entre la fase austenita y martensita en la distibución de carbono en las aceros. Finalmente, un modelo multi-campo es propuesto mediante la incorporación del modelo de dislocación en grano-grueso al modelo desarrollado de Landau para incluir las diferencias morfológicas entre aceros y aleaciones con memoria de forma con la misma ruptura de simetría. La nucleación de dislocaciones, la formación de la martensita ’butterfly’, y la redistribución del carbono después del revenido son bien representadas en las simulaciones 2D del estudio de la evolución de la microstructura en aceros representativos. Con dicha simulación demostramos que incluyendo las dislocaciones obtenemos para dichos aceros, una buena comparación frente a los datos experimentales de la morfología de los bordes de macla, la existencia de austenita retenida dentro de la martensita, etc. Por tanto, basado en un modelo integral y en el desarrollo de códigos durante esta tesis, se ha creado una herramienta de modelización multiescala y multi-campo. Dicha herramienta acopla la termodinámica y la mecánica del continuo en la macroescala con la cinética de difusión y los modelos de campo de fase/Landau en la mesoescala, y también incluye los principios de la cristalografía y de la dinámica de red cristalina en la microescala. ABSTRACT Martensitic transformation (MT), in a narrow sense, is defined as the change of the crystal structure to form a coherent phase, or multi-variant domain structures out from a parent phase with the same composition, by small shuffles or co-operative movements of atoms. Over the past century, MTs have been discovered in different materials from steels to shape memory alloys, ceramics, and smart materials. They lead to remarkable properties such as high strength, shape memory/superelasticity effects or ferroic functionalities including piezoelectricity, electro- and magneto-striction, etc. Various theories/models have been developed, in synergy with development of solid state physics, to understand why MT can generate these rich microstructures and give rise to intriguing properties. Among the well-established theories, the Phenomenological Theory of Martensitic Crystallography (PTMC) is able to predict the habit plane and the orientation relationship between austenite and martensite. The re-interpretation of the PTMC theory within a continuum mechanics framework (CM-PTMC) explains the formation of the multivariant domain structures, while the Landau theory with inertial dynamics unravels the physical origins of precursors and other dynamic behaviors. The crystal lattice dynamics unveils the acoustic softening of the lattice strain waves leading to the weak first-order displacive transformation, etc. Though differing in statics or dynamics due to their origins in different branches of physics (e.g. continuum mechanics or crystal lattice dynamics), these theories should be inherently connected with each other and show certain elements in common within a unified perspective of physics. However, the physical connections and distinctions among the theories/models have not been addressed yet, although they are critical to further improving the models of MTs and to develop integrated models for more complex displacivediffusive coupled transformations. Therefore, this thesis started with two objectives. The first one was to reveal the physical connections and distinctions among the models of MT by means of detailed theoretical analyses and numerical simulations. The second objective was to expand the Landau model to be able to study MTs in polycrystals, in the case of displacive-diffusive coupled transformations, and in the presence of the dislocations. Starting with a comprehensive review, the physical kernels of the current models of MTs are presented. Their ability to predict MTs is clarified by means of theoretical analyses and simulations of the microstructure evolution of cubic-to-tetragonal and cubic-to-trigonal MTs in 3D. This analysis reveals that the Landau model with irreducible representation of the transformed strain is equivalent to the CM-PTMC theory and microelasticity model to predict the static features during MTs but provides better interpretation of the dynamic behaviors. However, the applications of the Landau model in structural materials are limited due its the complexity. Thus, the first result of this thesis is the development of a nonlinear Landau model with irreducible representation of strains and the inertial dynamics for polycrystals. The simulation demonstrates that the updated model is physically consistent with the CM-PTMC in statics, and also permits a prediction of a classical ’C shaped’ phase diagram of martensitic nucleation modes activated by the combination of quenching temperature and applied stress conditions interplaying with Landau transformation energy. Next, the Landau model of MT is further integrated with a quantitative diffusional transformation model to elucidate atomic relaxation and short range diffusion of elements during the MT in steel. The model for displacive-diffusive transformations includes the effects of grain boundary relaxation for heterogeneous nucleation and the spatio-temporal evolution of diffusion potentials and chemical mobility by means of coupling with a CALPHAD-type thermo-kinetic calculation engine and database. The model is applied to study for the microstructure evolution of polycrystalline carbon steels processed by the Quenching and Partitioning (Q&P) process in 2D. The simulated mixed microstructure and composition distribution are compared with available experimental data. The results show that the important role played by the differences in diffusion mobility between austenite and martensite to the partitioning in carbon steels. Finally, a multi-field model is proposed by incorporating the coarse-grained dislocation model to the developed Landau model to account for the morphological difference between steels and shape memory alloys with same symmetry breaking. The dislocation nucleation, the formation of the ’butterfly’ martensite, and the redistribution of carbon after tempering are well represented in the 2D simulations for the microstructure evolution of the representative steels. With the simulation, we demonstrate that the dislocations account for the experimental observation of rough twin boundaries, retained austenite within martensite, etc. in steels. Thus, based on the integrated model and the in-house codes developed in thesis, a preliminary multi-field, multiscale modeling tool is built up. The new tool couples thermodynamics and continuum mechanics at the macroscale with diffusion kinetics and phase field/Landau model at the mesoscale, and also includes the essentials of crystallography and crystal lattice dynamics at microscale.

The kinesin walk: a dynamic model with elastically coupled heads.

Recently individual two-headed kinesin molecules have been studied in in vitro motility assays revealing a number of their peculiar transport properties. In this paper we propose a simple and robust model for the kinesin stepping process with elastically coupled Brownian heads that show all of these properties. The analytic and numerical treatment of our model results in a very good fit to the experimental data and practically has no free parameters. Changing the values of the parameters in the restricted range allowed by the related experimental estimates has almost no effect on the shape of the curves and results mainly in a variation of the zero load velocity that can be directly fitted to the measured data. In addition, the model is consistent with the measured pathway of the kinesin ATPase.

Climate simulation for 125 kyr BP with a coupled ocean-atmosphere general circulation model

The ECHAM-1 T21/LSG coupled ocean-atmosphere general circulation model (GCM) is used to simulate climatic conditions at the last interglacial maximum (Eemian. 125 kyr BP). The results reflect thc expected surface temperature changes (with respect to the control run) due to the amplification (reduction) of the seasonal cycle of insolation in the Northern (Southern) Hemisphere. A number of simulated features agree with previous results from atmospheric GCM simulations e.g. intensified summer southwest monsoons) except in the Northern Hemisphere poleward of 30 degrees N. where dynamical feedback, in the North Atlantic and North Pacific increase zonal temperatures about 1 degrees C above what would be predicted from simple energy balance considerations. As this is the same area where most of the terrestrial geological data originate, this result suggests that previous estimates of Eemian global average temperature might have been biased by sample distribution. This conclusion is supported by the fact that the estimated global temperature increase of only 0.3 degrees C greater than the control run ha, been previously shown to be consistent a with CLIMAP sea surface temperature estimates. Although the Northern Hemisphere summer monsoon is intensified. globally averaged precipitation over land is within about 1% of the present, contravening some geological inferences bur not the deep-sea delta(13)C estimates of terrestrial carbon storage changes. Winter circulation changes in the northern Arabian Sea. driven by strong cooling on land, are as large as summer circulation changes that are the usual focus of interest, suggesting that interpreting variations in the Arabian Sea. sedimentary record solely in terms of the summer monsoon response could sometimes lead to errors. A small monsoonal response over northern South America suggests that interglacial paleotrends in this region were not just due to El Nino variations.