Mica fish in mylonites

Mögliche Verformungsmechanismen, die zu den verschiedenen Glimmer- und Mineralfischen führen, sind: intrakristalline Verformung, Kristallrotation, Biegung und Faltung, Drucklösung in Kombination mit Ausfällung und dynamische Rekristallisation oder Mechanismen, die ein großes Mineral in mehrere kleine, fischförmige Kristalle aufspalten.Experimente mit ein neues Verformungsgerät und Objekten in zwei verschiedenen Matrixmaterialien werden beschrieben. Das eine ist PDMS, (Newtonianisch viskoses Polymer), und das andere Tapioca Perlen (Mohr-Couloumb Verhalten). Die Rotation von fischförmigen Objekten in PDMS stimmt mit der theoretischen Rotationsrate für ellipsenförmige Objekte in einem Newtonianischen Material überein. In einer Matrix von Tapioca Perlen nehmen die Objekte eine stabile Lage ein. Diese Orientierung ist vergleichbar mit der von Glimmerfischen. Die Verformung in der Matrix von Tapioca Perlen ist konzentriert auf dünne Scherzonen. Diese Ergebnisse implizieren, daß die Verformung in natürlichen Gesteinen auch in dünnen Scherzonen konzentriert ist.Computersimulationen werden beschrieben, mit denen der Einfluß der Eigenschaften einer Matrix auf die Rotation von Objekten und Verteilung von Deformation untersucht wird.Mit diesen Experimenten wird gezeigt, daß die Orientierung von Glimmerfischen nicht mit Verformung in einem nicht-linearen viskosen Material erklärt werden kann. Eine solche nicht-lineare Rheologie wird im Allgemeinen für die Erdkurste angenommen. Die stabile Orientierung eines Objektes kann mit weicheren Lagen in der Matrix erklärt werden.

Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Magnetic anisotropy in clinopyroxene and orthopyroxene single crystals

Pyroxenes constitute an important component in mafic igneous and metamorphic rocks. They often possess a prismatic habit, and their long axis, the crystallographic c axis, helps define a lineation in a textured rock. Anisotropy of magnetic susceptibility (AMS) serves as a fabric indicator in igneous and metamorphic rocks. If a rock’s AMS is carried by pyroxenes, it can be related to their crystallographic preferred orientation and degree of alignment. This requires knowing the intrinsic AMS of pyroxene single crystals. This study provides a comprehensive low-field and high-field AMS investigation of chemically diverse orthopyroxene and clinopyroxene crystals in relation to crystal structure, chemical composition, oxidation state of Fe, and the possible presence of ferromagnetic inclusions. The paramagnetic anisotropy, extracted from high-field data, shows clear relationships to crystallographic directions and Fe concentration both in clinopyroxene and orthopyroxene. In the diopside-augite series, the intermediate susceptibility is parallel to b, and the maximum is at 45° to the c axis. In aegirine, the intermediate axis remains parallel to b, while the maximum susceptibility is parallel to c. The AMS of spodumene depends on Fe concentration. In enstatite, the maximum susceptibility aligns with c and the minimum with b, and in the case of hypersthene, the maximum susceptibility is normal to the exsolution lamellae. Magnetite inclusions within augite possess a ferromagnetic anisotropy with consistent orientation of the principal susceptibilities, which dominates the low-field anisotropy. These results provide better understanding of magnetic anisotropy in pyroxenes and form a solid basis for interpretation of magnetic fabrics in pyroxene-bearing rocks.

