High-resolution reconstruction of Holocene climate variability and environmental changes in the North Pacific using bivalve shells

Bivalve mollusk shells are useful tools for multi-species and multi-proxy paleoenvironmental reconstructions with a high temporal and spatial resolution. Past environmental conditions can be reconstructed from shell growth and stable oxygen and carbon isotope ratios, which present an archive for temperature, freshwater fluxes and primary productivity. The purpose of this thesis is the reconstruction of Holocene climate and environmental variations in the North Pacific with a high spatial and temporal resolution using marine bivalve shells. This thesis focuses on several different Holocene time periods and multiple regions in the North Pacific, including: Japan, Alaska (AK), British Columbia (BC) and Washington State, which are affected by the monsoon, Pacific Decadal Oscillation (PDO) and El Niño/Southern Oscillation (ENSO). Such high-resolution proxy data from the marine realm of mid- and high-latitudes are still rare. Therefore, this study contributes to the optimization and verification of climate models. However, before using bivalves for environmental reconstructions and seasonality studies, life history traits must be well studied to temporally align and interpret the geochemical record. These calibration studies are essential to ascertain the usefulness of selected bivalve species as paleoclimate proxy archives. This work focuses on two bivalve species, the short-lived Saxidomus gigantea and the long-lived Panopea abrupta. Sclerochronology and oxygen isotope ratios of different shell layers of P. abrupta were studied in order to test the reliability of this species as a climate archive. The annual increments are clearly discernable in umbonal shell portions and the increments widths should be measured in these shell portions. A reliable reconstruction of paleotemperatures may only be achieved by exclusively sampling the outer shell layer of multiple contemporaneous specimens. Life history traits (e.g., timing of growth line formation, duration of the growing season and growth rates) and stable isotope ratios of recent S. gigantea from AK and BC were analyzed in detail. Furthermore, a growth-temperature model based on S. gigantea shells from Alaska was established, which provides a better understanding of the hydrological changes related to the Alaska Coastal Current (ACC). This approach allows the independent measurement of water temperature and salinity from variations in the width of lunar daily growth increments of S. gigantea. Temperature explains 70% of the variability in shell growth. The model was calibrated and tested with modern shells and then applied to archaeological specimens. The time period between 988 and 1447 cal yrs BP was characterized by colder (~1-2°C) and much drier (2-5 PSU) summers, and a likely much slower flowing ACC than at present. In contrast, the summers during the time interval of 599-1014 cal yrs BP were colder (up to 3°C) and fresher (1-2 PSU) than today. The Aleutian Low may have been stronger and the ACC was probably flowing faster during this time.

Study of the effect of minor compounds on the oxidative stability and physical properties of bulk oil, oil-in-water emulsion, and food emulsions

Minor components are of particular interest due to their antioxidant and biological properties. Various classes of lipophilic minor components (plant sterols (PS) and α-tocopherol) were selected as they are widely used in the food industry. A Fast GC-MS method for PS analysis in functional dairy products was set up. The analytical performance and significant reduction of the analysis time and consumables, demonstrated that Fast GC-MS could be suitable for the PS analysis in functional dairy products. Due to their chemical structure, PS can undergo oxidation, which could be greatly impacted by matrix nature/composition and thermal treatments. The oxidative stability of PS during microwave heating was evaluated. Two different model systems (PS alone and in combination) were heated up to 30 min at 1000 W. PS degraded faster when they were alone than in presence of TAG. The extent of PS degradation depends on both heating time and the surrounding medium, which can impact the quality and safety of the food product destined to microwave heating/cooking. Many minor lipid components are included in emulsion systems and can affect the rate of lipid oxidation. The oxidative stability of oil-in-water (O/W) emulsions containing PS esters, ω-3 FA and phenolic compounds, were evaluated after a 14-day storage at room temperature. Due to their surface active character, PS could be particularly prone to oxidation when they are incorporated in emulsions, as they are more exposed to water-soluble prooxidants. Finally, some minor lipophilic components may increase oxidative stability of food systems due to their antioxidant activity. á-tocopherol partitioning and antioxidant activity was determined in the presence of excess SDS in stripped soybean O/W emulsions. Results showed that surfactant micelles could play a key role as an antioxidant carrier, by potentially increasing the accessibility of hydrophobic antioxidant to the interface.

