Development of a continuum mechanics model of passive skeletal muscle

Skeletal muscle force evaluation is difficult to implement in a clinical setting. Muscle force is typically assessed through either manual muscle testing, isokinetic/isometric dynamometry, or electromyography (EMG). Manual muscle testing is a subjective evaluation of a patient’s ability to move voluntarily against gravity and to resist force applied by an examiner. Muscle testing using dynamometers adds accuracy by quantifying functional mechanical output of a limb. However, like manual muscle testing, dynamometry only provides estimates of the joint moment. EMG quantifies neuromuscular activation signals of individual muscles, and is used to infer muscle function. Despite the abundance of work performed to determine the degree to which EMG signals and muscle forces are related, the basic problem remains that EMG cannot provide a quantitative measurement of muscle force. Intramuscular pressure (IMP), the pressure applied by muscle fibers on interstitial fluid, has been considered as a correlate for muscle force. Numerous studies have shown that an approximately linear relationship exists between IMP and muscle force. A microsensor has recently been developed that is accurate, biocompatible, and appropriately sized for clinical use. While muscle force and pressure have been shown to be correlates, IMP has been shown to be non-uniform within the muscle. As it would not be practicable to experimentally evaluate how IMP is distributed, computational modeling may provide the means to fully evaluate IMP generation in muscles of various shapes and operating conditions. The work presented in this dissertation focuses on the development and validation of computational models of passive skeletal muscle and the evaluation of their performance for prediction of IMP. A transversly isotropic, hyperelastic, and nearly incompressible model will be evaluated along with a poroelastic model.

Spectral bounds and basis results for non-self-adjoint pencils, with an application to Hagen-Poiseuille flow

We obtain eigenvalue enclosures and basisness results for eigen- and associated functions of a non-self-adjoint unbounded linear operator pencil A−λBA−λB in which BB is uniformly positive and the essential spectrum of the pencil is empty. Both Riesz basisness and Bari basisness results are obtained. The results are applied to a system of singular differential equations arising in the study of Hagen–Poiseuille flow with non-axisymmetric disturbances.

Conservation of amino acid transporters in fungi, plants and animals

When comparing the transporters of three completely sequenced eukaryotic genomes - Saccharomyces cerevisiae, Arabidopsis thaliana and Homo sapiens - transporter types can be distinguished according to phylogeny, substrate spectrum, transport mechanism and cell specificity. The known amino acid transporters belong to five different superfamilies. Two preferentially Na+-coupled transporter superfamilies are not represented in them yeast and Arabidopsis genomes, whereas the other three groups, which often function as H+-coupled systems, have members in all investigated genomes. Additional superfamilies exist for organellar transport, including mitochondrial and plastidic carriers. When used in combination with phylogenetic analyses, functional comparison might aid our prediction of physiological functions for related but uncharacterized open reading frames.

Experimental Characterization and Quantification of Cement-Bentonite Interaction using Core Infiltration Techniques Coupled with X-ray Tomography

