Horseshoe Structures Research Articles

Nuclear morphology is shaped by loop-extrusion programs.

It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces1-3. However, how polymorphonuclear structures are assembled remains unknown4. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin5-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted inenrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.

Large Eddy Simulation of Transitional Separated Flow Over a Low Reynolds Number Cambered Airfoil

Abstract The accurate simulation of the aerodynamic behavior of low Reynolds number (Re) cambered airfoils requires the ability to capture the transitional separated boundary layer (BL) that occurs naturally on the surface of the airfoil. In this study, simulations are performed using a modern cambered airfoil designed for use in low Re applications, which are an advancement from previous studies using flat plate geometries or symmetric NACA airfoils. The cambered SD 7037 airfoil is simulated using wall-resolved large eddy simulation (LES) at a modest Re of 4.1×104 and at 1 deg, 5 deg, and 7 deg angles of attack (AOAs), with results validated against experimental data. Simulated predictions of pressure and skin friction coefficients clearly capture the correct location of the laminar separated bubble (LSB) which forms during the natural BL transition process. Sensitivity to elevated inflow turbulence is found to cause early BL reattachment at higher AOAs without impacting the location of BL separation. An integral BL analysis verifies the accuracy of the simulated velocity profiles against experimental values. The scale of horseshoe structures visualized in the transitional BL is larger in comparison to airfoil chord length than what is seen in previous simulations at Re of the order of 105, which highlights the importance of investigating cambered airfoils at a modest Re.

The unsteady wake transition behind a wall-mounted large-depth-ratio prism

The wake of a long rectangular wall-mounted prism is investigated at Reynolds numbers of $Re=250\unicode{x2013}1200$ by directly solving the Navier–Stokes equations. The aim of this study was to examine the unsteady transition mechanism in the wake of a large-depth-ratio (streamwise length to width) prism as well as to characterize the unsteady wake evolution at low Reynolds numbers. The results highlighted that increasing Reynolds number significantly altered the dominance of upwash and downwash flows in the time-averaged flow and changed the characteristics of coherent structures, including their size, dominant frequency and interaction with other structures in the flow. The wake is, therefore, categorized into three regimes within the transition process: steady regime at $Re \leq 625$ , regular unsteady regime at $625 < Re < 750$ and irregular unsteady regime at $Re \geq 750$ . Particularly, the wake started to exhibit unsteady features at $Re=625\unicode{x2013}650$ , which transitioned to an early irregular unsteady wake topology at $Re=750$ . At $Re \geq 675$ , horseshoe vortices transformed to vortex loops. There were hairpin-like structures formed on the upper and side faces of the long prism. The results further indicated that the transition to unsteadiness is attributed to separated leading-edge shear-layer instabilities and interactions of the shear layer with the horseshoe structures. The wake was more complex due to the interactions of multiple coherent structures in the flow, which resulted in a multiple-periodicity wake system. A skeleton model is proposed for a large-depth-ratio prism, to incorporate details of the unsteady flow features and specify various flow coherent structures at low Reynolds numbers.

Three-dimensional large-scale and very-large-scale coherent structures in a turbulent axisymmetric jet

The direct numerical simulation database from Shin et al. (J. Fluid Mech., vol. 823, 2017, pp. 1–25) is used to study three-dimensional vortical and very-large-scale coherent structures in a turbulent round jet at a Reynolds number of $7300$ . In particular, horseshoe vortices and their role in the formation of very-large-scale coherent structures in the jet near and intermediate fields are assessed. The swirling strength criterion together with conditional averaging are used to visualize volumetric vortical structures. It is shown that, similar to wall-bounded turbulent flows, the turbulent jet is populated with symmetric and asymmetric horseshoe-like vortices, which induce high-momentum and low-momentum regions in the flow. However, unlike what is found for wall-bounded flows, inverse horseshoe-like vortices are common in the turbulent jet. They prevail in the shear region around the potential core in the jet near field and contribute to the mixing of the potential core in the jet. In the jet near field, groups of axially aligned horseshoe structures induce long streaky structures, which are periodic in the azimuthal and streamwise directions. In the jet intermediate field, very-large-scale motions (VLSMs) consisting of high-momentum regions, flanked on either side by low-momentum regions, are found to be associated with groups of horseshoe vortices. Instantaneous three-dimensional flow fields suggest that horseshoe vortices tend to concatenate and form organized spiral as well as axially aligned coherent VLSMs. A detection scheme is introduced to identify and average over these VLSMs. This conditional averaging reveals that spiral VLSMs and axially aligned VLSMs constitute $72\,\%$ and $28\,\%$ of the total VLSMs, respectively.