Exact quantum Monte Carlo methods for correlated electron systems

Thema dieser Arbeit ist die Entwicklung und Kombination verschiedener numerischer Methoden, sowie deren Anwendung auf Probleme stark korrelierter Elektronensysteme. Solche Materialien zeigen viele interessante physikalische Eigenschaften, wie z.B. Supraleitung und magnetische Ordnung und spielen eine bedeutende Rolle in technischen Anwendungen. Es werden zwei verschiedene Modelle behandelt: das Hubbard-Modell und das Kondo-Gitter-Modell (KLM). In den letzten Jahrzehnten konnten bereits viele Erkenntnisse durch die numerische Lösung dieser Modelle gewonnen werden. Dennoch bleibt der physikalische Ursprung vieler Effekte verborgen. Grund dafür ist die Beschränkung aktueller Methoden auf bestimmte Parameterbereiche. Eine der stärksten Einschränkungen ist das Fehlen effizienter Algorithmen für tiefe Temperaturen.rnrnBasierend auf dem Blankenbecler-Scalapino-Sugar Quanten-Monte-Carlo (BSS-QMC) Algorithmus präsentieren wir eine numerisch exakte Methode, die das Hubbard-Modell und das KLM effizient bei sehr tiefen Temperaturen löst. Diese Methode wird auf den Mott-Übergang im zweidimensionalen Hubbard-Modell angewendet. Im Gegensatz zu früheren Studien können wir einen Mott-Übergang bei endlichen Temperaturen und endlichen Wechselwirkungen klar ausschließen.rnrnAuf der Basis dieses exakten BSS-QMC Algorithmus, haben wir einen Störstellenlöser für die dynamische Molekularfeld Theorie (DMFT) sowie ihre Cluster Erweiterungen (CDMFT) entwickelt. Die DMFT ist die vorherrschende Theorie stark korrelierter Systeme, bei denen übliche Bandstrukturrechnungen versagen. Eine Hauptlimitation ist dabei die Verfügbarkeit effizienter Störstellenlöser für das intrinsische Quantenproblem. Der in dieser Arbeit entwickelte Algorithmus hat das gleiche überlegene Skalierungsverhalten mit der inversen Temperatur wie BSS-QMC. Wir untersuchen den Mott-Übergang im Rahmen der DMFT und analysieren den Einfluss von systematischen Fehlern auf diesen Übergang.rnrnEin weiteres prominentes Thema ist die Vernachlässigung von nicht-lokalen Wechselwirkungen in der DMFT. Hierzu kombinieren wir direkte BSS-QMC Gitterrechnungen mit CDMFT für das halb gefüllte zweidimensionale anisotrope Hubbard Modell, das dotierte Hubbard Modell und das KLM. Die Ergebnisse für die verschiedenen Modelle unterscheiden sich stark: während nicht-lokale Korrelationen eine wichtige Rolle im zweidimensionalen (anisotropen) Modell spielen, ist in der paramagnetischen Phase die Impulsabhängigkeit der Selbstenergie für stark dotierte Systeme und für das KLM deutlich schwächer. Eine bemerkenswerte Erkenntnis ist, dass die Selbstenergie sich durch die nicht-wechselwirkende Dispersion parametrisieren lässt. Die spezielle Struktur der Selbstenergie im Impulsraum kann sehr nützlich für die Klassifizierung von elektronischen Korrelationseffekten sein und öffnet den Weg für die Entwicklung neuer Schemata über die Grenzen der DMFT hinaus.

