Negative Twist Research Articles

Discerning the Role of DNA Sequence, Shape, and Flexibility in Recognition by Drosophila Transcription Factors.

The precise spatial and temporal orchestration of gene expression is crucial for the ontogeny of an organism and is mainly governed by transcription factors (TFs). The mechanism of recognition of cognate sites amid millions of base pairs in the genome by TFs is still incompletely understood. In this study, we focus on DNA sequence composition, shape, and flexibility preferences of 28 quintessential TFs from Drosophila melanogaster that are critical to development and body patterning mechanisms. Our study finds that TFs exhibit distinct predilections for DNA shape, flexibility, and sequence compositions in the proximity of transcription factor binding sites (TFBSs). Notably, certain zinc finger proteins prefer GC-rich areas with less negative propeller twist, while homeodomains mainly seek AT-rich regions with a more negative propeller twist at their sites. Intriguingly, while numerous cofactors share similar binding site preferences and bind closer to each other in the genome, some cofactors that have different preferences bind farther apart. These findings shed light on TF DNA recognition and provide novel insights into possible cofactor binding and transcriptional regulation mechanisms.

Numerical studies on the aeroelasticity of a shipboard helicopter rotor during engagement and disengagement with ship motions using CFD/CSD coupling approach

When the shipboard helicopter rotor engages and disengages on a ship deck, due to the influence of wind-over-deck environment and ship airwake, the heterogeneity of rotor airload is large. This large heterogeneity leads to the fluctuation of blade deflection which changes the aerodynamic forces and causes danger of over deflection. To investigate the aeroelasticity of a rotor blade and find the rule of deflection and the deformed blade aerodynamic force in the rotor/ship coupling flow field, we establish a loose computational fluid dynamics/computational structural dynamics (CFD/CSD) coupling model. This coupling model simulates the aeroelastic characteristics of the shipboard helicopter rotor during engagement and disengagement with ship motions. In the simulation, the CFD solver is based on Reynolds-averaged Navier-Stokes (RANS) equations and the CSD solver is based on the moderate deflection beam model. We compare the results with the experimental data and verify the effectiveness of the simulation. Through the analysis of the flow field, blade deflection, and aerodynamic forces under various wind-over-deck conditions at different positions, we find in certain cases, that the elastic deflection has a significant impaction the blade aerodynamic force. As the wind direction anglesincrease, the rotor blade is more likely to have a large negative elastic twist deflection, causing drop of aerodynamic forces and danger of over deflection.

Locally maximising orbits for the non-standard generating function of convex billiards and applications

Given an exact symplectic map T of a cylinder with a generating function H satisfying the so-called negative twist condition, , we study the locally maximising orbits of T, that is, configurations which are local maxima of the action functional . We provide a necessary and sufficient condition for a configuration to be locally maximising. Using it, we consider a situation where T has two generating functions with respect to two different sets of symplectic coordinates. We suggest a simple geometric condition which guarantees that the set of locally maximising orbits with respect to both of these generating functions coincide. As the main application we show that the two generating functions for planar Birkhoff billiards satisfy this geometric condition. We apply it to get the following result: consider a centrally symmetric curve γ, for which the Birkhoff billiard map has a rotational invariant curve α of four-periodic orbits. We prove that a certain L 2-distance between γ and its ‘best approximating’ ellipse can be bounded from above in terms of the measure of the complement of the set filled by locally maximising orbits lying between α and the boundary of the phase cylinder. Moreover, this estimate is sharp, giving an effective version of a recent result on Birkhoff conjecture for centrally symmetric curves (Bialy and Mironov 2022 Ann. Math. 196 389–413). We also get a similar bound for arbitrary curves γ, that relates the measure of the complement of the set of locally maximising orbits with the L 2-distance between γ and its ‘best approximating’ circle.