Tunable hyperbolic out-of-plane deformation of 3D-printed auxetic PLA shape memory arrays

Auxetic metamaterials attract wide attention due to their unusual mechanical behaviours. This work explores the tunability of the bidirectionally hyperbolic deformation of thin plates under uniaxial compression, instead of the Euler buckling deformation. Inspired by the horseshoe structures, through tuning the radius and thickness of the central circles of the horseshoes, as well as the thickness and subtending arc angles of the four branches, bidirectionally hyperbolic out of plane deformation was achieved together with auxetic behaviour. Finally, finite element simulations, theoretical analyses, and experimental verifications have been carried out to design the out of plane bidirectionally hyperbolic deformation by the tailorable temperature sensitivity and shape memory effect in unit cells.

Fabrication strategy for joints in 3D printed continuous fiber reinforced composite lattice structures

Three-dimensional (3D) printing has revolutionized the fabrication process of continuous fiber reinforced composite lattice structures (CFRCLSs) with complex designs. However, optimal strategies for fabricating specific features of lattice structures, particularly joints, are not established, limiting the fabricated parts’ geometry accuracy and mechanical property. To address the above issues, we propose an interlayer-based adaptive process planning strategy for printing joints of CFRCLSs. More specifically, six strategies with different printing paths and parameter settings were used to fabricate an orthogrid structure. Their mechanical properties were compared and the part fabricated with the proposed strategy outstands the others. In addition, the failure modes and internal microstructure at the joints were analyzed using the digital image correlation (DIC) and micro-CT techniques for providing deep insights. Results indicate that the proposed strategy can significantly improve the geometry accuracy and mechanical properties of fabricated parts. Moreover, the effectiveness of the proposed joint strategy has been validated with two representative metamaterial designs, i.e., horseshoe and auxetic structures.

A numerical study on suspended sediment transport in a partially vegetated channel flow

Turbulent structures generated by vegetation patches play a dominant role in the dispersion of suspended sediment, which in turn is of great significance for ecosystem cycling and river geomorphology development. High fidelity Large Eddy Simulations (LES) coupled with the Discrete Phase Method (DPM) were used to explore the particle distribution and its variance (the non-uniformity in temporal and spatial space) in a partially vegetated straight channel. The novel findings and conclusions are outlined here. Firstly, the contour of the vertical vorticity component coincides well with particle preferential gatherings in the outer edge of the mixing layer in the near-bed region. Large-scale turbulent structures grow in mixing layer along the side of a vegetation patch (VP), which deplete particles away from the mixing layer into the neighbouring region. Also, higher vegetation densities (Dn) promote this depletion trend. Secondly, the Probability Density Function (PDF) and its variance were defined to quantify these phenomena, illustrating that the VP continuously interrupts the flow condition and promotes higher non-uniformity of particle distribution among the vegetated and non-vegetated regions. The variance of the PDF in the non-vegetated region is significantly higher than that in the neighbouring vegetated region located in the same streamwise location. The particle parcels are highly unevenly located along the periphery of the large eddies and are exchanged by the mixing flow between the non-vegetated and vegetated regions. Finally, the vertical entrainment of particles occurs in the vegetated region of the present cases. This is because the horseshoe structures provide an upwards velocity for the current Dn conditions (Dn < 0.1) and an increase of Dn (Dn < 0.1) accelerates the upward suspension. These findings complete our understanding of particles’ transportation in both spanwise and vertical directions.

