Size effects in indentation of hydrated biological tissues

Fluid flow in biological tissues is important in both mechanical and biological contexts. Given the hierarchical nature of tissues, there are varying length scales at which time-dependent mechanical behavior due to fluid flow may be exhibited. Here, spherical nanoindentation and microindentation testings are used for the characterization of length scale effects in the mechanical response of hydrated tissues. Although elastic properties were consistent across length scales, there was a substantial difference between the time-dependent mechanical responses for large and small contact radii in the same tissue specimens. This difference was far more obvious when poroelastic analysis was used instead of viscoelastic analysis. Overall, indentation testing is a fast and robust technique for characterizing the hierarchical structure of biological materials from nanometer to micrometer length scales and is capable of making quantitative material property measurements to do with fluid flow. © 2011 Materials Research Society.

Monitoring offshore pipelines using forced transverse vibration: Data analysis

Vibration methods are used to identify faults, such as spanning and loss of cover, in long off-shore pipelines. A pipeline `pig', propelled by fluid flow, generates transverse vibration in the pipeline and the measured vibration amplitude reflects the nature of the support condition. Large quantities of vibration data are collected and analyzed by Fourier and wavelet methods.

Biofluid behaviour in 3D microchannel systems: Numerical analysis and design development of 3D microchannel biochip separators

This paper describes the design and development cycle of a 3D biochip separator and the modelling analysis of flow behaviour in the biochip microchannel features. The focus is on identifying the difference between 2D and 3D implementations as well as developing basic forms of 3D microfluidic separators. Five variants, based around the device are proposed and analysed. These include three variations of the branch channels (circular, rectangular, disc) and two variations of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming steady state flow has been established, the efficiencies of the flow between the main and side channels for the different designs are analysed and compared with regard to relevant biomicrofluidic laws or effects (bifurcation law, Fahraeus effect, cell-free phenomenon, bending channel effect and laminar flow behaviour). The modelling results identify flow features in microchannels, a constriction and bifurcations and show detailed differences in flow fields between the various designs. The manufacturing process using injection moulding for the initial base case design is also presented and discussed. The work reported here is supported as part of the UK funded 3D-MINTEGRATION project. © 2010 IEEE.

Separating poroviscoelastic deformation mechanisms in hydrogels

Hydrogels have applications in drug delivery, mechanical actuation, and regenerative medicine. When hydrogels are deformed, load-relaxation arising from fluid flow - poroelasticity - and from rearrangement of the polymer network - viscoelasticity - is observed. The physical mechanisms are different in that poroelastic relaxation varies with experimental length-scale while viscoelastic does not. Here, we show that poroviscoelastic load-relaxation is the product of the two individual responses. The difference in length-scale dependence of the two mechanisms can be exploited to uniquely determine poroviscoelastic properties from simultaneous analysis of multi-scale indentation experiments, providing insight into hydrogel physical behavior. © 2013 American Institute of Physics.

Numerical simulation of single-stream jets from a serrated nozzle

Hybrid large-eddy type simulations for cold jet flows from a serrated nozzle are performed at an acoustic Mach number Ma ac = 0.9 and Re = 1.03×10 6. Since the solver being used tends towards having dissipative qualities, the subgrid scale (SGS) model is omitted, giving a numerical type LES (NLES) or implicit LES (ILES) reminiscent procedure. To overcome near wall streak resolution problems a near wall RANS (Reynolds averaged Navier-Stokes) model is smoothly blended to the LES making a hybrid RANS-ILES. The geometric complexity of the serrated nozzle is fully considered without simplification or emulation. An improved but still modest hexahedral multi-block grid with circa 20 million grid points (with respect to 12.5 million in Xia et al.; Int J Heat Fluid Flow 30:1067-1079, 2009) is used. Despite the modest grid size, encouraging and improved results are obtained. Directly resolved mean and second-order fluctuating quantities along the jet centerline and in the jet shear layer compare favorably with measurements. The radiated far-field sound predicted using the Ffowcs Williams and Hawkings (FW-H) surface integral method shows good agreement with the measurements in directivity and sound spectra. © 2011 Springer Science+Business Media B.V.

