Structural Insights into Viral Membrane Fusion Machinery via Cryo-Electron Tomography: Influenza Virus and Human Parainfluenza Virus

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

Martensite Crystallography - the apparent controversy between the infinitesimal deformation approach and the phenomenological theory of martensitic transformations

The aim of this article is to demonstrate that the apparent controversy between the infinitesimal deformation (ID) approach and the phenomenological theory of martensitic transformations (PTMTs) in predicting the crystallographic characteristics of a martensitic transformation is entirely based on unjustified approximations associated with the way in which the ID calculations are performed. When applied correctly, the ID approach is shown to be absolutely identical to the PTMT. Nevertheless, there may be some advantages in using the ID approach. In particular, it is somewhat simpler than the PTMT; it is based on a physical concept that is easier to understand and, most important, it may provide a tool for investigating some of the features of martensitic transformations that have eluded explanation via the PTMT.

Partitioning of deformation within a subduction channel during exhumation of high-pressure rocks: a case study from the Western Alps

The metamorphic belt of the Western Alps was subjected to widespread extensional tectonism at the end of the Eocene (ca. 45-35 Ma). Extension was accommodated by hinterland-directed movements along gently inclined extensional shear zones, which facilitated rapid exhumation of high-pressure and ultra-high-pressure rocks. This deformation resulted in a normal metamorphic sequence. Extension in the inner parts of the Western Alps was coeval with shortening at the front of the belt (foreland-directed thrusts), which took place during decompression, and emplaced higher grade metamorphic units over lower grade metamorphic rocks, thus forming an inverse metamorphic sequence. Two mechanisms for this extensional episode are discussed: (1) collapse of an overthickened lithosphere, and (2) internal readjustments within the orogenic wedge due to subduction channel dynamics. We favour the latter mechanism because it can account for the development of the observed inverse and normal metamorphic sequences along foreland-directed thrusts and hinterland-directed detachments, respectively. This hypothesis is supported by published structural, metamorphic and geochronological data from four geological transects through the Western Alps. This study also emphasizes the importance of post-shearing deformation (e.g. horizontal buckling versus vertical flattening), which can modify the distribution of hinterland- and foreland-directed shear zones in orogenic belts. (c) 2006 Elsevier Ltd. All rights reserved.

Structural behaviour of glass reinforced plastics

The aim of this research is to promote the use of G.R.P. as a structural material. In the past, the use of G.R.P. has been confined to non-load carrying applications. Such uses are still rapidly increasing but in addition significant changes have been made during the last decade in the development of semi-structural and now even fully structural applications. Glass-reinforced plastic is characterized by a high strength but a relatively low modulus of elasticity. For this reasona G.R.P. structure can expect to show large deformations as a result of which the individual structural members will fail under load due to a loss of stability rather than approaching the ultimate strength of the material. For this reason the selection of the geometrical shapes of G.R.P. structural elements is considered to be an important factor in designing G.R.P. structures. The first chapter of this thesis deals with a general review of the theoretical and experimental methods used to describe the structural properties of G.R.P. The research programme includes five stages dealing with the structural behaviour of G.R.P. The first stage (Chapter 2) begins with selecting and designing an optimum box beam cross-section which gives the maximum flexural and torsional rigidity. The second stage of investigation (Chapter 3) deals with beam to beam connections. A joint was designed and manufactured with different types of fasteners used to connect two beam units. A suitable fastener was selected and the research extended to cover the behaviour of long span beams using multiple joints. The third part of the investigation includes a study of the behaviour of box beams subjected to combined bending, shear and torsion. A special torque rig was developed to perform the tests. Creep deformation of 6 m span G.R.P. was investigated as the fourth stage under a range of loading conditions. As a result of the phenomenon of post buckling behaviour exhibited in the compression flange during testing of box beams during earlier stages of the investigation it was decided to consider this phenomenon in more detail in the final stage of the investigation. G.R.P. plates with different fibre orientation were subjected to uniaxial compression and tested up to failure. In all stages of the investigation theoretical predictions and experimental results were compared and generally good correlation between theory and experimental data was observed.