A 950 yr temperature reconstruction from Duckhole Lake, southern Tasmania, Australia

A lack of quantitative high resolution paleoclimate data from the Southern Hemisphere limits the ability to examine current trends within the context of long-term natural climate variability. This study presents a temperature reconstruction for southern Tasmania based on analyses of a sediment core from Duckhole Lake (43.365°S, 146.875°E). The relationship between non-destructive whole core scanning reflectance spectroscopy measurements in the visible spectrum (380–730 nm) and the instrumental temperature record (ad 1911–2000) was used to develop a calibration-in-time reflectance spectroscopy-based temperature model. Results showed that a trough in reflectance from 650 to 700 nm, which represents chlorophyll and its derivatives, was significantly correlated to annual mean temperature. A calibration model was developed (R = 0.56, p auto < 0.05, root mean squared error of prediction (RMSEP) = 0.21°C, five-year filtered data, calibration period 1911–2000) and applied down-core to reconstruct annual mean temperatures in southern Tasmania over the last c. 950 years. This indicated that temperatures were initially cool c. ad 1050, but steadily increased until the late ad 1100s. After a brief cool period in the ad 1200s, temperatures again increased. Temperatures steadily decreased during the ad 1600s and remained relatively stable until the start of the 20th century when they rapidly decreased, before increasing from ad 1960s onwards. Comparisons with high resolution temperature records from western Tasmania, New Zealand and South America revealed some similarities, but also highlighted differences in temperature variability across the mid-latitudes of the Southern Hemisphere. These are likely due to a combination of factors including the spatial variability in climate between and within regions, and differences between records that document seasonal (i.e. warm season/late summer) versus annual temperature variability. This highlights the need for further records from the mid-latitudes of the Southern Hemisphere in order to constrain past natural spatial and seasonal/annual temperature variability in the region, and to accurately identify and attribute changes to natural variability and/or anthropogenic activities.

Dominance and the maintenance of polymorphism in multiallelic migration-selection models with two demes

The maintenance of genetic variation in a spatially heterogeneous environment has been one of the main research themes in theoretical population genetics. Despite considerable progress in understanding the consequences of spatially structured environments on genetic variation, many problems remain unsolved. One of them concerns the relationship between the number of demes, the degree of dominance, and the maximum number of alleles that can be maintained by selection in a subdivided population. In this work, we study the potential of maintaining genetic variation in a two-deme model with deme-independent degree of intermediate dominance, which includes absence of G x E interaction as a special case. We present a thorough numerical analysis of a two-deme three-allele model, which allows us to identify dominance and selection patterns that harbor the potential for stable triallelic equilibria. The information gained by this approach is then used to construct an example in which existence and asymptotic stability of a fully polymorphic equilibrium can be proved analytically. Noteworthy, in this example the parameter range in which three alleles can coexist is maximized for intermediate migration rates. Our results can be interpreted in a specialist-generalist context and (among others) show when two specialists can coexist with a generalist in two demes if the degree of dominance is deme independent and intermediate. The dominance relation between the generalist allele and the specialist alleles play a decisive role. We also discuss linear selection on a quantitative trait and show that G x E interaction is not necessary for the maintenance of more than two alleles in two demes.

An empirical model to estimate the demand for primary care in urban settings

Objective. To measure the demand for primary care and its associated factors by building and estimating a demand model of primary care in urban settings.^ Data source. Secondary data from 2005 California Health Interview Survey (CHIS 2005), a population-based random-digit dial telephone survey, conducted by the UCLA Center for Health Policy Research in collaboration with the California Department of Health Services, and the Public Health Institute between July 2005 and April 2006.^ Study design. A literature review was done to specify the demand model by identifying relevant predictors and indicators. CHIS 2005 data was utilized for demand estimation.^ Analytical methods. The probit regression was used to estimate the use/non-use equation and the negative binomial regression was applied to the utilization equation with the non-negative integer dependent variable.^ Results. The model included two equations in which the use/non-use equation explained the probability of making a doctor visit in the past twelve months, and the utilization equation estimated the demand for primary conditional on at least one visit. Among independent variables, wage rate and income did not affect the primary care demand whereas age had a negative effect on demand. People with college and graduate educational level were associated with 1.03 (p < 0.05) and 1.58 (p < 0.01) more visits, respectively, compared to those with no formal education. Insurance was significantly and positively related to the demand for primary care (p < 0.01). Need for care variables exhibited positive effects on demand (p < 0.01). Existence of chronic disease was associated with 0.63 more visits, disability status was associated with 1.05 more visits, and people with poor health status had 4.24 more visits than those with excellent health status. ^ Conclusions. The average probability of visiting doctors in the past twelve months was 85% and the average number of visits was 3.45. The study emphasized the importance of need variables in explaining healthcare utilization, as well as the impact of insurance, employment and education on demand. The two-equation model of decision-making, and the probit and negative binomial regression methods, was a useful approach to demand estimation for primary care in urban settings.^