The study of miRNA-200c expression and epithelial-to-mesenchymal transition-related transcription factors in the primary bladder urothelial carcinoma

Epithelial-mesenchymal transition (EMT) plays an important role in bladder carcinoma (BC) invasiveness and metastasis. Studies have shown that muscle-invasive BC (MIBC) and non-MIBC (NMIBC) are different at the molecular level owing to different EMT-related programming. Recent studies suggest that dysregulation of specific miRNAs is linked to EMT in BC. With this background, we aimed to study the immunoexpression of EMT-markers and its correlation with miRNA-200c expression in a series of MIBCs and NMIBCs. Quantitative real-time-polymerase chain reaction for the quantification of miR-200c expression was performed on 50 cases of urinary BC obtained from transurethral resection of bladder tumor (TURBT), cystectomy specimens, and ten peritumoral bladder tissue. Immunohistochemistry for ZEB1, ZEB2, TWIST, E-cadherin, and β-catenin was performed on tumor and peritumoral bladder tissue. Thirty-five TURBT and 15 cystectomy specimens were assessed. Among MIBC, loss of expression of E-cadherin (72.3%), β-catenin (66.7%), and ZEB1, ZEB2, and TWIST2 immunoreactivity was noted in 53.3%, 86.7%, and 73.3% of cases, respectively. Among NMIBC, loss of expression of E-cadherin (22.5%), β-catenin (17.1%) and ZEB1, ZEB2, and TWIST immunoreactivity was noted in 11.5%, 51.4%, and 91.4% of cases, respectively. Upregulation of miRNA-200c was noted in cases with retained E-cadherin and negative TWIST expression. Downregulation of miRNA-200c expression was noted in all the cases showing loss of E-cadherin, β-catenin, and in cases immunoreactive for ZEB1, ZEB2, and TWIST in MIBC. Downregulation of miRNA-200c expression was also noted in cases of MIBC with retained β-catenin and those immunonegative for ZEB1 and ZEB2. A similar trend was noted in NMIBC. Median miRNA-200c expression was low in both high-grade and low-grade NMIBC compared to peritumoral bladder tissue and was not statistically significant. This study for the first time explores the relation of miR200C with E-cadherin, b-catenin, and its direct transcriptional regulators, namely Zeb1, Zeb2, and Twist in the same cohort of BC. We observed that miRNA-200c is downregulated in both MIBC and NMIBC. We identified novel expression of TWIST in cases of BC showing downregulation of miR200Cs suggesting that it is one of the protein targets of altered miRNA-200c expression contributing to EMT and can serve as a promising diagnostic marker and therapeutic target. Loss of E-cadherin and ZEB1 immunoexpression in high-grade NMIBC suggests an aggressive clinical behavior. However, ZEB2 heterogeneous expression in BC limits its diagnostic and prognostic utility.

First-return maps of Birkhoff sections of the geodesic flow

This paper compares different pseudo-Anosov maps coming from different Birkhoff sections of a given flow. More precisely, given a hyperbolic surface and a collection of periodic geodesics on it, we study those Birkhoff sections for the geodesic flow on the unit bundle to the surface bounded by the collection. We show that there is a canonical identification of all those surfaces, and that the first-return maps induced by the flow can all be expressed as a composition of negative Dehn twists along the same family of curves: only the order depends on the choice of a particular surface.

Aerodynamic characteristics of flexible flapping wings depending on aspect ratio and slack angle

Experimental investigations are made for the combined effects of aspect ratio (AR), slack (βS), and pitch angles on the aerodynamic characteristics of flexible flapping wings in hover. βS is introduced as a way to indirectly alter the flexibility of the wing. An optimum AR range of 3–5 based on the lift coefficient is observed depending on the flexibility. For a constant AR, the intensity of the leading-edge vortex (LEV) with corresponding circulatory-based lift mitigates as βS increases beyond 2.5°. The variation of βS affects the magnitude of the shed trailing-edge vortices (TEVs) but the vorticity core is maintained. We found the shed TEVs to be the key vortical feature of twistable flexible wings in comparison with the rigid (untwisted) cases. More intriguingly, the negative wing twist played a significant role in sustaining the circulatory lift at the outboard section for even high AR cases. The primary LEV trace is found to be an indicator for the effective spanwise limit of the LEV. Although an increase in AR reduces the effective spanwise limit, it is found that wing flexibility further decreases the radial distance. Again, the study reveals that lift enhancement in the rigid wing requires a wider effective downwash area induced by the outward movement of the LEV traces to merge with the tip vortex. Contrarily, the flexible wing requires an elongated downwash area induced by the wing twist to enhance the aerodynamic performance.

Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules

Microtubules (MTs) are polymers of αβ-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here, we use cryo-electron microscopy and total internal reflection fluorescence microscopy of GTP hydrolysis-deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wild-type GDP-MTs. End-binding proteins of the EB family have the ability to compact both mutant GTP lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wild-type MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these structures of catalytically inactive MTs add mechanistic insight into the GTP state of MTs, the stability of the GTP- and GDP-bound lattice, and our overall understanding of MT dynamic instability.

Torus knots obtained by negatively twisting torus knots

Twisted torus knots are torus knots with some full twists added along some number of adjacent strands. There are infinitely many known examples of twisted torus knots which are actually torus knots. We give eight more infinite families of such twisted torus knots with a single negative twist.

Numerical Investigation of Aeroelastic Deformation Effect on the NASA Common Research Model

The risk of the aeroelastic deformation of the wings to the flight safety has become increasingly prominent for commercial transport aircraft due to the requirements for lightweight structure. In this work, Reynolds averaged Navier-Stokes (RANS) method coupled with transfinite interpolation were employed to investigate the influence of static elastic deformation of wing on aerodynamic characteristics of NASA CRM. Both bend and twist distributions were scaled in numerical simulations based on dynamic pressure, which was shown to be reasonable by the compassions between the calculations and measurements. The numerical results show premature flow separation in the middle and outboard of the wing for original configuration. Furthermore, the flow separation was supressed by the upward bending of the wing and negative twist in the leading edge, and the aerodynamic characteristics of the aircraft were improved by the aeroelastic deformation.

The effect of cyclic twist angle on mechanical properties for AISI 1038 medium carbon steel

A group of 11 specimens AISI 1038 Medium carbon steel alloy fabricated according to ASTM standard D790-02 torsion test were twisted cyclically one in positive another to negative angle in range of angles (0o-50o), step 5 degrees for each specimen. The data from torsion test device help to get actual torques and shear stresses, later the specimens tested the tensile test to figure out the effects of cyclic angle of twist on mechanical properties for AISI 1038 Medium carbon steel. The results showed a good agreement between the theoretical and actual data (torque, shear stress) for specimens with positive angle of twist by the percentage: 98%, 91%, 96%, 93%, 91%, 89%, 88%, 85%, 82%, 81%, 80%. In other side the results for experimental tests showed a dangerous decrements in mechanical properties for cyclic or negative twist angles, the yield stress for reference specimen without twist angle is 490 Mpa, yield stress increased for angels (5o,10o,15o) by 1%, 3%, 6%, then decreased for angels (20o,25o,30o,35o,40o,45o) by 3%, 5%, 13%, 18%, 24% and 35% Respectively and the final specimen with 50o angle of twist had been broken torsional before tensile test as a result specimens groups consequent of the extrusion – intrusion defects concomitant from twisting load.

Effect of geometrical features on the contra-rotating propeller hydrodynamic performances

New contra-rotating four-bladed DTMB propeller configurations operating in open water are numerically studied to determine their hydrodynamic performances. The unsteady turbulent flow around propellers is modelled by RANS equations with Kω SST model then solved by a CFD code. The computational domain is divided in two blocks linked with a rotating interface. The obtained results show that thrust and efficiency of the contra-rotating (CRP) increase compared to the single propeller, leading to a significant reduction of the propeller diameter. The variation in axial spacing and angular displacement seems to have little effect on the CRP efficiency. The results also show that the thrust can be further improved by adopting a moderate negative twist angle of the rear propeller.
 Keywords: CRP contra-rotating propeller, axial spacing, angular spacing, twist angle, CFD.

Parametric analysis and optimization of a simple wind turbine in high speed railway tunnels