Computer simulation of horse shoes made of polymeric composite subjected to external loading

A horse shoe is designed to protect a horse’s hoof from wear. Like the human shoes, the horse shoes should also meet the ergonomic design, i.e. strong enough to withstand external loadings, comfort, and safe. Conventional horseshoes made of iron, for example, have good mechanical properties, but they are not comfort enough for horses due to its higher weight to size ratio. The internal stresses due to the external loading of the shoes to the soil surface, rocks, asphalt or hard surface will transfer the force of the horse’s foot pounding against the horse’s foot, so that it can hurt the horse’s foot if used for a long time. Therefore, a new research on polymeric foam alternative materials is the main concern to reduce existing problems. The purpose of this study was to conduct a static loading simulation of horse shoes made of polymeric foam reinforced with glass fiber using ANSYS software. In the simulation specimens are modelled with SolidWork. The aims are to determine the stress distribution of to two horse shoes models. It was found that the stresses on z-direction for both commercial and polymeric composite horse shoes material were not significantly difference in values. Stress in z-direction constitutes the bending stresses due to external loadings. The stress contours on both modes are also similar. The stress concentration occurs around the vicinity of the shoe connectors. The maximum normal stresses in z-direction at those locations for steel and polymeric composite are 7.819 MPa and 7.850 MPa, respectively. Comparing those stresses with the static tensile strength of both materials we may conclude that both horseshoe structures are acceptable to be used. However, in terms of the applicability the one made of polymeric composite are more easily to be used.

On-chip simultaneous rotation of large-scale cells by acoustically oscillating bubble array.

Bubbles locating in microfluidic chamber can produce acoustic streaming vortices by applying travelling surface acoustic wave oscillation in an ultrasonic range, which can be used to drive bio-samples to move within the flow field. In this paper, a strategy of bubble array configured in a large number of regularly arranged horseshoe structures is proposed to capture and rotate cells simultaneously. By modifying the geometric parameters of the horseshoe structure and microfluidic setting, high bubble homogeneity and cell trapping percentage was achieved. The simulation and experimental results of the bubble-induced streaming vortices were confirmed to be consistent. Through experiments, we achieved both in-plane and out-of-plane rotation of arrayed HeLa cells trapped by the bubbles. Out-of-plane rotation was used to reconstruct the 3D (three-dimensional) cell morphology, which was demonstrated to be useful in calculating cell geometry related parameters. We believe that this bubble array based cell rotation method is expected to be a promising tool for the investigation of bioengineering, biophysics, medicine, and cell biology.

Turbulence structures over realistic and synthetic wall roughness in open channel flow at Reτ = 1000

ABSTRACTTurbulence structures in flow over three types of wall roughness: sand-grain, cube roughness and a realistic, multi-scale turbine-blade roughness, are compared to structures observed in flow over a smooth wall in open channel flow at , using direct numerical simulations. Two-point velocity correlations, length scales, inclination angles, and velocity spectra are analysed, and the applicability of Townsend's outer layer similarity hypothesis [Townsend. The structure of turbulent shear flow. Cambridge: Cambridge University Press; 1976] to these parameters was examined. Results from linear stochastic estimation suggest that, near the wall, the quasi-streamwise vortices observed in smooth-wall flow are present in the large-scale recessed regions of multi-scale roughness, whereas they are replaced by a pair of ‘head-up, head-down’ horseshoe structures in sandgrain and cube roughness, similar to those observed by Talapatra and Katz [Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV. J Fluid Mech. 2012;711:161–170]. The configuration of conditional eddies near the wall suggests that the kinematical process of vortices differ for each kind of rough surface. Eddies over multiscale roughness are conjectured to obey a growth mechanism similar to those over smooth walls, while around the cube roughness the head-down horse-shoe vortices of Talapatra and Katz [Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV. J Fluid Mech. 2012;711:161–170] may undergo solid-body rotation on top of a cube roughness on account of the strong shear layer, shortening the longitudinal extent of near-wall structure and promoting turbulence production during this process. These results illustrate the sensitivity of turbulence structure to the roughness texture, particularly within the roughness sublayer.