Deep geological storage of radioactive waste foresees cementitious materials as reinforcement of tunnels and as backfill. Bentonite is proposed to enclose spent fuel canisters and as drift seals. Sand/bentonite (s/b) is foreseen as backfill material of access galleries or as drift seals. The emplacement of cementitious material next to clay material generates an enormous chemical gradient in pore-water composition that drives diffusive solute transport. Laboratory studies and reactive transport modeling predicted significant mineral alteration at and near interfaces, mainly resulting in a decrease of porosity in bentonite. The goal of this thesis was to characterize and quantify the cement/bentonite interactions both spatially and temporally in laboratory experiments. A newly developed mobile X-ray transparent core infiltration device was used to perform X-ray computed tomography (CT) scans without interruption of running experiments. CT scans allowed tracking the evolution of the reaction plume and changes in core volume/diameter/density during the experiments. In total 4 core infiltration experiments were carried out for this study with the compacted and saturated cores consisting of MX-80 bentonite and sand/MX-80 bentonite mixture (s/b; 65/35%). Two different high-pH cementitious pore-fluids were infiltrated: a young (early) ordinary Portland cement pore-fluid (APWOPC; K+–Na+–OH-; pH 13.4; ionic strength 0.28 mol/kg) and a young ‘low-pH’ ESDRED shotcrete pore-fluid (APWESDRED; Ca2+–Na+–K+–formate; pH 11.4; ionic strength 0.11 mol/kg). The experiments lasted between 1 and 2 years. In both bentonite experiments, the hydraulic conductivity was strongly reduced after switching to high-pH fluids, changing eventually from an advective to a diffusion-dominated transport regime. The reduction was mainly induced by mineral precipitation and possibly partly also by high ionic strength pore-fluids. Both bentonite cores showed a volume reduction and a resulting transient flow in which pore-water was squeezed out during high-pH infiltration. The outflow chemistry was characterized by a high ionic strength, while chloride in the initial pore water got replaced as main anionic charge carrier by sulfate, originating from gypsum dissolution. The chemistry of the high-pH fluids got strongly buffered by the bentonite, consuming hydroxide and in case of APWESDRED also formate. Hydroxide got consumed by mineral reactions (saponite and possibly talc and brucite precipitation), while formate being affected by bacterial degradation. Post-mortem analysis showed reaction zones near the inlet of the bentonite core, characterized by calcium and magnesium enrichment, consisting predominately of calcite and saponite, respectively. Silica got enriched in the outflow, indicating dissolution of silicate-minerals, identified as preferentially cristobalite. In s/b, infiltration of APWOPC reduced the hydraulic conductivity strongly, while APWESDRED infiltration had no effect. The reduction was mainly induced by mineral precipitation and probably partly also by high ionic strength pore-fluids. Not clear is why the observed mineral precipitates in the APWESDRED experiment had no effect on the fluid flow. Both s/b cores showed a volume expansion along with decreasing ionic strengths of the outflow, due to mineral reactions or in case of APWESDRED infiltration also mediated by microbiological activity, consuming hydroxide and formate, respectively. The chemistry of the high-pH fluids got strongly buffered by the s/b. In the case of APWESDRED infiltration, formate reached the outflow only for a short time, followed by enrichment in acetate, indicating most likely biological activity. This was in agreement to post-mortem analysis of the core, observing black spots on the inflow surface, while the sample had a rotten-egg smell indicative of some sulfate reduction. Post-mortem analysis showed further in both cores a Ca-enrichment in the first 10 mm of the core due to calcite precipitation. Mg-enrichment was only observed in the APWOPC experiment, originating from newly formed saponite. Silica got enriched in the outflow of both experiments, indicating dissolution of silicate-minerals, identified in the OPC experiment as cristobalite. The experiments attested an effective buffering capacity for bentonite and s/b, a progressing coupled hydraulic-chemical sealing process and also the preservation of the physical integrity of the interface region in this setup with a total pressure boundary condition on the core sample. No complete pore-clogging was observed but the hydraulic conductivity got rather strongly reduced in 3 experiments, explained by clogging of the intergranular porosity (macroporosity). Such a drop in hydraulic conductivity may impact the saturation time of the buffer in a nuclear waste repository, although the processes and geometry will be more complex in repository situation.

Oxygen isotope record of oceanic and high-pressure metasomatism: a P-T-time-fluid path for the Monviso eclogites (Italy)

Fluids are considered a fundamental agent for chemical exchanges between different rock types in the subduction system. Constraints on the sources and pathways of subduction fluids thus provide crucial information to reconstruct subduction processes. The Monviso ophiolitic sequence is composed of mafic, ultramafic and minor sediments that have been subducted to ~80 km depth. In this sequence, both localized fluid flow and channelized fluids along major shear zones have been documented. We investigate the timing and source of the fluids that affected the dominant mafic rocks using microscale U-Pb dating of zircon and oxygen isotope analysis of mineral zones (garnet, zircon and antigorite) in high pressure rocks with variable degree of metasomatic modification. In mafic eclogites, Jurassic zircon cores are the only mineralogical relicts of the protolith gabbros and retain δ18O values of 4.5–6 ‰, typical of mantle melts. Garnet and metamorphic zircon that grew during prograde to peak metamorphism display low δ18O values between 0.2 and 3.8 ‰, which are likely inherited from high-temperature alteration of the protolith on the sea floor. This is corroborated by δ18O values of 3.0 and 3.6 ‰ in antigorite from surrounding serpentinites. In metasomatised eclogites within the Lower Shear Zone, garnet rim formed at the metamorphic peak shows a shift to higher δ18O up to 6‰. The age of zircons in high-pressure veins and metasomatised eclogites constrains the timing of fluid flow at high pressure at around 45–46 Ma. Although the oxygen data do not contradict previous reports of interaction with serpentinite-derived fluids, the shift to isotopically heavier oxygen compositions requires contribution from sediment-derived fluids. The scarcity of metasediments in the Monviso sequence suggests that such fluids were concentrated and fluxed along the Lower Shear Zone in a sufficient amount to modify the oxygen composition of the eclogitic minerals.