Concentrations of natural and anthropogenic organohalogens in water and air samples in the Canadian Arctic during IPY (2007-2008)

Shipboard measurements of organohalogen compounds in air and surface seawater were conducted in the Canadian Arctic in 2007-2008. Study areas included the Labrador Sea, Hudson Bay, and the southern Beaufort Sea. High volume air samples were collected at deck level (6 m), while low volume samples were taken at 1 and 15 m above the water or ice surface. Water samples were taken within 7 m. Water concentration ranges (pg/L) were as follows: alpha-hexachlorocyclohexane (alpha-HCH) 465-1013, gamma-HCH 150-254, hexachlorobenzene (HCB) 4.0-6.4, 2,4-dibromoanisole (DBA) 8.5-38, and 2,4,6-tribromoanisole (TBA) 4.7-163. Air concentration ranges (pg/m**3) were as follows: alpha-HCH 7.5-48, gamma-HCH 2.1-7.7, HCB 48-71, DBA 4.8-25, and TBA 6.4-39. Fugacity gradients predicted net deposition of HCB in all areas, while exchange directions varied for the other chemicals by season and locations. Net evasion of alpha-HCH from Hudson Bay and the Beaufort Sea during open water conditions was shown by air concentrations that averaged 14% higher at 1 m than 15 m. No significant difference between the two heights was found over ice cover. The alpha-HCH in air over the Beaufort Sea was racemic in winter (mean enantiomer fraction, EF = 0.504 ± 0.008) and nonracemic in late spring-early summer (mean EF = 0.476 ± 0.010). This decrease in EF was accompanied by a rise in air concentrations due to volatilization of nonracemic alpha-HCH from surface water (EF = 0.457 ± 0.019). Fluxes of chemicals during the southern Beaufort Sea open water season (i.e., Leg 9) were estimated using the Whitman two-film model, where volatilization fluxes are positive and deposition fluxes are negative. The means ± SD (and ranges) of net fluxes (ng/m**2/d) were as follows: alpha-HCH 6.8 ± 3.2 (2.7-13), gamma-HCH 0.76 ± 0.40 (0.26-1.4), HCB -9.6 ± 2.7 (-6.1 to -15), DBA 1.2 ± 0.69 (0.04-2.0), and TBA 0.46 ± 1.1 ng/m**2/d (-1.6 to 2.0).

Noble gases sampled from three cruises in the eastern tropical Atlantic in September 2005 and June/July 2006

Upwelling velocities w in the equatorial band are too small to be directly observed. Here, we apply a recently proposed indirect method, using the observed helium isotope (3He or 4He) disequilibria in the mixed layer. The helium data were sampled from three cruises in the eastern tropical Atlantic in September 2005 and June/July 2006. A one-dimensional two-box model was applied, where the helium air-sea gas exchange is balanced by upwelling from 3He-rich water below the mixed layer and by vertical mixing. The mixing coefficients Kv were estimated from microstructure measurements, and on two of the cruises, Kv exceeded 1 x 10**-4 m**2/s, making the vertical mixing term of the same order of magnitude as the gas exchange and the upwelling term. In total, helium disequilibrium was observed on 54 stations. Of the calculated upwelling velocities, 48% were smaller than 1.0 x 10**-5 m/s, 19% were between 1.0 and 2.0 x 10**-5 m/s, 22% were between 2.0 and 4.0 x 10**-5 m/s, and on 11% of upwelling velocities exceeded this limit. The highest upwelling velocities were found in late June 2006. Meridional upwelling distribution indicated an equatorial asymmetry with higher vertical velocities between the equator and 1° to 2° south compared to north of the equator, particularly at 10°W. Associated heat flux into the mixed layer could be as high as 138 W/m**2, but this depends strongly on the chosen depths where the upwelled water comes from. By combining upwelling velocities with sea surface temperature and productivity distributions, a mean monthly equatorial upwelling rate of 19 Sv was estimated for June 2006 and a biweekly mean of 24 Sv was estimated for September 2005.