Effect of turbulence models' choice on the aero-thermal flow numerical validations within a ribbed trailing edge geometry

In this paper, the commercial ANSYS Fluent software was used to achieve a numerical survey of the effect of five (05) turbulence models’ formulation on the aero-thermal computational fluid dynamics validation of two 30:1 scaled models reproducing an original internal ribbed trailing edge prototype. Tests were conducted for stationary and rotation conditions, for Re = 10,000–40,000 and Ro = 0–0.23. Particle image velocimetry and thermochromic liquid crystal experimental data were employed to check the consistence computational fluid dynamics results qualitatively and quantitatively, aerodynamically and thermally, for various working conditions. Numerical predictions revealed that the choice of the turbulence model affects the accuracy of results. Concerning the shear stress transport k-w model, limiters defined in the eddy viscosity formulation induce a surplus estimation of the turbulence kinetic energy ( k) which leads to noticeable discrepancies in terms of velocity profiles and recirculation zones. Also, numerical calculations confirmed former experimental assumptions concerning origins of the aerodynamic structures and heat transfer's features, especially, those related to the increase of the cooling temperature balance efficiency, the appearance/disappearance of the horseshoe structures within the trailing edge region and velocities/boundary layers’ profile variations. The obtained results assist the understanding and the forecast of the flow field behavior, throughout the design process, by the assessment of the aerodynamic and thermal performances within the considered blade's cooling system.

Short-crested wave breaking

Peregrine (1998, 1999), in discussing the effect of local variations of wave energy dissipation as a generation mechanism for vorticity at the scale of individual waves, spurred a wave of study of vorticity dynamics and mixing processes in the wave-driven ocean. In deep water, the limited depth of penetration of breaking effects leads to the conceptual forcing of a smoke-ring resulting from the localized cross-section of impulsive forcing, as elaborated by Pizzo and Melville (2013). In shallow water, depth limitations favor the generation of a quasi-two-dimensional field of vertical vortex structures, with a resulting inverse cascade of energy to low wavenumbers and the evolution of flows such as transient rip currents (Johnson and Pattiaratchi, 2006). In this presentation, we consider vorticity-generating mechanisms ranging from the generation of patterns of vertical vorticity in 2D, depth-averaged flows, to a more detailed picture of the vorticity field evolving during a localized breaking event. Using an LES/VOF model (Derakhti and Kirby, 2014), we examine the evolution of coherent vortex structures whose initial scales are determined by the width of the breaking region, and are much larger than the locally-controlled reverse horseshoe structures seen in typical studies of along-crest uniform breaking. We study the persistence of three-dimensionality of these structures and their contribution to the development of depth-integrated vertical vorticity, but also point out the persistent presence of both components of horizontal vorticity as a result of the isolated breaking event.

Roughness effects on the second-order turbulence statistics in oscillatory flows

Effects of roughness on the near-bed turbulence characteristics in oscillatory flows are studied by means of particle-resolved direct numerical simulations (DNS). Two particle sizes of diameter 375 and 125 in wall units in a very rough turbulent flow regime are studied. A double-averaging technique is employed to study the nature of the wake field, i.e., the spatial inhomogeneity at the roughness length scale. This introduced dispersive stresses along with additional production and transport terms in the double-averaged Reynolds stress budget, indicating alternate pathways of turbulent energy transfer mechanisms. While overall nature of the elementary processes responsible for energy transport in both flow cases remains identical, there are some discernible differences with regards to the near-bed turbulence structure. It is shown that the roughness modulates the near-bed turbulence, distorts and breaks the streamwise horseshoe structures, and therefore reduces the large-scale anisotropy; a result of redistribution of energy from streamwise component to other two components of the Reynolds stress and is illustrated by studying their individual budgets. In comparison to the small diameter, such effects are found to be significant in the case of large diameter particle-bed. In addition, redistribution of energy in the large diameter particle case shows reduced dependence on the flow oscillations, while for the small diameter particle it is more pronounced towards the end of an acceleration cycle.