Chemical and isotope compositions of bottom sediments from ODP Leg 168, Eastern Flank of the Juan de Fuca Ridge

Ten sites were drilled in the eastern flank of the Juan de Fuca Ridge (North East Pacific) along a 100 km-long east-west transect during Leg ODP 168. This study focuses on the mineralogical and chemical study of sediments that overly basaltic basement through which seawater circulates. Silicate authigenesis was observed in the sediment layer just above basement at sites located more than 30 km from the ridge axis. This sediment alteration is particularly abundant at ODP Sites 1031 and 1029 where authigenic formation of Fe-Mg rich smectite and zeolite and the dissolution of biogenic calcite are observed. Comparison of the distribution of the alteration in the basal sediment collected along this transect suggests that diffusional transport of aqueous solutes from the basement into the overlying sediment cannot produce the mineralogical and chemical changes in the basal sediments at Sites 1031 located on a basement topographic high, and at Site 1029 located at about 50 km from the ridge axis on a buried basement area. Vertical advection of basement fluid though the sediment section is required to produce this alteration. These processes are still active at Site 1031, based on systematic variations in pore-water profiles and temperatures obtained from stable isotopic data on calcium carbonates and the nature of authigenic minerals. At Site 1029, there is no present-day advection of basement fluids though the sediment section, suggesting that this is a relic site for fluid flow.

Mineral, chemical and isotopic compositions of hydrothermally altered sediments from the Middle Valley (Juan de Fuca Ridge), ODP Site 139-858

Li and Li isotopes have been measured in the clay fraction of sediments recovered from the Middle Valley hydrothermal site on the Juan De Fuca Ridge. The Li content of pure detrital clays is 51 ppm while hydrothermal clays and carbonates have lower Li (22+/-11 ppm). However, there is no clear relationship between the mineralogy of the hydrothermal alteration products and their Li content. The d7Li value of the detrital clays is +5.8?. Hydrothermal clays and carbonates have d7Li in the range of -3.9? to +7.8?; these values do not seem to be dependent on the temperature at which they formed. Modelling of the Li and Li isotope systematics indicates that the fluid from which the alteration products form is significantly enriched in Li (higher than 10000 µmol/kg) relative to pore fluids recovered from within the sediments (up to 589 µmol/kg; [Wheat, C.G., M.J. Mottl, 1994. Data report: trace metal composition of pore water from Sites 855 through 858, Middle valley, Juan De Fuca Ridge. In Mottl, M.J., Davis, E.E., Fisher, A.T., Slack, J.F. (Eds.), Proc. ODP, Sci. Res. 139: 749-755; doi:10.2973/odp.proc.sr.139.269.1994]), and that this Li is derived from sediment. Thus, the alteration products are not in equilibrium with their conjugate pore fluids; rather, the alteration minerals formed at lower water/sediment ratios. This suggests that fluid flow pathways at Middle Valley were more diffuse in the past than they are today.