C and H geochemistry of altered oceanic crus of ODP/IODP Hole 1256D

Carbon and hydrogen concentrations and isotopic compositions were measured in 19 samples from altered oceanic crust cored in ODP/IODP Hole 1256D through lavas, dikes down to the gabbroic rocks. Bulk water content varies from 0.32 to 2.14 wt% with dD values from -64per mil to -25per mil. All samples are enriched in water relative to fresh basalts. The dD values are interpreted in terms of mixing between magmatic water and another source that can be either secondary hydrous minerals and/or H contained in organic compounds such as hydrocarbons. Total CO2, extracted by step-heating technique, ranges between 564 and 2823 ppm with d13C values from -14.9per mil to -26.6per mil. As for water, these altered samples are enriched in carbon relative to fresh basalts. The carbon isotope compositions are interpreted in terms of a mixing between two components: (1) a carbonate with d13C = -4.5per mil and (2) an organic compound with d13C = -26.6per mil. A mixing model calculation indicates that, for most samples (17 of 19), more than 75% of the total C occurs as organic compounds while carbonates represent less than 25%. This result is also supported by independent estimates of carbonate content from CO2 yield after H3PO4 attack. A comparison between the carbon concentration in our samples, seawater DIC (Dissolved Inorganic Carbon) and DOC (Dissolved Organic Carbon), and hydrothermal fluids suggests that CO2 degassed from magmatic reservoirs is the main source of organic C addition to the crust during the alteration process. A reduction step of dissolved CO2 is thus required, and can be either biologically mediated or not. Abiotic processes are necessary for the deeper part of the crust (>1000 mbsf) because alteration temperatures are greater than any hyperthermophilic living organism (i.e. T > 110 °C). Even if not required, we cannot rule out the contribution of microbial activity in the low-temperature alteration zones. We propose a two-step model for carbon cycling during crustal alteration: (1) when "fresh" oceanic crust forms at or close to ridge axis, alteration starts with hot hydrothermal fluids enriched in magmatic CO2, leading to the formation of organic compounds during Fischer-Tropsch-type reactions; (2) when the crust moves away from the ridge axis, these interactions with hot hydrothermal fluids decrease and are replaced by seawater interactions with carbonate precipitation in fractures. Taking into account this organic carbon, we estimate C isotope composition of mean altered oceanic crust at ? -4.7per mil, similar to the d13C of the C degassed from the mantle at ridge axis, and discuss the global carbon budget. The total flux of C stored in the altered oceanic crust, as carbonate and organic compound, is 2.9 ± 0.4 * 10**12 molC/yr.

Analysis of Magnetic Nozzles For Space Plasma Thrusters = Análisis de Toberas Magnéticas para Motores Espaciales de Plasma