Magnetic anisotropy in natural amphibole crystals

Anisotropy of magnetic susceptibility (AMS) is often used as a proxy for mineral fabric in deformed rocks. To do so quantitatively, it is necessary to quantify the intrinsic magnetic anisotropy of single crystals of rock-forming minerals. Amphiboles are common in mafic igneous and metamorphic rocks and often define rock texture due to their general prismatic crystal habits. Amphiboles may dominate the magnetic anisotropy in intermediate to felsic igneous rocks and in some metamorphic rock types, because they have a high Fe concentration and they can develop a strong crystallographic preferred orientation. In this study, the AMS is characterized in 28 single crystals and I crystal aggregate of compositionally diverse clino- and ortho-amphiboles. High-field methods were used to isolate the paramagnetic component of the anisotropy, which is unaffected by ferromagnetic inclusions that often occur in amphibole crystals. Laue imaging, laser ablation-inductively coupled plasma-mass spectrometry, and Mossbauer spectroscopy were performed to relate the magnetic anisotropy to crystal structure and Fe concentration. The minimum susceptibility is parallel to the crystallographic a*-axis and the maximum susceptibility is generally parallel to the crystallographic b-axis in tremolite, actinolite, and hornblende. Gedrite has its minimum susceptibility along the a-axis, and maximum susceptibility aligned with c. In richterite, however, the intermediate susceptibility is parallel to the b-axis and the minimum and maximum susceptibility directions are distributed in the a-c plane. The degree of anisotropy, k', increases generally with Fe concentration, following a linear trend: k' = 1.61 x 10(-9) Fe - 1.17 x 10(-9) m(3)/kg. Additionally, it may depend on the Fe2+/Fe3+ ratio. For most samples, the degree of anisotropy increases by a factor of approximately 8 upon cooling from room temperature to 77 K. Fen-oactinolite, one pargasite crystal and riebeckite show a larger increase, which is related to the onset of local ferromagnetic (s.l.) interactions below about 100 K. This comprehensive data set increases our understanding of the magnetic structure of amphiboles, and it is central to interpreting magnetic fabrics of rocks whose AMS is controlled by amphibole minerals.

Physical properties and neutron texture measuerments of deep-sea carbonates of DSDP Holes 62-463 and 62-465A

In weakly indurated, nannofossil-rich, deep-sea carbonates compressional wave velocity is up to twice as fast parallel to bedding than normal to it. It has been suggested that this anisotropy is due to alignment of calcite c-axes perpendicular to the shields of coccoliths and shield deposition parallel to bedding. This hypothesis was tested by measuring the preferred orientation (fabric) of calcite c-axes in acoustic anisotropic, calcareous DSDP sediment samples by X-ray goniometry, and it was found that the maximum c-axis concentrations are by far too low to explain the anisotropies. The X-ray method is subject to a number of uncertainties due to preparatory and technical shortcomings in weakly indurated rocks. The most serious weaknesses are: sample preparation, volume of measured sample (fraction of a mm3), beam defocusing and background intensity corrections, combination of incomplete pole figures, and necessity of recalculation of the c-axis orientations from other crystallographic directions. Goniometry using thermal neutrons overcomes most of these difficulties, but it is time consuming. We test the interferences made about velocity anisotropy by X-ray studies about the concentration of c-axes in deep-sea carbonates by employing neutron texture goniometry to eight DSDP samples comprising mostly nannofossil material. Fabric and sonic velocity were determined directly on the core specimens, thus from the same rock volume and requiring no preparation. The c-axis orientation is obtained directly from the [0006] calcite diffraction peak without corrections. The fabrics are clearly defined, but weak (1.1 to 1.86 times uniform) with the maximum about normal to bedding. They have crudely orthorhombic symmetry, but are not axisymmetric around the bedding normal. The observed c-axis intensities, although higher than determined by the X-ray method on other samples, are by far too low to explain the observed acoustic anisotropies.

Physical properties and bulk minerals from IODP Holes 308-U1322B, U1322D and U1324B

How the micro-scale fabric of clay-rich mudstone evolves during consolidation in early burial is critical to how they are interpreted in the deeper portions of sedimentary basins. Core samples from the Integrated Ocean Drilling Program Expedition 308, Ursa Basin, Gulf of Mexico, covering seafloor to 600 meters below sea floor (mbsf) are ideal for studying the micro-scale fabric of mudstones. Mudstones of consistent composition and grain size decrease in porosity from 80% at the seafloor to 37% at 600 mbsf. Argon-ion milling produces flat surfaces to image this pore evolution over a vertical effective stress range of 0.25 (71 mbsf) to 4.05 MPa (597 mbsf). With increasing burial, pores become elongated, mean pore size decreases, and there is preferential loss of the largest pores. There is a small increase in clay mineral preferred orientation as recorded by high resolution X-ray goniometry with burial.