Optimization of compound serpentine–spiral structure for ultra-stretchable electronics

Stretchable electronics is a rising technology, promising to replace the conventional, brittle and rigid electronics for applications that demand mechanical compliance to irregular, complex and mobile shapes. Several approaches have been proposed to find an optimum balance between electrical and mechanical characteristics. These include finding new flexible electronic materials, integrating both organic and inorganic materials or incorporating structural modifications to conventional materials, thus achieving flexibility and stretchability. Previously, the use of spiral-based structures made entirely out of silicon, a well-mature and high-performing material, has been proposed as a platform for ultra-stretchable electronic applications. In this paper we have demonstrated the use of spiral-based compound, fractal-inspired structures to optimize and greatly reduce the stress and strain distribution along them. The integration of double-arm spirals with variants of serpentine and horseshoe structures has been considered and their mechanical response to an applied deformation has been performed through finite element analysis (FEA). The proposed compound structures provide outstanding stretching capabilities and demonstrate up to ∼55% reduction in stress/strain, as well as a more uniform distribution as compared to the original, un-optimized spiral-based structure. These results show the remarkable potential of combining structures to optimize their mechanical behavior, thus accomplishing more robust platforms that will leverage the development of stretchable electronics.

DNS study of particle-bed–turbulence interactions in an oscillatory wall-bounded flow

Particle-resolved direct numerical simulations (DNS) are performed to investigate the behaviour of an oscillatory flow field over a rough bed, corresponding to the experimental set-up of Keiller &amp; Sleath (J. Fluid Mech., vol. 73 (04), 1976, pp. 673–691) for transitional and turbulent flows over a range of Reynolds numbers (95–400) based on the Stokes-layer thickness. It is shown that the roughness modulates the near-bed turbulence, produces streamwise horseshoe structures which then undergo distortion and breaking, and therefore reduces the large-scale anisotropy. A fully developed equilibrium turbulence is observed in the central part of the oscillation cycle, with two-component turbulence in the near-bed region and cigar-shaped turbulence in the outer region. A double averaging of the flow field reveals spatial inhomogeneities at the roughness scale and alternate paths of energy transport in the turbulent kinetic energy (TKE) budget. Contrary to the unidirectional, steady flow over rough beds, bed-induced production terms are important and comparable to the shear production term. It is shown that the near-bed velocity and pressure fluctuations are non-Gaussian, a result of critical importance for the modelling of incipient motion of sediment grains.

Three-dimensional wavelet analysis on turbulent structure of dune wake flow

The three-dimensional (3D) turbulent structure was simulated by large eddy simulation (LES), and then the numerical result was validated by PIV experiment. In order to give a detailed description of dune wake flow, the instantaneous velocity, vorticity, and pressure were decomposed into the large-, intermediate- and relatively small-scale components by 3D wavelet multi-resolution technique. To get a further understanding of coherent structure, the decomposed wavelet components were employed to calculate Q-criterion. It was found that the rollers and horse-shoe structures in the separation bubble were mainly contributed from large-scale structures and it made the most significance to the vorticity concentration. The observations of intermediate-scale horse-shoe structures indicated that the coherent structure was the combined effect of large- and intermediate-scale structures. Besides, from the visualization of 3D streamlines and pressure iso-surfaces, the separation bubble and pressure distribution are found to be dominated by large-scale structure.

