Universal scaling law in drag-to-thrust wake transition of flapping foils

Reversed von K\'arm\'an streets are responsible for a velocity surplus in the wake of flapping foils, indicating the onset of thrust generation. However, the wake pattern cannot be predicted based solely on the flapping peak-to-peak amplitude $A$ and frequency $f$ because the transition also depends sensitively on other details of the kinematics. In this work we replace $A$ with the cycle-averaged swept trajectory $\mathcal{T}$ of the foil chord-line. Two dimensional simulations are performed for pure heave, pure pitch and a variety of heave-to-pitch coupling. In a phase space of dimensionless $\mathcal{T}-f$ we show that the drag-to-thrust wake transition of all tested modes occurs for a modified Strouhal $St_{\mathcal{T}}\sim 1$. Physically the product $\mathcal{T}\cdot f$ expresses the induced velocity of the foil and indicates that propulsive jets occur when this velocity exceeds $U_{\infty}$. The new metric offers a unique insight into the thrust producing strategies of biological swimmers and flyers alike as it directly connects the wake development to the chosen kinematics enabling a self similar characterisation of flapping foil propulsion.Comment: Rev

Ultra-fast escape maneuver of an octopus-inspired robot

We design and test an octopus-inspired flexible hull robot that demonstrates outstanding fast-starting performance. The robot is hyper-inflated with water, and then rapidly deflates to expel the fluid so as to power the escape maneuver. Using this robot we verify for the first time in laboratory testing that rapid size-change can substantially reduce separation in bluff bodies traveling several body lengths, and recover fluid energy which can be employed to improve the propulsive performance. The robot is found to experience speeds over ten body lengths per second, exceeding that of a similarly propelled optimally streamlined rigid rocket. The peak net thrust force on the robot is more than 2.6 times that on an optimal rigid body performing the same maneuver, experimentally demonstrating large energy recovery and enabling acceleration greater than 14 body lengths per second squared. Finally, over 53% of the available energy is converted into payload kinetic energy, a performance that exceeds the estimated energy conversion efficiency of fast-starting fish. The Reynolds number based on final speed and robot length is $Re \approx 700,000$. We use the experimental data to establish a fundamental deflation scaling parameter $\sigma^*$ which characterizes the mechanisms of flow control via shape change. Based on this scaling parameter, we find that the fast-starting performance improves with increasing size.Comment: Submitted July 10th to Bioinspiration & Biomimetic

‘Our Global Family’: Using Storytelling to Develop Compassion and Acceptance of Cultural Others in Primary School Pupils

The aim of this project was to develop a teaching model that develops understanding, acceptance and compassion amongst primary school pupils towards others, particularly refugees and migrants

Amplitude dependence of image quality in atomically-resolved bimodal atomic microscopy

In bimodal FM-AFM, two flexural modes are excited simultaneously. The total vertical oscillation deflection range of the tip is the sum of the peak-to-peak amplitudes of both flexural modes (sum amplitude). We show atomically resolved images of KBr(100) in ambient conditions in bimodal AFM that display a strong correlation between image quality and sum amplitude. When the sum amplitude becomes larger than about 200 pm, the signal-to-noise ratio (SNR) is drastically decreased. We propose this is caused by the temporary presence of one or more water layers in the tip-sample gap. These water layers screen the short range interaction and must be displaced with each oscillation cycle. Further decreasing the sum amplitude, however, causes a decrease in SNR. Therefore, the highest SNR in ambient conditions is achieved when the sum amplitude is slightly less than the thickness of the primary hydration layer.Comment: 3000 words, 3 Figures, 3 supplimentary figure

