Nitrogen incorporation into tetrahedral hydrogenated amorphous carbon

Structural changes induced by the incorporation of nitrogen into ta-C : H films have been studied by Electron Energy Loss Spectroscopy, X-Ray Photoelectron Spectroscopy, Fourier Transformed Infrared Spectroscopy and Ultraviolet-Visible Spectroscopy. ta-C:H films have been synthesised using a low pressure Electron Cyclotron Wave Resonance (ECWR) source which provides a plasma beam with a high degree of ionisation and dissociation. Nitrogen was incorporated by adding N2 to the C2H2 plasma used for the deposition of ta-C : H films. The N/C atomic ratio in the films rises rapidly until the N2/C2H2 gas ratio reaches three, and then increases more gradually, while the deposition rate decreases steeply. Chemical sputtering of the forming films and the formation of molecular nitrogen within the films limit the maximum nitrogen content to about N/C = 0.6. For low nitrogen content the films retain their diamond-like properties, however as N/C atomic ratio increases, a polymeric-like material is formed, with >C=N- structures and terminating C=N and NH groups that decrease the connectivity of the network.

Perturbation of the stability of amyloid fibrils through alteration of electrostatic interactions.

The self-assembly of proteins and peptides into polymeric amyloid fibrils is a process that has important implications ranging from the understanding of protein misfolding disorders to the discovery of novel nanobiomaterials. In this study, we probe the stability of fibrils prepared at pH 2.0 and composed of the protein insulin by manipulating electrostatic interactions within the fibril architecture. We demonstrate that strong electrostatic repulsion is sufficient to disrupt the hydrogen-bonded, cross-β network that links insulin molecules and ultimately results in fibril dissociation. The extent of this dissociation correlates well with predictions for colloidal models considering the net global charge of the polypeptide chain, although the kinetics of the process is regulated by the charge state of a single amino acid. We found the fibrils to be maximally stable under their formation conditions. Partial disruption of the cross-β network under conditions where the fibrils remain intact leads to a reduction in their stability. Together, these results support the contention that a major determinant of amyloid stability stems from the interactions in the structured core, and show how the control of electrostatic interactions can be used to characterize the factors that modulate fibril stability.

Physical and numerical modeling of horizontal gas-hydrate wells

Methane hydrate, which is usually found under deep seabed or permafrost zones, is a potential energy resource for future years. Depressurization of horizontal wells bored in methane hydrate layer is considered as one possible method for hydrate dissociation and methane extraction from the hosting soil. Since hydrate is likely to behave as a bonding material to sandy soils, supported well construction is necessary to avoid well-collapse due to the loss of the apparent cohesion during depressurization. This paper describes both physical and numerical modeling of such horizontal support wells. The experimental part involves depressurization of small well models in a large pressure cell, while the numerical part simulates the corresponding problem. While the experiment models simulate only gas saturated initial conditions, the numerical analysis simulates both gas-saturated and more realistic water-saturated conditions based on effective stress coupled flow-deformation formulation of these three phases. © 2006 Taylor & Francis Group.

Physical and numerical modeling of horizontal gas-hydrate wells

Methane hydrate, which is usually found under deep seabed or permafrost zones, is a potential energy resource for future years. Depressurization of horizontalwells bored in methane hydrate layer is considered as one possible method for hydrate dissociation and methane extraction from the hosting soil. Since hydrate is likely to behave as a bonding material to sandy soils, supported well construction is necessary to avoid wellcollapse due to the loss of the apparent cohesion during depressurization. This paper describes both physical and numerical modeling of such horizontal support wells. The experimental part involves depressurization of small well models in a large pressure cell, while the numerical part simulates the corresponding problem. While the experiment models simulate only gas saturated initial conditions, the numerical analysis simulates both gas-saturated and more realistic water-saturated conditions based on effective stress coupled flow-deformation formulation of these three phases. © 2006 Taylor & Francis Group, London.

Stress-strain response of hydrate-bearing sands: Numerical study using discrete element method simulations

Gas hydrate is a crystalline solid found within marine and subpermafrost sediments. While the presence of hydrates can have a profound effect on sediment properties, the stress-strain behavior of hydrate-bearing sediments is poorly understood due to inherent limitations in laboratory testing. In this study, we use numerical simulations to improve our understanding of the mechanical behavior of hydrate-bearing sands. The hydrate mass is simulated as either small randomly distributed bonded grains or as "ripened hydrate" forming patchy saturation, whereby sediment clusters with 100% pore-filled hydrate saturation are distributed within a hydrate-free sediment. Simulation results reveal that reduced sand porosity and higher hydrate saturation cause an increase in stiffness, strength, and dilative tendency, and the critical state line shifts toward higher void ratio and higher shear strength. In particular, the critical state friction angle increases in sands with patchy saturation, while the apparent cohesion is affected the most when the hydrate mass is distributed in pores. Sediments with patchy hydrate distribution exhibit a slightly lower strength than sediments with randomly distributed hydrate. Finally, hydrate dissociation under drained conditions leads to volume contraction and/or stress relaxation, and pronounced shear strains can develop if the hydrate-bearing sand is subjected to deviatoric loading during dissociation.

The effect of remodelling and contractility of the actin cytoskeleton on the shear resistance of single cells: a computational and experimental investigation.