NUMERICAL MODELING OF VORTEX STRUCTURES UNDER A BROKEN SOLITARY WAVE USING SMOOTHED PARTICLE HYDRODYNAMICS METHOD

Water wave breaking and the resulting surf-zone turbulence play a role in sediment transport, wave damping, and mixing processes. The vortex structures associated with wave breaking carry large amount of turbulent momentum and turbulent kinetic energy and therefore have a crucial effect on the safety of vessels and structures located in the surf zone. In this study, turbulent vortical structures under a broken solitary waves is studied using a three-dimensional Smoothed Particle Hydrodynamics (SPH) method. A broken solitary wave is of interest since the generation and evolution of the three-dimensional vortex structures under a broken wave can be isolated from the case of a periodic wave train, which has undertow and residual turbulence induced from previously broken waves. Further, a solitary wave is a first approximation to a tsunami wave. The numerical model predicts water surface evolution very well in comparison with the experimental results of Ting (2006). The numerical results show organized coherent structures trailing the wave and characterized by reversed horseshoe (hairpin) vortices, traveling downward, which appear to be the previously found obliquely descending eddies. These horseshoe coherent structures transport momentum and turbulent kinetic energy downward into the water column and likely have a significant role in bed and beach erosion. Different terms of vorticity equations are studied and it is concluded that vortex stretching and vortex bending play an important role on the generation and evolution of reversed horseshoe structures.

Numerical simulation of initial mixing of marine wastewater discharge from multiport diffusers

Purpose – The purpose of this paper is to examine the initial mixing of wastewater discharged from submerged outfall diffusers and the influence of port configurations on wastewater distribution based on computational results. Design/methodology/approach – Marine wastewater discharges from multiport diffusers are investigated by numerically solving three-dimensional and uncompressible two-phase flow fields. A mixture model simulates this flow and the standard k-e model to resolve flow turbulence; inter-phase interactions were described in terms of relative slip velocity between phases. Computations were performed for two values of the port spacings s/H with different current Froude numbers F. Findings – Computational results compared well with previous laboratory measurements. Numerical results reveal that for both the closely spaced (s/H=0.21) and widely spaced (s/H=3.0) ports, the normalized dilution Sn becomes independent of F; further, the length of the near field xn and the spreading layer thickness hn are functions of F. For the closely spaced ports, the wastewater discharge behaves like a line plume, the Coanda effect is obvious, quasi-bifurcation is present, horseshoe structures of the jets in the planes are rapidly produced and then squashed and elongated, and the jet trajectories based on maximum velocity precede those based on maximum concentration. For the widely spaced ports, the wastewater discharge behaves like a point plume, the Coanda effect is not obvious, bifurcation is present, horseshoe structures of the jets in the planes are gradually produced and become ellipses, and the jet trajectories based on maximum velocity are similar to those based on maximum concentration. Originality/value – Semi-empirical equations are presented to predict major near field characteristics. These provide guidance for designing multiport diffusers and assessing environmental impact.

Prediction of horseshoe configuration in neural receptors: Dscam isoforms

Dscam (Down Syndrome Cell Adhesion Molecule), a member of immunoglobulin superfamily (IgSF), is a receptor for netrin-1 [1,2], a classical axon guidance cue. The interaction between netrin-1 and Dscam plays an important role in the development of the nervous system. Here, we present the crystal structure of the N-terminal four Ig-like domains of Dscam. The molecule folds into a horseshoe-like configuration. A comparison of this Dscam horseshoe with the previously described horseshoe structures of other cell-surface receptors has revealed fascinating conserved structural features and important sequence markers for these IgSF proteins. This discovery can help us predict the horseshoe configuration N-terminal arrangements in a number of other structurally unknown neural receptors. The N-terminal horseshoe has been shown to be engaged in homophilic and heterophilic interactions between two cell-surface receptors.

Three-dimensional reversed horseshoe vortex structures under broken solitary waves

Turbulent vortical structures under broken solitary waves are studied using three-dimensional smoothed particle hydrodynamics (SPH) method. The numerical model predicts water surface evolution and horizontal velocity very well in comparison with the experimental results. The numerical results detect organized coherent structures characterized as reversed horseshoe (hairpin) vortices being generated at the back of the broken spilling wave and traveling downward. The counter rotating legs of the reversed horseshoe structures appear to be a continuous form of the previously found obliquely descending eddies. The reversed horseshoe structures are associated with the turbulence motion of sweep events (downwelling motion) and transport momentum and turbulent kinetic energy downward into the water column. Vortex turning play an important role on the generation and evolution of three dimensional reversed horseshoe structures from the spanwise breaking wave rollers.