Esta tesis presenta un análisis teórico del funcionamiento de toberas magnéticas para la propulsión espacial por plasmas. El estudio está basado en un modelo tridimensional y bi-fluido de la expansión supersónica de un plasma caliente en un campo magnético divergente. El modelo básico es ampliado progresivamente con la inclusión de términos convectivos dominantes de electrones, el campo magnético inducido por el plasma, poblaciones electrónicas múltiples a distintas temperaturas, y la capacidad de integrar el flujo en la región de expansión lejana. La respuesta hiperbólica del plasma es integrada con alta precisión y eficiencia haciendo uso del método de las líneas características. Se realiza una caracterización paramétrica de la expansión 2D del plasma en términos del grado de magnetización de iones, la geometría del campo magnético, y el perfil inicial del plasma. Se investigan los mecanismos de aceleración, mostrando que el campo ambipolar convierte la energía interna de electrones en energía dirigida de iones. Las corrientes diamagnéticas de Hall, que pueden hallarse distribuidas en el volumen del plasma o localizadas en una delgada capa de corriente en el borde del chorro, son esenciales para la operación de la tobera, ya que la fuerza magnética repulsiva sobre ellas es la encargada de confinar radialmente y acelerar axialmente el plasma. El empuje magnético es la reacción a esta fuerza sobre el motor. La respuesta del plasma muestra la separación gradual hacia adentro de los tubos de iones respecto de los magnéticos, lo cual produce la formación de corrientes eléctricas longitudinales y pone el plasma en rotación. La ganancia de empuje obtenida y las pérdidas radiales de la pluma de plasma se evalúan en función de los parámetros de diseño. Se analiza en detalle la separación magnética del plasma aguas abajo respecto a las líneas magnéticas (cerradas sobre sí mismas), necesaria para la aplicación de la tobera magnética a fines propulsivos. Se demuestra que tres teorías existentes sobre separación, que se fundamentan en la resistividad del plasma, la inercia de electrones, y el campo magnético que induce el plasma, son inadecuadas para la tobera magnética propulsiva, ya que producen separación hacia afuera en lugar de hacia adentro, aumentando la divergencia de la pluma. En su lugar, se muestra que la separación del plasma tiene lugar gracias a la inercia de iones y la desmagnetización gradual del plasma que tiene lugar aguas abajo, que permiten la separación ilimitada del flujo de iones respecto a las líneas de campo en condiciones muy generales. Se evalúa la cantidad de plasma que permanece unida al campo magnético y retorna hacia el motor a lo largo de las líneas cerradas de campo, mostrando que es marginal. Se muestra cómo el campo magnético inducido por el plasma incrementa la divergencia de la tobera magnética y por ende de la pluma de plasma en el caso propulsivo, contrariamente a las predicciones existentes. Se muestra también cómo el inducido favorece la desmagnetización del núcleo del chorro, acelerando la separación magnética. La hipótesis de ambipolaridad de corriente local, común a varios modelos de tobera magnética existentes, es discutida críticamente, mostrando que es inadecuada para el estudio de la separación de plasma. Una inconsistencia grave en la derivación matemática de uno de los modelos más aceptados es señalada y comentada. Incluyendo una especie adicional de electrones supratérmicos en el modelo, se estudia la formación y geometría de dobles capas eléctricas en el interior del plasma. Cuando dicha capa se forma, su curvatura aumenta cuanto más periféricamente se inyecten los electrones supratérmicos, cuanto menor sea el campo magnético, y cuanto más divergente sea la tobera magnética. El plasma con dos temperaturas electrónicas posee un mayor ratio de empuje magnético frente a total. A pesar de ello, no se encuentra ninguna ventaja propulsiva de las dobles capas, reforzando las críticas existentes frente a las propuestas de estas formaciones como un mecanismo de empuje. Por último, se presenta una formulación general de modelos autosemejantes de la expansión 2D de una pluma no magnetizada en el vacío. El error asociado a la hipótesis de autosemejanza es calculado, mostrando que es pequeño para plumas hipersónicas. Tres modelos de la literatura son particularizados a partir de la formulación general y comparados. Abstract This Thesis presents a theoretical analysis of the operation of magnetic nozzles for plasma space propulsion. The study is based on a two-dimensional, two-fluid model of the supersonic expansion of a hot plasma in a divergent magnetic field. The basic model is extended progressively to include the dominant electron convective terms, the plasma-induced magnetic field, multi-temperature electron populations, and the capability to integrate the plasma flow in the far expansion region. The hyperbolic plasma response is integrated accurately and efficiently with the method of the characteristic lines. The 2D plasma expansion is characterized parametrically in terms of the ion magnetization strength, the magnetic field geometry, and the initial plasma profile. Acceleration mechanisms are investigated, showing that the ambipolar electric field converts the internal electron energy into directed ion energy. The diamagnetic electron Hall current, which can be distributed in the plasma volume or localized in a thin current sheet at the jet edge, is shown to be central for the operation of the magnetic nozzle. The repelling magnetic force on this current is responsible for the radial confinement and axial acceleration of the plasma, and magnetic thrust is the reaction to this force on the magnetic coils of the thruster. The plasma response exhibits a gradual inward separation of the ion streamtubes from the magnetic streamtubes, which focuses the jet about the nozzle axis, gives rise to the formation of longitudinal currents and sets the plasma into rotation. The obtained thrust gain in the magnetic nozzle and radial plasma losses are evaluated as a function of the design parameters. The downstream plasma detachment from the closed magnetic field lines, required for the propulsive application of the magnetic nozzle, is investigated in detail. Three prevailing detachment theories for magnetic nozzles, relying on plasma resistivity, electron inertia, and the plasma-induced magnetic field, are shown to be inadequate for the propulsive magnetic nozzle, as these mechanisms detach the plume outward, increasing its divergence, rather than focusing it as desired. Instead, plasma detachment is shown to occur essentially due to ion inertia and the gradual demagnetization that takes place downstream, which enable the unbounded inward ion separation from the magnetic lines beyond the turning point of the outermost plasma streamline under rather general conditions. The plasma fraction that remains attached to the field and turns around along the magnetic field back to the thruster is evaluated and shown to be marginal. The plasmainduced magnetic field is shown to increase the divergence of the nozzle and the resulting plasma plume in the propulsive case, and to enhance the demagnetization of the central part of the plasma jet, contrary to existing predictions. The increased demagnetization favors the earlier ion inward separation from the magnetic field. The local current ambipolarity assumption, common to many existing magnetic nozzle models, is critically discussed, showing that it is unsuitable for the study of plasma detachment. A grave mathematical inconsistency in a well-accepted model, related to the acceptance of this assumption, is found out and commented on. The formation and 2D shape of electric double layers in the plasma expansion is studied with the inclusion of an additional suprathermal electron population in the model. When a double layer forms, its curvature is shown to increase the more peripherally suprathermal electrons are injected, the lower the magnetic field strength, and the more divergent the magnetic nozzle is. The twoelectron- temperature plasma is seen to have a greater magnetic-to-total thrust ratio. Notwithstanding, no propulsive advantage of the double layer is found, supporting and reinforcing previous critiques to their proposal as a thrust mechanism. Finally, a general framework of self-similar models of a 2D unmagnetized plasma plume expansion into vacuum is presented and discussed. The error associated with the self-similarity assumption is calculated and shown to be small for hypersonic plasma plumes. Three models of the literature are recovered as particularizations from the general framework and compared.