The structural properties of glassfibre reinforced plastics

The research work described in this thesis is concerned with the development of glassfibre reinforced plastics for structural uses in Civil Engineering construction. The first stage was primarily concerned with the design of GRP lamintes with structura1 properties and method of manufacture suitable for use with relatively large structural components. A cold setting, pressure moulding technique was developed which proved to be efficient in reducing the void content in the composite and minimising the exothermic effect due to curing. The effect of fibre content and fibre arrangement on strength and stiffness of the cornposite was studied and the maximum amount of' fibre content that could be reached by the adopted type of moulding technique was determined. The second stage of the project was concerned with the introduction of steel-wire "sheets" into the GRP cornposites, to take advantage of the high modulus of steel wire to improve the GRP stiffness and to reduce deformation. The experimental observations agreed reasonably well with theoretical predictions in both first and second stages of the work. The third stage was concerned with studying the stability of GRP flat rectangular plates subjected to uniaxial compression or pure shear, to simulate compression flanges or shear webs respectively. The investigation was concentrated on the effect of fibre arrangement in the plate on buckling load. The effect of the introduction of steel-wire sheets on the plate stability in compression was also investigated. The boundary conditions were chosen to be close to those usually assumed in built-up box-sections for both compression flanges and webs. The orthotropic plate and the mid-plane symmetric were used successfully in predicting the buckling load theoretically. In determining the buckling load experimentally, two methods were used. The Southwell plot method and electrical strain gauge method. The latter proved to be more reliable in predicting the buckling load than the former, especially for plates under uniaxial compression. Sample design charts for GRP plates that yield and buckle simultaneously under compression are also presented in the thesis. The final stage of the work dealt with the design and test of GRP beams. The investigation began by finding the optimum cross-section for a GRP beam. The cross-section which was developed was a thin walled corrugated section which showed higher stiffness than other cross-sections for the same cross-sectional area (i.e. box, I, and rectangular sections). A cold setting, hand layings technique was used in manufacturing these beams wbich were of nine types depending on the type of glass reinforcement employed and the arrangement of layers in the beam. The simple bending theory was used in the beam design and proved to be satisfactory in predicting the stresses and deflections. A factor of safety of 4 was chosen for design purposes and considered to be suitable for long term use under static load. Because of its relatively low modulus, GRP beams allowable deflection was limited to 1/120th of the span which was found to be adequate for design purposes. A general discussion of the behaviour of GRP composites and their place relative to the more conventional structural material was also presented in the thesis.

Deformation microstructures and recrystallization in heavily worked copper

Deformation microstructures in two batches of commercially pure copper (A and B) of allnost similar composition have been studied after rolling reductions from 5% to 95%. X- ray diffraction, optical metallography, scanning electron microscopy in the back-scattered mode, transmission and scanning electron microscopy have been used to examine the deformation microstructure. At low strains (~10 %) the deformation is accommodated by uniform octahedral slip. Microbands that occur as sheet like features usually on the {111} slip planes are formed after 10% reduction. The misorientations between rnicrobonds ond the matrix are usually small (1 - 2° ) and the dislocations within the bands suggest that a single slip system has been operative. The number of microbands increases with strain, they start to cluster and rotate after 60% reduction and, after 90 %, they become almost perfectly aligned with the rolling direction. There were no detectable differences in deformation microstructure between the two materials up to a deformation level of 60% but subsequently, copper B started to develop shear bands which became very profuse by 90% reduction. By contrast, copper A at this stage of deformation developed a smooth laminated structure. This difference in the deformation microstructures has been attributed to traces of unknown impurity in D which inhibit recovery of work hardening. The preferred orientations of both were typical of deformed copper although the presence of shear bands was associated wth a slightly weaker texture. The effects of rolling temperature and grain size on deformation microstructure were also investigated. It was concluded that lowering the rolling temperature or increasing the initial grain size encourages the material to develop shear bands after heavy deformation. Recovery and recrystallization have been studied in both materials during annealing. During recrystallization the growth of new grains showed quite different characteristics in the two cases. Where shear bands were present these acted as nucleation sites and produced a wide spread of recrystallized grain orientations. The resulting annealing textures were very weak. In the absence of shear bands, nucleation occurs by a remarkably long range bulging process which creates the cube orientation and an intensely sharp annealing texture. Cube oriented regions occur in long bands of highly elongated and well recovered cells which contain long range cumulative micorientations. They are transition bands with structural characteristics ideally suited for nucleation of recrystallization. Shear banding inhibits the cube texture both by creating alternative nuclei and by destroying the microstructural features necessary for cube nucleation.