Stable oxygen isotope ratios of pore waters from ODP Leg 166 sites

This study investigates the d18O of pore waters from Sites 1003 through 1007, drilled along the western margin of the Great Bahama Bank during Leg 166 of the Ocean Drilling Program. These pore waters generally show a positive correlation between d18O and the concentration of chloride. The exception to this trend is Site 1006, where the pore waters exhibit nonlinear behavior with respect to chloride. The correlation between the concentration of Cl- and d18O at most of the sites appears to be a coincidence because although the increase in Cl- is a result of diffusion from an underlying source, the increases in d18O result from the recrystallization of metastable carbonates in the presence of a geothermal gradient. The difference in behavior in the d18O of the pore water at Site 1006 is probably a result of the relative reduced rate of carbonate recrystallization at this site. The d18O of the pore waters in the upper portion of the cores shows a pattern similar to the concentration of chloride in that there is an interval of 30-50 m in which neither the d18O nor the concentration of Cl- changes. This interval is consistent with either an interval of very rapid deposition of sediment or the advection of fluid through the platform. Both the d18O and the concentration of Cl- increase toward the platform, suggesting an input of saline and isotopically heavy water from the platform surface.

Biogeochemical measurements of cold seep sediments inhabit by vesicomyid clams in the Japan Deep Sea Trench

Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities associated with tectonic faults where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. During the cruise YK06-05 in 2006 with the RV Yokosuka to the Japan Trench, we investigated a clam colony inhabited by Abyssogena phaseoliformis (former known as Calyptogena phaseoliformis) and Isorropodon fossajaponicum (former known as Calyptogena fossajaponica). The targeted sampling and precise positioning of the in situ instruments were achieved with the manned research submersible Shinkai 6500 (JAMSTEC, Nankoku, Kochi, Japan). Sampling was first performed close to the rim of the JTC colony and then at the center. Immediately after sample recovery onboard, the sediment core was sub-sampled for ex situ rate measurements or preserved for later analyses. In sediment of the clam colony, low sulfate reduction (SR) rates (max. 128 nmol ml**-1 d**-1) were coupled to the anaerobic oxidation of methane (AOM). They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity was low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench.

Hydrogen, carbon, and oxygen isotope ratios of interstitial fluides of ODP Leg 104 holes

Carbon, hydrogen, and oxygen isotope ratios determined on 32 squeezed interstitial fluid samples show remarkable variations with depth. For the most part these variations are related to diagenetic and alteration reactions taking place in the sediments, and in the underlying basalts. delta13C SumCO2 depth distributions at Sites 642 and 643 are the result of mixing of original SumCO2 of the paleo bottom water with SumCO2 released by remineralization of organic matter. At Site 644, where sulfate exhaustion occurs, the processes of methanogenesis by CO2 reduction and anaerobic methanotrophy strongly influence the delta13C SumCO2 distribution. Hydrogen and oxygen isotopes roughly covary, and become enriched in 16O and1H with depth. This effect is most pronounced at Sites 642 and 643, possibly due to the influence of the directly underlying basalts. Isotope depletions at Site 644 are much lower, corresponding to the greater sediment depth to basement. The alternative, that the O, H isotope shifts are due primarily to autochthonous diagenetic and exchange reactions, is not supported by the data available.

Pore pressure measurements on IODP Exp308 sites

Overpressures measured with pore pressure penetrometers during Integrated Ocean Drilling Program (IODP) Expedition 308 reach 70% and 60% of the hydrostatic effective stress (View the MathML source) in the first 200 meters below sea floor (mbsf) at Sites U1322 and U1324, respectively, in the deepwater Gulf of Mexico, offshore Louisiana. High overpressures are present within low permeability mudstones where there have been multiple, very large, submarine landslides during the Pleistocene. Beneath 200 mbsf at Site U1324, pore pressures drop significantly: there are no submarine landslides in this mixture of mudstone, siltstone, and sandstone. The penetrometer measurements did not reach the in situ pressure at the end of the deployment. We used a soil model to determine that an extrapolation approach based on the inverse of square route of time (View the MathML source) requires much less decay time to achieve a desirable accuracy than an inverse time (1/t) extrapolation. Expedition 308 examined how rapid and asymmetric sedimentation above a permeable aquifer drives lateral fluid flow, extreme pore pressures, and submarine landslides. We interpret that the high overpressures observed are driven by rapid sedimentation of low permeability material from the ancestral Mississippi River. Reduced overpressure at depth at Site U1324 suggests lateral flow (drainage) whereas high overpressure at Site U1322 requires inflow from below: lateral flow in the underlying permeable aquifer provides one mechanism for these observations. High overpressure near the seafloor reduces slope stability and provides a mechanism for the large submarine landslides and low regional gradient (2°) offshore from the Mississippi delta.