c-axis preferential orientation of hydroxyapatite accounts for the high wear resistance of the teeth of black carp (Mylopharyngodon piceus)

Biological armors such as mollusk shells have long been recognized and studied for their values in inspiring novel designs of engineering materials with higher toughness and strength. However, no material is invincible and biological armors also have their rivals. In this paper, our attention is focused on the teeth of black carp (Mylopharyngodon piceus) which is a predator of shelled mollusks like snails and mussels. Nanoscratching test on the enameloid, the outermost layer of the teeth, indicates that the natural occlusal surface (OS) has much higher wear resistance compared to the other sections. Subsequent X-ray diffraction analysis reveals that the hydroxyapatite (HAp) crystallites in the vicinity of OS possess c-axis preferential orientation. The superior wear resistance of black carp teeth is attributed to the c-axis preferential orientation of HAp near the OS since the (001) surface of HAp crystal, which is perpendicular to the c-axis, exhibits much better wear resistance compared to the other surfaces as demonstrated by the molecular dynamics simulation. Our results not only shed light on the origin of the good wear resistance exhibited by the black carp teeth but are of great value to the design of engineering materials with better abrasion resistance

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Wake Dynamics Study of an H-type Vertical Axis Wind Turbine

Recent developments in wind energy have identified vertical axis wind turbines as a favored candidate for megawatt-scale offshore systems. Compared with the direct horizontal axis competitors they poss higher potentials for scalability and mechanical simplicity. The wake dynamics of an H-type vertical axis wind turbine is investigated using Particle Image Velocimetry (PIV). The experiments are conducted in an open jet wind tunnel with a turbine model of 1 m diameter constituted of 2 straight blades generated from a NACA0018. The turbine model is operated at a tip speed ratio of 4.5 and at a maximum chord Reynolds of 210,000. Two-component planar PIV measurements at the mid-span plane focus on vorticity shedding and horizontal wake expansion. Stereoscopic PIV measurements at 7 cross-stream vertical planes are performed to study tip vortex dynamics and evolution of 3D wake structures. Measurement at the turbine mid-span plane shows that the roll-up of shed vortex is triggered by wake interactions. Vorticity decay is asymmetrical with the faster decay rate at the leeward side. The faster windward wake expansion is attributed to the windward deflection of the tower wake. Wake recovery has not been observed in the horizontal measurement plane up to 4R downstream of the rotor. Experimental results on the vertical planes show that the tip vortex is stronger than the shed vortex in the horizontal plane. The strongest tip vortex is produced near the turbine axial plane (y/R = 0), and the in-rotor vorticity decay accounts for 60% - 90% of the overall decay. Near y/R = 0, tip vortices move inboard behind the rotor, whereas the turbine tower and the horizontal struts obstruct the inboard motion within the rotor swept volume. The rate of inboard motion is proportional to the vorticity strength. Due to weak vortex strength and strong blade blockage, tip vortices move outboard at two sides of the rotor primarily towards the windward side. Roll-over of vortex pairs contributes to the breakdown of vortical structure behind the rotor. Vertical wake recovery begins 4R downstream of the rotor, and the fastest recovery is observed near y/R = 0.Aerospace EngineeringAerodynamics & Wind Energ

Comparison of some preconditioners for the incompressible Navier-Stokes equations

In this report we explore the performance of the SIMPLER , augmented Lagrangian, ’grad-div’ preconditioners and their variants for the two-by-two block systems arising in the incompressible Navier-Stokes equations. The lid-driven cavity and flow over a finite flat plate are chosen as the benchmark problems. For each problem Reynolds number varies from a low to the limiting number for a laminar flow.Delft Institute of Applied MathematicsElectrical Engineering, Mathematics and Computer Scienc

How important is mud transport on large scale estuarine and deltaic morphodynamics?

Sediment transport provides a critical bridge between hydrodynamics and morphodynamics. Sediment transport behaviour has obvious impacts on morphodynamic development. Long-term morphodynamic modelling enables examination of large scale morphological patterns, such as channel-shoal patterns in estuaries and deltaic channel structures. Non-cohesive sand is mostly used as the material in shaping morphology. However, most of estuaries and deltas in nature are partly or fully dominated by cohesive sediment or mud. There are researches on sand-mud interactions and their implications on total sediment transport (van Ledden, 2003). It is increasingly aware that adding mud to the system can make a big differences on the large scale morphodynamic development behaviour (Edmond and Slinger, 2009; Gelynese et al., 2010; Caldwel and Edmond, 2014). However mud transport is notoriously difficult to be defined properly in the model given the combined sensitivity to a few fundamental parameters (Partheniades, 1965; Mehta, 2014). It is thus not clearly known how mud have controls on development of large scale morphodynamics and the sensitivity to the mud property.Coastal Engineerin

Comprehensive validation of three-dimensional finite element modelling of wheel-rail high-frequency interaction via the V-Track test rig

Wheel-rail high-frequency interaction is closely related to the formation of railway short-wave defects. Finite element (FE) method has been widely used to simulate wheel-rail dynamic systems, but its validity in modelling high-frequency interaction has not been fully demonstrated in three dimensions (3D). This work aims at comprehensively validating the 3D FE modelling of wheel-rail high-frequency interaction using a downscale V-Track test rig. First, the FE model of the V-Track is developed that comprehensively includes the 3D track elasticity. The simulated track dynamic behaviours are validated against hammer tests, and the major vibration modes are analyzed employing modal analysis. Afterwards, the simulate wheel-rail dynamic responses are comprehensively compared with measurement results up to 10 kHz. Their characteristic frequencies are identified and correlated to the eigenmodes of the vehicle-track system. The results indicate that the proposed 3D FE model is capable of comprehensively and accurately simulating the 3D track dynamics and wheel-rail dynamic interaction of the V-Track up to 10 kHz. Rail vibrations dominate the wheel-rail dynamic contact within 10 kHz, while the wheel vibrations play an increasingly important role at higher frequencies and become decisive near the wheel eigenmode frequencies. The V-Track overall achieves dynamic similarity to the real vehicle-track system.Railway Engineerin