Industrial structural geology : principles, techniques and integration : an introduction

The authors wish to acknowledge the generous financial support provided in association with this volume to the Geological Society and the Petroleum Group by Badley Geoscience Ltd, BP, CGG Robertson, Dana Petroleum Ltd, Getech Group plc, Maersk Oil North Sea UK Ltd, Midland Valley Exploration Ltd, Rock Deformation Research (Schlumberger) and Borehole Image & Core Specialists (Wildcat Geoscience, Walker Geoscience and Prolog Geoscience). We would like to thank the fine team at the Geological Society’s Publishing House for the excellent support and encouragement that they have provided to the editors and authors of this Special Publication.

Industrial structural geology : principles, techniques and integration : an introduction

The authors wish to acknowledge the generous financial support provided in association with this volume to the Geological Society and the Petroleum Group by Badley Geoscience Ltd, BP, CGG Robertson, Dana Petroleum Ltd, Getech Group plc, Maersk Oil North Sea UK Ltd, Midland Valley Exploration Ltd, Rock Deformation Research (Schlumberger) and Borehole Image & Core Specialists (Wildcat Geoscience, Walker Geoscience and Prolog Geoscience). We would like to thank the fine team at the Geological Society’s Publishing House for the excellent support and encouragement that they have provided to the editors and authors of this Special Publication.

Sedimentary and structural controls on seismogenic slumping within mass transport deposits from the Dead Sea basin

GIA acknowledges funding from the Carnegie Trust to undertake fieldwork for this project. SM acknowledges the Israel Science Foundation (ISF grant no. 1436/14) and the Ministry of National Infrastructures, Energy and Water Resources (grant no. #214-17-027). RW was supported by the Israel Science Foundation (ISF grant no. 1245/11). We thank Hugo Ortner and Pedro Alfaro for careful and constructive reviews.

Stochastically forced dislocation density distribution in plastic deformation

The dynamical evolution of dislocations in plastically deformed metals is controlled by both deterministic factors arising out of applied loads and stochastic effects appearing due to fluctuations of internal stress. Such type of stochastic dislocation processes and the associated spatially inhomogeneous modes lead to randomness in the observed deformation structure. Previous studies have analyzed the role of randomness in such textural evolution but none of these models have considered the impact of a finite decay time (all previous models assumed instantaneous relaxation which is "unphysical") of the stochastic perturbations in the overall dynamics of the system. The present article bridges this knowledge gap by introducing a colored noise in the form of an Ornstein-Uhlenbeck noise in the analysis of a class of linear and nonlinear Wiener and Ornstein-Uhlenbeck processes that these structural dislocation dynamics could be mapped on to. Based on an analysis of the relevant Fokker-Planck model, our results show that linear Wiener processes remain unaffected by the second time scale in the problem but all nonlinear processes, both Wiener type and Ornstein-Uhlenbeck type, scale as a function of the noise decay time τ. The results are expected to ramify existing experimental observations and inspire new numerical and laboratory tests to gain further insight into the competition between deterministic and random effects in modeling plastically deformed samples.

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.

Simulating Granite Emplacement and Deformation with Centrifuge Analogue Modelling

The Greater Himalayan leucogranites are a discontinuous suite of intrusions emplaced in a thickened crust during the Miocene southward ductile extrusion of the Himalayan metamorphic core. Melt-induced weakening is thought to have played a critical role in strain localization that facilitated the extrusion. Recent advancements in centrifuge analogue modelling techniques allow for the replication of a broader range of crustal deformation behaviors, enhancing our understanding of large hot orogens. Polydimethylsiloxane (PDMS) is commonly used in centrifuge experiments to model weak melt zones. Difficulties in handling PDMS had, until now, limited its emplacement in models prior to any deformation. A new modelling technique has been developed where PDMS is emplaced into models that have been subjected to some shortening. This technique aims to better understand the effects of melt on strain localization and potential decoupling between structural levels within an evolving orogenic system. Models are subjected to an early stage of shortening, followed by the introduction of PDMS, and then a final stage of shortening. Theoretical percentages of partial melt and their effect on rock strength are considered when adding a specific percentage of PDMS in each model. Due to the limited size of the models, only PDMS sheets of 3 mm thickness were used, which varied in length and width. Within undeformed packages, minimal surface and internal deformation occurred when PDMS is emplaced in the lower layer of the model, showing a vertical volume increase of ~20% within the package; whereas the emplacement of PDMS into the middle layer showed internal dragging of the middle laminations into the lower layer and a vertical volume increase ~30%. Emplacement of PDMS results in ~7% shortening for undeformed and deformed models. Deformed models undergo ~20% additional shortening after two rounds of deformation. Strain localization and decoupling between units occur in deformed models where the degree of deformation changes based on the amount of partial melt present. Surface deformation visible by the formation of a bulge, mode 1 extension cracks and varying surface strain ellipses varies depending if PDMS is present. Better control during emplacement is exhibited when PDMS is added into cooler models, resulting in reduced internal deformation within the middle layer.