Added mass energy recovery of octopus-inspired shape change

Dynamic shape change of the octopus mantle during fast jet escape manoeuvres results in added mass energy recovery to the energetic advantage of the octopus, giving escape thrust and speed additional to that due to jetting alone. We show through numerical simulations and experimental validation of overall wake behaviour, that the success of the energy recovery is highly dependent on shrinking speed and Reynolds number, with secondary dependence on shape considerations and shrinking amplitude. The added mass energy recovery ratio η[subscript ma], which measures momentum recovery in relation to the maximum momentum recovery possible in an ideal flow, increases with increasing the non-dimensional shrinking parameter σ[superscript ∗]=ȧ[subscript max]/U√(Re[subscript 0]), where ȧ[subscript max] is the maximum shrinking speed, U is the characteristic flow velocity and √(Re0) is the Reynolds number at the beginning of the shrinking motion. An estimated threshold σ[superscript ∗]≈10 determines whether or not enough energy is recovered to the body to produce net thrust. Since there is a region of high transition for 10100 added mass energy is recovered at diminishing returns, we propose a design criterion for shrinking bodies to be in the range of 50<σ[superscript ∗]<100, resulting in 61–82 % energy recovery

IDENTIFYING GENETIC VARIANTS AND CHARACTERIZING THEIR ROLE IN CLUBFOOT

Clubfoot is a common, complex birth defect affecting 4,000 newborns in the United States and 135,000 world-wide each year. The clubfoot deformity is characterized by inward and rigid downward displacement of one or both feet, along with persistent calf muscle hypoplasia. Despite strong evidence for a genetic liability, there is a limited understanding of the genetic and environmental factors contributing to the etiology of clubfoot. The studies described in this dissertation were performed to identify variants and/or genes associated with clubfoot. Genome-wide linkage scan performed on ten multiplex clubfoot families identified seven new chromosomal regions that provide new areas to search for clubfoot genes. Troponin C (TNNC2) the strongest candidate gene, located in 20q12-q13.11, is involved in muscle contraction. Exon sequencing of TNNC2 did not identify any novel coding variants. Interrogation of fifteen muscle contraction genes found strong associations with SNPs located in potential regulatory regions of TPM1 (rs4075583 and rs3805965), TPM2 (rs2025126 and rs2145925) and TNNC2 (rs383112 and rs437122). In previous studies, a strong association was found with rs3801776 located in the basal promoter of HOXA9, a gene also involved in muscle development and patterning. Altogether, this data suggests that SNPs located in potential regulatory regions of genes involved in muscle development and function could alter transcription factor binding leading to changes in gene expression. Functional analysis of 3801776/HOXA9, rs2025126/TPM2 and rs2145925/TPM2 showed altered protein binding, which significantly influenced promoter activity. Although the ancestral allele (G) of rs4075583/TPM1 creates a DNA-protein complex, it did not affect TPM1 promoter activity. However and importantly, in the context of a haplotype, rs4075583/G significantly decreased TPM1 promoter activity. These results suggest dysregulation of multiple skeletal muscle genes, TPM1, TPM2, TNNC2 and HOXA9, working in concert may contribute to clubfoot. However, specific allelic combinations involving these four regulatory SNPs did not confer a significantly higher risk for clubfoot. Other combinations of these variants are being evaluated. Moreover, these variants may interact with yet to be discovered variants in other genes to confer a higher clubfoot risk. Collectively, we show novel evidence for the role of skeletal muscle genes in clubfoot indicating that there are multiple genetic factors contributing to this complex birth defect

Shape of retracting foils that model morphing bodies controls shed energy and wake structure