Semi-implicit second order finite volume jet stream computations

Semi-implicit, second order temporal and spatial finite volume computations of the flow in a differentially heated rotating annulus are presented. For the regime considered, three cyclones and anticyclones separated by a relatively fast moving jet of fluid or "jet stream" are predicted. Two second order methods are compared with, first order spatial predictions, and experimental measurements. Velocity vector plots are used to illustrate the predicted flow structure. Computations made using second order central differences are shown to agree best with experimental measurements, and to be stable for integrations over long time periods (> 1000s). No periodic smoothing is required to prevent divergence.

Mechanical and hydraulic properties of Nankai accretionary prism sediments: Effect of stress path

We have conducted triaxial deformation experiments along different loading paths on prism sediments from the Nankai Trough. Different load paths of isotropic loading, uniaxial strain loading, triaxial compression (at constant confining pressure, Pc), undrained Pc reduction, drained Pc reduction, and triaxial unloading at constant Pc, were used to understand the evolution of mechanical and hydraulic properties under complicated stress states and loading histories in accretionary subduction zones. Five deformation experiments were conducted on three sediment core samples for the Nankai prism, specifically from older accreted sediments at the forearc basin, underthrust slope sediments beneath the megasplay fault, and overthrust Upper Shikoku Basin sediments along the frontal thrust. Yield envelopes for each sample were constructed based on the stress paths of Pc-reduction using the modified Cam-clay model, and in situ stress states of the prism were constrained using the results from the other load paths and accounting for horizontal stress. Results suggest that the sediments in the vicinity of the megasplay fault and frontal thrust are highly overconsolidated, and thus likely to deform brittle rather than ductile. The porosity of sediments decreases as the yield envelope expands, while the reduction in permeability mainly depends on the effective mean stress before yield, and the differential stress after yield. An improved understanding of sediment yield strength and hydromechanical properties along different load paths is necessary to treat accurately the coupling of deformation and fluid flow in accretionary subduction zones. © 2012 American Geophysical Union All Rights Reserved.

Large eddy simulations in low-pressure turbines: Effect of wakes at elevated free-stream turbulence

The transition of a separated shear layer over a flat plate, in the presence of periodic wakes and elevated free-stream turbulence (FST), is numerically investigated using Large Eddy Simulation (LES). The upper wall of the test section is inviscid and specifically contoured to impose a streamwise pressure distribution over the flat plate to simulate the suction surface of a low-pressure turbine (LPT) blade. Two different distributions representative of a 'high-lift' and an 'ultra high-lift' turbine blade are examined. Results obtained from the current LES compare favourably with the extensive experimental data previously obtained for these configurations. The LES results are then used to further investigate the flow physics involved in the transition process.In line with experimental experience, the benefit of wakes and FST obtained by suppressing the separation bubble, is more pronounced in 'ultra high-lift' design when compared to the 'high-lift' design. Stronger 'Klebanoff streaks' are formed in the presence of wakes when compared to the streaks due to FST alone. These streaks promoted much early transition. The weak Klebanoff streaks due to FST continued to trigger transition in between the wake passing cycles.The experimental inference regarding the origin of Klebanoff streaks at the leading edge has been confirmed by the current simulations. While the wake convects at local free-stream velocity, its impression in the boundary layer in the form of streaks convects much slowly. The 'part-span' Kelvin-Helmholtz structures, which were observed in the experiments when the wake passes over the separation bubble, are also captured. The non-phase averaged space-time plots manifest that reattachment is a localized process across the span unlike the impression of global reattachment portrayed by phase averaging. © 2013 Elsevier Inc.

Age-related changes in mouse bone permeability.

The determination of lacunar-canalicular permeability is essential for understanding local fluid flow in bone, which may indicate how bone senses changes in the mechanical environment to regulate mechano-adaptation. The estimates of lacunar-canalicular permeability found in the literature vary by up to eight orders of magnitude, and age-related permeability changes have not been measured in non-osteonal mouse bone. The objective of this study is to use a poroelastic approach based on nanoindentation data to characterize lacunar-canalicular permeability in murine bone as a function of age. Nine wild type C57BL/6 mice of different ages (2, 7 and 12 months) were used. Three tibiae from each age group were embedded in epoxy resin, cut in half and indented in the longitudinal direction in the mid-cortex using two spherical fluid indenter tips (R=238 μm and 500 μm). Results suggest that the lacunar-canalicular intrinsic permeability of mouse bone decreases from 2 to 7 months, with no significant changes from 7 to 12 months. The large indenter tip imposed larger contact sizes and sampled larger ranges of permeabilities, particularly for the old bone. This age-related difference in the distribution was not seen for indents with the smaller radius tip. We conclude that the small tip effectively measured lacunar-canalicular permeability, while larger tip indents were influenced by vascular permeability. Exploring the age-related changes in permeability of bone measured by nanoindentation will lead to a better understanding of the role of fluid flow in mechano-transduction. This understanding may help indicate alterations in bone adaptation and remodeling.