Deformation mechanisms in second-phase affected microstructures and their energy balance

Based on the relationship Zener parameter (Z=second-phase size/second-phase volume fraction) vs. calcite grain size (dg), second-phase controlled aggregates and microstructures that are weakly affected by second-phases are discriminated. The latter are characterized by large but constant grain sizes, high calcite grain boundary fractions and crystallographic preferred orientations (CPO), while calcite grain size and calcite grain boundary fraction decrease continuously and CPO weakens with decreasing Z in second-phase controlled microstructures. These observations suggest that second-phase controlled microstructures predominantly deform via granular flow because pinning of calcite grain boundaries reduces the efficiency of dynamic recrystallization favoring mass transfer processes and grain boundary sliding. In contrast, the balance of grain size reduction and growth by dynamic recrystallization maintains a steady state grain size in microstructures that are only weakly affected by second-phases promoting a predominance of dislocation creep. With increasing temperature, the relationship between Z and dg persists but the calcite grain size increases continuously. Based on microstructures, the energy of each modifying process is calculated and its relative contribution is compared with energies of the competing processes (surface energy, dragging energy, dynamic recrystallization energy). The steady state microstructures result from a temperature-dependent energy minimization procedure of the system.

The influence of nano-scale second-phase particles on deformation of fine grained calcite mylonites

Grey and white carbonate mylonites were collected along thrust planes of the Helvetic Alps. They are characterised by very small grain sizes and non-random grain shape (SPO) and crystallographic preferred orientation (CPO). Presumably they deformed in the field of grain size sensitive flow by recrystallisation accommodated intracrystalline deformation in combination with granular flow. Both mylonites show a similar mean grain size, but in the grey mylonites the grain size range is larger, the grain shapes are more elongate and the dynamically recrystallised calcite grains are more often twinned. Grey mylonites have an oblique CPO, while the CPO in white mylonites is symmetric with respect to the shear plane. Combustion analysis and TEM investigations revealed that grey mylonites contain a higher amount of highly structured kerogens with particle sizes of a few tens of nanometers, which are finely dispersed at the grain boundaries. During deformation of the rock, nano-scale particles reduced the migration velocity of grain boundaries by Zener drag resulting in slower recrystallisation rates of the calcite aggregate. In the grey mylonites, more strain increments were accommodated by individual grains before they became refreshed by dynamic recrystallisation than in white mylonites, where grain boundary migration was less hindered and recrystallisation cycles were faster. Consequently, grey mylonites represent ‘deformation’ microfabrics while white mylonites are characterised by ‘recrystallisation’ microfabrics. Field geologists must utilise this different deformation behavior when applying the obliquity in CPO and SPO of the respective mylonites as reliable shear sense indicators.

Inverse identification of the bending stiffness of a braided polyethylene twine subject to large deformation: application to the identification of the mesh opening rigidity of fishing nets.

The evaluation of the mesh opening stiffness of fishing nets is an important issue in assessing the selectivity of trawls. It appeared that a larger bending rigidity of twines decreases the mesh opening and could reduce the escapement of fish. Nevertheless, netting structure is complex. A netting is made up of braided twines made of polyethylene or polyamide. These twines are tied with non-symmetrical knots. Thus, these assemblies develop contact-friction interactions. Moreover, the netting can be subject to large deformation. In this study, we investigate the responses of netting samples to different types of solicitations. Samples are loaded and unloaded with creep and relaxation stages, with different boundary conditions. Then, two models have been developed: an analytical model and a finite element model. The last one was used to assess, with an inverse identification algorithm, the bending stiffness of twines. In this paper, experimental results and a model for netting structures made up of braided twines are presented. During dry forming of a composite, for example, the matrix is not present or not active, and relative sliding can occur between constitutive fibres. So an accurate modelling of the mechanical behaviour of fibrous material is necessary. This study offers experimental data which could permit to improve current models of contact-friction interactions [4], to validate models for large deformation analysis of fibrous materials [1] on a new experimental case, then to improve the evaluation of the mesh opening stiffness of a fishing net