Physical properties and AMS characteristics of ODP Site 185-1149 sediments

During Ocean Drilling Program Leg 185, we studied progressive changes of microfabrics of unconsolidated pelagic and hemipelagic sediments in Holes 1149A and 1149B in the northwest Pacific at 5818 m water depth. We paid particular attention to the early consolidation and diagenetic processes without tectonic deformation before the Pacific plate subduction at the Izu-Bonin Trench. Shape, size, and arrangement of pores were analyzed by scanning electron microscope (SEM) and were compared to anisotropy of magnetic susceptibility (AMS) data. The microfabric in Unit I is nondirectional fabric and is characterized by large peds of ~10-100 µm diameter, which are made up of clay platelets (mainly illite) and siliceous biogenic fragments. They are ovoid in shape and are mechanically packed by benthic animals. Porosity decreases from 0 to 60 meters below seafloor (mbsf) in Unit I (from 60% to 50%) in association with macropore size decreases. The microfabric of coarser grain particles other than clay in Unit II is characterized by horizontal preferred orientation because of depositional processes in Subunit IIA and burial compaction in Subunit IIB. On the other hand, small peds, which are probably made of fragments of fecal pellets and are composed of smectite and illite (3-30 µm diameter), are characterized by random orientation of clay platelets. The clay platelets in the small peds in Subunit IIA are in low-angle edge-to-face (EF) or face-to-face (FF) contact. These peds are electrostatically connected by long-chained clay platelets, which are interconnected by high-angle EF contact. Breaking of these long chains by overburden pressure diminishes the macropores, and the clay platelets in the peds become FF in contact, resulting in decreases in the volume of the micropores between clay platelets. Thus, porosity in Subunits IIA and IIB decreases remarkably downward. The AMS indicates random fabric and horizontal preferred orientation fabric in Units I and II, respectively. This result corresponds to that of SEM microfabric observations.In Subunit IIB, pressure solutions around radiolarian tests and clinoptilolite veins with normal displacement sense are seen distinctively below ~170 mbsf, probably in correspondence to the transition zone from opal-A to opal-CT.

Results from Purgatory Conglomerate investigations

Quartz Crystallographic Preferred Orientation (CPO) patterns are most commonly a result of deformation by dislocation creep. We investigated whether Dissolution-Precipitation Creep (DPC) a process that occur at lower differential stresses and temperatures, may result in CPO in quartz. Within the Purgatory Conglomerate, DPC led to quartz dissolution along cobble surfaces perpendicular to the shortening direction, and quartz precipitation in overgrowths at the ends of the cobbles (strain shadows), parallel to the maximum extension direction. The Purgatory Conglomerate is part of the SE Narragansett basin where strain intensity increases from west to east and is associated with top-to-the-west transport and folding during the Alleghanian orogeny. Quartz c-axis orientations as revealed by Electron Backscatter Diffraction (EBSD) methods, were random in all analyzed domains within the cobbles and strain shadows irrespective of the intensity of strain or metamorphic grade of the sample. Quartz dissolution probably occurred exclusively along the cobbles' margins, leaving the remaining grains unaffected by DPC. The fact that quartz precipitated in random orientations may indicate that the strain shadows were regions of little or no differential stress.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos–Jun–AP-1 complex may contribute to its functional versatility at different promoters.

Dynamics of Fos-Jun-NFAT1 complexes

Transcription initiation in eukaryotes is controlled by nucleoprotein complexes formed through cooperative interactions among multiple transcription regulatory proteins. These complexes may be assembled via stochastic collisions or defined pathways. We investigated the dynamics of Fos-Jun-NFAT1 complexes by using a multicolor fluorescence resonance energy transfer assay. Fos-Jun heterodimers can bind to AP-1 sites in two opposite orientations, only one of which is populated in mature Fos-Jun-NFAT1 complexes. We studied the reversal of Fos-Jun binding orientation in response to NFAT1 by measuring the efficiencies of energy transfer from donor fluorophores linked to opposite ends of an oligonucleotide to an acceptor fluorophore linked to one subunit of the heterodimer. The reorientation of Fos-Jun by NFAT1 was not inhibited by competitor oligonucleotides or heterodimers. The rate of Fos-Jun reorientation was faster than the rate of heterodimer dissociation at some binding sites. The facilitated reorientation of Fos-Jun heterodimers therefore can enhance the efficiency of Fos-Jun-NFAT1 complex formation. We also examined the influence of the preferred orientation of Fos-Jun binding on the stability and transcriptional activity of Fos-Jun-NFAT1 complexes. Complexes formed at sites where Fos-Jun favored the same binding orientation in the presence and absence of NFAT1 exhibited an 8-fold slower dissociation rate than complexes formed at sites where Fos-Jun favored the opposite binding orientation. Fos-Jun-NFAT1 complexes also exhibited greater transcription activation at promoter elements that favored the same orientation of Fos-Jun binding in the presence and absence of NFAT1. Thus, the orientation of heterodimer binding can influence both the dynamics and promoter selectivity of multiprotein transcription regulatory complexes.