On preconditioning incompressible non-Newtonian flow problems

This paper deals with fast and reliable numerical solution methods for the incompressible non-Newtonian Navier-Stokes equations. To handle the nonlinearity of the governing equations, the Picard and Newton methods are used to linearize these coupled partial differential equations. For space discretization we use the finite element method and utilize the two-by-two block structure of the matrices in the arising algebraic systems of equations. The Krylov subspace iterative methods are chosen to solve the linearized discrete systems and the development of computationally and numerically efficient preconditioners for the two-by-two block matrices is the main concern in this paper. In non-Newtonian flows, the viscosity is not constant and its variation is an important factor that effects the performance of some already known preconditioning techniques. In this paper we examine the performance of several preconditioners for variable viscosity applications, and improve them further to be robust with respect to variations in viscosity.Electrical Engineering, Mathematics and Computer Scienc

Review of the action of organic matter on mineral sediment flocculation

Sediment is found throughout the world’s alluvial plain rivers, estuarine coasts and adjacent seas and is thereby a key factor in major ecosystems. Suspended mineral sediment can affect the biological activity of microorganisms and plants, by reducing light penetration in the water column or by binding to organic matter. Biological processes can, in turn, affect the physical and chemical properties of the sediment particles and influence the adhesion between particles. They can facilitate the sediment aggregation (flocculation) through bridging, patching and sweep, while biological decay will mainly help to disintegrate organic matter rich flocs. Biological activity also affects the properties of flocs (structure, density, sedimentation rate and composition). This activity is itself influenced by environmental conditions (like temperature, light and nutrient fluxes). Sediment flocculation thus involves complex relationships between several physical, chemical and biological factors. The role of biology in particular needs to be better integrated in sediment transport models, through the interaction between mineral clay particles, microorganisms and their excreted polymers (Extra Polymeric Substances, i.e., EPS). In this article, a summary of the state-of-the-art research regarding sediment flocculation is given. In particular, the action of organic matter on fine-grained sediment flocculation is discussed. The aim of the article is to provide a more comprehensive understanding of bio-sediment dynamics and give an outlook on remaining research questions.Environmental Fluid Mechanic

Seasonal variation of floc population influenced by the presence of algae in the Changjiang (Yangtze River) Estuary

The variation of the floc population in the Changjiang Estuary has been studied for both winter and summer season as a function of the presence of living (micro)algae. The influence of algae has been characterized through the use of the chlorophyll-a concentration to suspended sediment concentration (CC/SSC) ratio. Two whole tidal cycle sampling campaigns were carried out and a full set of parameters (particle size distribution, particle concentration, salinity, velocities, chlorophyll-a concentration) was recorded as function of time for 6 vertical depths. It is found that the floc population can be described by three particle classes. The two most dynamic classes (microflocs and macroflocs) co-exist in the water column. It was nonetheless found, due to the correlation between CC/SSC and particle sizes that the system is at steady state, both in summer and in winter. This can be explained by the limited flocculation ability between the classes due to their segregation in the water column. In winter, macroflocs are found at the top of the water column but their amount and size are very reduced with a mean CC/SSC value of 13 ± 11 μg g−1. In summer, algae-rich macroflocs are abundant at the top of the water column with a mean CC/SSC value of 21 ± 18 μg g−1, especially at flood tide. Microflocs, on the other hand, have a higher density and are generally found deeper in the water column. At high water slack, both macroflocs and microflocs will settle but will never catch-up. The fact that the flocs are at steady-state in terms of flocculation is of importance for sediment transport modelling.Accepted Author ManuscriptCoastal EngineeringEnvironmental Fluid Mechanic

How have the river discharges and sediment loads changed in the Changjiang River basin downstream of the Three Gorges Dam?

Streamflow and sediment loads undergo remarkable changes in worldwide rivers in response to climatic changes and human interferences. Understanding their variability and the causes is of vital importance regarding river management. With respect to the Changjiang River (CJR), one of the largest river systems on earth, we provide a comprehensive overview of its hydrological regime changes by analyzing long time series of river discharges and sediment loads data at multiple gauge stations in the basin downstream of Three Gorges Dam (TGD). We find profound river discharge reduction during flood peaks and in the wet-to-dry transition period, and slightly increased discharges in the dry season. Sediment loads have reduced progressively since 1980s owing to sediment yield reduction and dams in the upper basin, with notably accelerated reduction since the start of TGD operation in 2003. Channel degradation occurs in downstream river, leading to considerable river stage drop. Lowered river stages have caused a ‘draining effect’ on lakes by fostering lake outflows following TGD impoundments. The altered river–lake interplay hastens low water occurrence inside the lakes which can worsen the drought given shrinking lake sizes in long-term. Moreover, lake sedimentation has decreased since 2002 with less sediment trapped in and more sediment flushed out of the lakes. These hydrological changes have broad impacts on river flood and drought occurrences, water security, fluvial ecosystem, and delta safety.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Coastal Engineerin