A regularised continuum damage model based on the mesoscopic scale for soft tissue

Material properties of soft fibrous tissues are highly conditioned by the hierarchical structure of this kind of composites. Collagen based tissues present, at decreasing length scales, a complex framework of fibres, fibrils, tropocollagen molecules and amino-acids. Understanding the mechanical behaviour at nano-scale level is critical to accurately incorporate this structural information in phenomenological damage models. In this work we derive a relationship between the mechanical and geometrical properties of the fibril constituents and the soft tissue material parameters at macroscopic scale. A Hodge–Petruska two-dimensional model has been used to describe the fibrils as staggered arrays of tropocollagen molecules. After a mechanical characterisation of each of the fibril components, two fibril failures modes have been defined related with two planes of weakness. A phenomenological continuous damage model with regularised softening was presented along with meso-structurally based definitions for its material parameters. Finally, numerical analysis at fibril, fibre and tissue levels are presented to show the capabilities of the model

Limited internal friction in the rate-limiting step of a two-state protein folding reaction

Small, single-domain proteins typically fold via a compact transition-state ensemble in a process well fitted by a simple, two-state model. To characterize the rate-limiting conformational changes that underlie two-state folding, we have investigated experimentally the effects of changing solvent viscosity on the refolding of the IgG binding domain of protein L. In conjunction with numerical simulations, our results indicate that the rate-limiting conformational changes of the folding of this domain are strongly coupled to solvent viscosity and lack any significant “internal friction” arising from intrachain collisions. When compared with the previously determined solvent viscosity dependencies of other, more restricted conformational changes, our results suggest that the rate-limiting folding transition involves conformational fluctuations that displace considerable amounts of solvent. Reconciling evidence that the folding transition state ensemble is comprised of highly collapsed species with these and similar, previously reported results should provide a significant constraint for theoretical models of the folding process.

Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.

Quantitative ER ↔ Golgi Transport Kinetics and Protein Separation upon Golgi Exit Revealed by Vesicular Integral Membrane Protein 36 Dynamics in Live CellsV⃞

To quantitatively investigate the trafficking of the transmembrane lectin VIP36 and its relation to cargo-containing transport carriers (TCs), we analyzed a C-terminal fluorescent-protein (FP) fusion, VIP36-SP-FP. When expressed at moderate levels, VIP36-SP-FP localized to the endoplasmic reticulum, Golgi apparatus, and intermediate transport structures, and colocalized with epitope-tagged VIP36. Temperature shift and pharmacological experiments indicated VIP36-SP-FP recycled in the early secretory pathway, exhibiting trafficking representative of a class of transmembrane cargo receptors, including the closely related lectin ERGIC53. VIP36-SP-FP trafficking structures comprised tubules and globular elements, which translocated in a saltatory manner. Simultaneous visualization of anterograde secretory cargo and VIP36-SP-FP indicated that the globular structures were pre-Golgi carriers, and that VIP36-SP-FP segregated from cargo within the Golgi and was not included in post-Golgi TCs. Organelle-specific bleach experiments directly measured the exchange of VIP36-SP-FP between the Golgi and endoplasmic reticulum (ER). Fitting a two-compartment model to the recovery data predicted first order rate constants of 1.22 ± 0.44%/min for ER → Golgi, and 7.68 ± 1.94%/min for Golgi → ER transport, revealing a half-time of 113 ± 70 min for leaving the ER and 1.67 ± 0.45 min for leaving the Golgi, and accounting for the measured steady-state distribution of VIP36-SP-FP (13% Golgi/87% ER). Perturbing transport with AlF4− treatment altered VIP36-SP-GFP distribution and changed the rate constants. The parameters of the model suggest that relatively small differences in the first order rate constants, perhaps manifested in subtle differences in the tendency to enter distinct TCs, result in large differences in the steady-state localization of secretory components.

The "allosteric three-site model" of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli.

For the functional role of the ribosomal tRNA exit (E) site, two different models have been proposed. It has been suggested that transient E-site binding of the tRNA leaving the peptidyl (P) site promotes elongation factor G (EF-G)-dependent translocation by lowering the energetic barrier of tRNA release [Lill, R., Robertson, J. M. & Wintermeyer, W. (1989) EMBO J. 8, 3933-3938]. The alternative "allosteric three-site model" [Nierhaus, K.H. (1990) Biochemistry 29, 4997-5008] features stable, codon-dependent tRNA binding to the E site and postulates a coupling between E and aminoacyl (A) sites that regulates the tRNA binding affinity of the two sites in an anticooperative manner. Extending our testing of the two conflicting models, we have performed translocation experiments with fully active ribosomes programmed with heteropolymeric mRNA. The results confirm that the deacylated tRNA released from the P site is bound to the E site in a kinetically labile fashion, and that the affinity of binding, i.e., the occupancy of the E site, is increased by Mg2+ or polyamines. At conditions of high E-site occupancy in the posttranslocation complex, filling the A site with aminoacyl-tRNA had no influence on the E site, i.e., there was no detectable anticooperative coupling between the two sites, provided that second-round translocation was avoided by removing EF-G. On the basis of these results, which are entirely consistent with our previous results, we consider the allosteric three-site model of elongation untenable. Rather, as proposed earlier, the E site-bound state of the leaving tRNA is a transient intermediate and, as such, is a mechanistic feature of the classic two-state model of the elongating ribosome.