Structural evolution of the Lesser Himalayan fold-thrust belt of west central Nepal

The Lesser Himalayan fold-thrust belt on the south flank of the Jajarkot klippe in west central Nepal was mapped in detail between the Main Central thrust in the north and the Main Boundary thrust in the south. South of the Jajarkot klippe, the fold-thrust belt involves sandstone, shale and carbonate rocks that are unmetamorphosed in the foreland and increase in metamorphic grade with higher structural position to sub-greenschist facies towards the hinterland. The exposed stratigraphy is correlative with the Proterozoic Ranimata, Sangram, Galyang, Syangia Formations and Lakharpata Group of Western Nepal and overlain by the Paleozoic Tansen and Kali Gandaki Groups. Based on field mapping and cross-section construction, three distinct thrust sheets were identified separated by top-to-the-south thrust faults. From the foreland (south) to the hinterland (north), the first thrust sheet in the immediate hanging wall of the Main Boundary thrust defines an open syncline. The second thrust sheet contains a very broad synformal duplex, which is structurally stacked against the third thrust sheet containing a homoclinal panel of the oldest exposed Proterozoic stratigraphy. Outcrop scale folds throughout the study area are predominantly south vergent, open, and asymmetric reflecting the larger regional scale folding style, which corroborate the top-to-the-south deformation style seen in the faults of the region. Field techniques were complemented with microstructural and quartz crystallographic c-axis preferred orientation analyses using a petrographic microscope and a fabric analyzer, respectively. Microstructural analysis identified abundant strain-induced recrystallization textures and occasional occurrences of top-to-the-south shear-sense indicators primarily in the hinterland rocks in the immediate footwall of the Main Central Thrust. Top-to-the-south shearing is also supported by quartz crystallographic c-axis preferred orientations. Quartz recrystallization textures indicate an increase in deformation temperature towards the Main Central thrust. A line balance estimate indicates that approximately 15 km of crustal shortening was accommodated by folding and faulting in the fold-thrust belt south of the Jajarkot klippe. Additionally, estimations of shortening velocity suggest that the shortening velocity operating in this section of the fold-thrust belt between 23 to 14 Ma was slower than what is currently observed as a result of the ongoing deformation of the Sub-Himalayan fold-thrust belt.

(Table 1) Physical properties at DSDP Hole 72-516F

Forty indurated sediment samples from Site 516 were studied to determine the cause of acoustic anisotropy in carbonate- bearing deep-sea sediments. Recovered from sub-bottom depths between 388 and 1222 m, the samples have properties exhibiting the following ranges: wet-bulk density, 1.90-2.49 g/cm3; fractional porosity, 0.45-0.14; carbonate content, 33-88%; compressional-wave velocity (at 0.1 kbar pressure), 1.87-4.87 km/s; and anisotropy, 1-13%. Velocities were measured in three mutually perpendicular directions through the same specimen in 29 of the 40 samples studied. Calcite fabric has been estimated by X-ray pole figure goniometry. The major findings of this study are: 1) Carbonate-bearing deep-sea sediments may be regarded as transversely isotropic media with symmetry axes normal to bedding. 2) Calcite c-axes are weakly concentrated in a direction perpendicular to bedding, but the preferred orientation of calcite does not contribute significantly to velocity anisotropy. 3) The properties of bedded and unbedded samples are distinctly different. Unbedded sediments exhibit low degrees of acoustic anisotropy (1-5%). By contrast, bedded samples show higher degrees of anisotropy (to 13%), and anisotropy increases markedly with depth of burial. Thus, bedding must be regarded as the principal cause of acoustic anisotropy in calcareous, deep-sea sediments.