The biomechanisms that govern the response of chondrocytes to mechanical stimuli are poorly understood. In this study, a series of in vitro tests are performed, in which single chondrocytes are subjected to shear deformation by a horizontally moving probe. Dramatically different probe force-indentation curves are obtained for untreated cells and for cells in which the actin cytoskeleton has been disrupted. Untreated cells exhibit a rapid increase in force upon probe contact followed by yielding behaviour. Cells in which the contractile actin cytoskeleton was removed exhibit a linear force-indentation response. In order to investigate the mechanisms underlying this behaviour, a three-dimensional active modelling framework incorporating stress fibre (SF) remodelling and contractility is used to simulate the in vitro tests. Simulations reveal that the characteristic force-indentation curve observed for untreated chondrocytes occurs as a result of two factors: (i) yielding of SFs due to stretching of the cytoplasm near the probe and (ii) dissociation of SFs due to reduced cytoplasm tension at the front of the cell. In contrast, a passive hyperelastic model predicts a linear force-indentation curve similar to that observed for cells in which the actin cytoskeleton has been disrupted. This combined modelling-experimental study offers a novel insight into the role of the active contractility and remodelling of the actin cytoskeleton in the response of chondrocytes to mechanical loading.

Increased gas production from hydrates by combining depressurization with heating of the wellbore

To extract gas from hydrate reservoirs, it has to be dissociated in situ. This endothermic dissociation process absorbs heat energy from the formation and pore fluid. The heat transfer governs the dissociation rate, which is proportional to the difference between the actual temperature and the equilibrium temperature. This study compares three potential gas production schemes from hydrate-bearing soil, where the radial heat transfer is governing. Cylindrical samples with 40% pore-filling hydrate saturation were tested. The production tests were carried out over 90 min by dissociating the hydrate from a centered miniature wellbore, by either lowering the pressure to 6, 4, or 6 MPa with simultaneous heating of the wellbore to 288 K. All tests were replicated by a numerical simulation. With additional heating at the same wellbore pressure, the gas production from hydrates could, on average, be increased by 1.8 and 3.6 times in the simulation and experiments, respectively. If the heat influx from the outer boundary is limited, a simulation showed that the specific heat of the formation is rapidly used up when the wellbore is only depressurized and not heated. © 2012 American Chemical Society.

Explicitly coupled thermal flow mechanical formulation for gas-hydrate sediments

This paper presents an explicit time-marching formulation for the solution of the coupled thermal flow mechanical behavior of gas- hydrate sediment. The formulation considers the soil skeleton as a deformable elastoplastic continuum, with an emphasis on the effect of hydrate (and its dissociation) on the stress-strain behavior of the soil. In the formulation, the hydrate is assumed to deform with the soil and may dissociate into gas and water. The formulation is explicitly coupled, such that the changes in temperature because of energy How and hydrate dissociation affect the skeleton stresses and fluid (water and gas) pressures. This, in return, affects the mechanical behavior. A simulation of a vertical well within a layered soil is presented. It is shown that the heterogeneity of hydrate saturation causes different rates of dissociation in the layers. The difference alters the overall gas production and also the mechanical-deformation pattern, which leads to loading/ unloading shearing along the interfaces between the layers. Copyright © 2013 Society of Petorlleum Engineers.

Cellular contractility and substrate elasticity: A numerical investigation of the actin cytoskeleton and cell adhesion

Numerous experimental studies have established that cells can sense the stiffness of underlying substrates and have quantified the effect of substrate stiffness on stress fibre formation, focal adhesion area, cell traction, and cell shape. In order to capture such behaviour, the current study couples a mixed mode thermodynamic and mechanical framework that predicts focal adhesion formation and growth with a material model that predicts stress fibre formation, contractility, and dissociation in a fully 3D implementation. Simulations reveal that SF contractility plays a critical role in the substrate-dependent response of cells. Compliant substrates do not provide sufficient tension for stress fibre persistence, causing dissociation of stress fibres and lower focal adhesion formation. In contrast, cells on stiffer substrates are predicted to contain large amounts of dominant stress fibres. Different levels of cellular contractility representative of different cell phenotypes are found to alter the range of substrate stiffness that cause the most significant changes in stress fibre and focal adhesion formation. Furthermore, stress fibre and focal adhesion formation evolve as a cell spreads on a substrate and leading to the formation of bands of fibres leading from the cell periphery over the nucleus. Inhibiting the formation of FAs during cell spreading is found to limit stress fibre formation. The predictions of this mutually dependent material-interface framework are strongly supported by experimental observations of cells adhered to elastic substrates and offer insight into the inter-dependent biomechanical processes regulating stress fibre and focal adhesion formation. © 2013 Springer-Verlag Berlin Heidelberg.

Numerical study on hydrate bearing sediments during gas production

The fully coupled methane hydrate model developed in Cambridge was adopted in this numerical study on gas production trial at the Eastern Nankai Trough, Japan 2013. Based on the latest experimental data of hydrate soil core samples, the clay parameters at Eastern Nankai site were successfully calibrated. With updated clay parameters and site geometry, a 50 days gas production trail was numerically simulated in FLAC2D. The geomechanical behaviour of hydrate bearing sediments under 3 different depressurization strategies were explored and discussed. The results from both axisymmetrical and plane-strain models suggest, the slope of the seabed only affects mechanical properties while no significant impact on the dissociation, temperature and pore pressure. For mechanical deformation after PT recovery, there are large settlements above the perforation zone and small uplift underneath the production zone. To validate the fully coupled model, numerical simulation with finer mesh in the hydrate production zone was carried out. The simulation results suggest good agreement between our model and JOE's results on history matching of gas and water production during trial. Parameter sensitivity of gas production is also investigated and concluded the sea water salinity is a dominant factor for gas production.