The flow mechanisms of shape-changing moving bodies are investigated through the simple model of a foil that is rapidly retracted over a spanwise distance as it is towed at constant angle of attack. It is shown experimentally and through simulation that by altering the shape of the tip of the retracting foil, different shape-changing conditions may be reproduced, corresponding to: (i) a vanishing body, (ii) a deflating body and (iii) a melting body. A sharp-edge, ‘vanishing-like’ foil manifests strong energy release to the fluid; however, it is accompanied by an additional release of energy, resulting in the formation of a strong ring vortex at the sharp tip edges of the foil during the retracting motion. This additional energy release introduces complex and quickly evolving vortex structures. By contrast, a streamlined, ‘shrinking-like’ foil avoids generating the ring vortex, leaving a structurally simpler wake. The ‘shrinking’ foil also recovers a large part of the initial energy from the fluid, resulting in much weaker wake structures. Finally, a sharp edged but hollow, ‘melting-like’ foil provides an energetic wake while avoiding the generation of a vortex ring. As a result, a melting-like body forms a simple and highly energetic and stable wake, that entrains all of the original added mass fluid energy. The three conditions studied correspond to different modes of flow control employed by aquatic animals and birds, and encountered in disappearing bodies, such as rising bubbles undergoing phase change to fluid

LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types

Abstract Background The relative contribution of epigenetic mechanisms to carcinogenesis is not well understood, including the extent to which epigenetic dysregulation and somatic mutations target similar genes and pathways. We hypothesize that during carcinogenesis, certain pathways or biological gene sets are commonly dysregulated via DNA methylation across cancer types. The ability of our logistic regression-based gene set enrichment method to implicate important biological pathways in high-throughput data is well established. Results We developed a web-based gene set enrichment application called LRpath with clustering functionality that allows for identification and comparison of pathway signatures across multiple studies. Here, we employed LRpath analysis to unravel the commonly altered pathways and other gene sets across ten cancer studies employing DNA methylation data profiled with the Illumina HumanMethylation27 BeadChip. We observed a surprising level of concordance in differential methylation across multiple cancer types. For example, among commonly hypomethylated groups, we identified immune-related functions, peptidase activity, and epidermis/keratinocyte development and differentiation. Commonly hypermethylated groups included homeobox and other DNA-binding genes, nervous system and embryonic development, and voltage-gated potassium channels. For many gene sets, we observed significant overlap in the specific subset of differentially methylated genes. Interestingly, fewer DNA repair genes were differentially methylated than expected by chance. Conclusions Clustering analysis performed with LRpath revealed tightly clustered concepts enriched for differential methylation. Several well-known cancer-related pathways were significantly affected, while others were depleted in differential methylation. We conclude that DNA methylation changes in cancer tend to target a subset of the known cancer pathways affected by genetic aberrations.http://deepblue.lib.umich.edu/bitstream/2027.42/112789/1/12864_2012_Article_4373.pd

Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot.

Clubfoot is a common birth defect that affects 135,000 newborns each year worldwide. It is characterized by equinus deformity of one or both feet and hypoplastic calf muscles. Despite numerous study approaches, the cause(s) remains poorly understood although a multifactorial etiology is generally accepted. We considered the HOXA and HOXD gene clusters and insulin-like growth factor binding protein 3 (IGFBP3) as candidate genes because of their important roles in limb and muscle morphogenesis. Twenty SNPs from the HOXA and HOXD gene clusters and 12 SNPs in IGFBP3 were genotyped in a sample composed of non-Hispanic white and Hispanic multiplex and simplex families (discovery samples) and a second sample of non-Hispanic white simplex trios (validation sample). Four SNPs (rs6668, rs2428431, rs3801776, and rs3779456) in the HOXA cluster demonstrated altered transmission in the discovery sample, but only rs3801776, located in the HOXA basal promoter region, showed altered transmission in both the discovery and validation samples (P = 0.004 and 0.028). Interestingly, HOXA9 is expressed in muscle during development. An SNP in IGFBP3, rs13223993, also showed altered transmission (P = 0.003) in the discovery sample. Gene-gene interactions were identified between variants in HOXA, HOXD, and IGFBP3 and with previously associated SNPs in mitochondrial-mediated apoptotic genes. The most significant interactions were found between CASP3 SNPS and variants in HOXA, HOXD, and IGFBP3. These results suggest a biologic model for clubfoot in which perturbation of HOX and apoptotic genes together affect muscle and limb development, which may cause the downstream failure of limb rotation into a plantar grade position