Age-related changes in mouse bone permeability

The determination of lacunar-canalicular permeability is essential for understanding local fluid flow in bone, which may indicate how bone senses changes in the mechanical environment to regulate mechano-adaptation. The estimates of lacunar-canalicular permeability found in the literature vary by up to eight orders of magnitude, and age-related permeability changes have not been measured in non-osteonal mouse bone. The objective of this study is to use a poroelastic approach based on nanoindentation data to characterize lacunar-canalicular permeability in murine bone as a function of age. Nine wild type C57BL/6 mice of different ages (2, 7 and 12 months) were used. Three tibiae from each age group were embedded in epoxy resin, cut in half and indented in the longitudinal direction in the mid-cortex using two spherical fluid indenter tips (R=238 μm and 500 μm). Results suggest that the lacunar-canalicular intrinsic permeability of mouse bone decreases from 2 to 7 months, with no significant changes from 7 to 12 months. The large indenter tip imposed larger contact sizes and sampled larger ranges of permeabilities, particularly for the old bone. This age-related difference in the distribution was not seen for indents with the smaller radius tip. We conclude that the small tip effectively measured lacunar-canalicular permeability, while larger tip indents were influenced by vascular permeability. Exploring the age-related changes in permeability of bone measured by nanoindentation will lead to a better understanding of the role of fluid flow in mechano-transduction. This understanding may help indicate alterations in bone adaptation and remodeling. © 2013 Elsevier Ltd.

Short and long peptidoglycan recognition proteins (PGRPs) in zebrafish, with findings of multiple PGRP homologs in teleost fish

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. Using a database mining approach and RT-PCR, multiple peptidoglycan recognition protein (PGRP) like genes have been discovered in fish including zebrafish Danio rerio, Japanese pufferfish TakiFugu rubripes and spotted green pufferfish Tetraodon nigroviridis. They share the common features of those PGRPs in arthropod and mammals, by containing a conserved PGRP domain. Based on the predicted structures, the identified zebrafish PGRP homologs resemble short and long PGRP members in arthropod and mammals. The identified PGRP genes in T. nigroviridis and TakiFugu rubripes resemble the long PGRPs, and the short PGRP genes have not been found in T. nigroviridis and TakiFugu rubripes databases. Computer modelling of these molecules revealed the presence of three alpha-helices and five or six beta-strands in all fish PGRPs reported in the present study. The long PGRP in teleost fish have multiple alternatively spliced forms, and some of the identified spliced variants, e.g., tnPGRP-L3 and tnPGRP-L4 (in: Tetraodon nigroviridis), exhibited no characters present in the PGRP homologs domain. The coding regions of zfPGRP6 (zf: zebrafish), zfPGRP2-A, zfPGRP2-B and zfPGRP-L contain five exons and four introns; however, the other PGRP-like genes including zfPGRPSC1a, zfPGRPSC2, tnPGRP-L1-, tnPGRP-L2 and frPGRP-L (fr: Takifugu rubripes) contain four exons and three introns. In zebrafish, long and short PGRP genes identified are located in different chromosomes, and an unknown locus containing another long PGRP-like gene has also been found in zebrafish, demonstrating that multiple PGRP loci may be present in fish. In zebrafish, the constitutive expressions of zfPGRP-L, zfPGRP-6 and zfPGRP-SC during ontogeny from unfertilized eggs to larvae, in different organs of adult, and the inductive expression following stimulation by Flavobacterium columnare, were detected by real-time PCR, but the levels and patterns varied for different PGRP genes, implying that different short and long PGRPs may play different roles in innate immune response. (c) 2007 Elsevier Ltd. All rights reserved.