The harvesting of wind energy from the slipstream generated when a train passes through a tunnel is a new way to produce renewable energy. From the perspective of CFD (Computed fluid dynamics), a three-dimensional URANS (unsteady Reynolds-averaged Navier–Stokes) model was used to study the energy harvesting performance of wind turbines with different design parameters inside the tunnel during the entire process of a train passing through a tunnel. A higher value of offset distance of blades could promote the power efficiency of the wind turbine inside the wind tunnel. The maximum power efficiency with regard to overlap distance was found when an overlap distance is 0 m. The turbine with a negative twist angle yielded a better performance than the turbine with a positive twist angle. The optimal wind turbine can generate up to 157.9 W power when a train passes at 350 km/h. Given the tunnel distribution in China, 4.8 × 10 12 J energy will be recovered each day by this way, which is sufficient to supply the emergency power for railway lighting. It can also effectively ease the pressure of daily lighting power in railway tunnels. • Harvesting wind energy from railway tunnels is considered feasible. • DFBI (dynamic fluid body interaction) was used to simulate the response of the turbine. • The power efficiency of turbines with various design parameters was quantitatively evaluated. • The optimal wind turbine can generate up to 157.9 W power when a train passes at 350 km/h.

Yield curve risks in currency carry forwards

AbstractWe provide empirical evidence that cross‐country yield curve gaps (parallel gap, twist gap, and butterfly gap) are predictive to the expected currency carry premiums using currency forward contracts. We find that the expected currency gains are more notable as these yield curve risk factors at time t indicate short‐term bond prices of investment currencies to go up (positive parallel movement, negative twist, and positive butterfly). We also find carry gains are more sensitively affected by cross‐country monetary shocks than currency‐country inflation pressures and business cycles. Our findings support that cross‐country yield curve risk premiums still exist even after considering transaction costs.

A combined experimental and numerical study on shape memory alloy rods under torsion

In this article, a study on modeling and experimental characterization of a shape memory alloy rod undergoing torsional loading is presented. According to former studies, the direction of twist is effective on the response of a shape memory alloy rod. Accordingly, we used Brinson’s improved model and adapted it for torsional loading. Referring a twist deformation in the clockwise direction to a positive twist and a twist deformation in the counter clockwise direction to a negative twist, the asymmetric response of the shape memory alloy rod is studied. The material parameters for Brinson model are derived from the experimental tests and there is a good agreement between the present asymmetric model and the experimental data. Also, material parameters are verified due to the experimental test in different temperatures. In one of the case studies, the average error of asymmetric and symmetric models with respect to the experimental test is 4% and 15%, respectively. A parametric study along with a study on the hysteresis inner loops in addition to model prediction for different temperatures is reported in the result section.

Rotor aerodynamic shape design for improving performance of an unmanned helicopter

In order to improve the effective load of an unmanned helicopter, a new blade shape with a new airfoil section, non-linear negative twist, varied chord length and double-swept blade tip was designed by employing a CFD method coupled with an optimization method. Firstly, a new airfoil is designed with improved aerodynamic characteristics. By comparing the numerical data, the new airfoil has better lift-drag ratio, i.e., the maximum lift-drag ratio increases from 63.03 to 66.29 at Mach number of 0.3 and from 70.17 to 72.13 at Mach number of 0.4, compared with the original NACA8H12 airfoil. In addition, a new blade shape is designed based on the new airfoil. By comparing the numerical data, the CT of the design rotor increases from 4.79×10−3 to 5.07×10−3, and the maximum FM increases from 0.67 to 0.72 at the design state. After that, a verification test is performed in hovering flight. The test data indicated the a maxumu thrust increase of 3.18% at the design state. Meanwhile, the FM of design rotor is improved about 3.41% compared with the original rotor.

Convection Electric Field and Plasma Convection in a Twisted Magnetotail: A THEMIS Case Study 1–2 January 2009

AbstractWe investigate THEMIS satellite measurements made in a tail‐aligned constellation during a time interval on 1–2 January 2009, which has previously been attributed to an interval of an interplanetary magnetic field By‐driven magnetotail twisting. We find evidence for that the orientation of the convection electric field in the tail is twist‐mode dependent. For earthward flow and a negative twist (induced tail By< 0), the electric field is found to have northward Ez and tailward Ex components. During a positive twist (induced tail By> 0), the directions of Ez and Ex are reversed. The Ey component shows the expected dawn‐to‐dusk direction for earthward flow. The electric field components preserve their orientation across the neutral sheet, and a quasi‐collinear field is observed irrespective to the tail distance. The electric field associated with the tailward flow has an opposite direction compared to the earthward flow for the negative twist. For the positive twist, the results are less clear. The corresponding plasma convection and thus the magnetic flux transport have an opposite dawn‐dusk direction above and below the neutral sheet. The directions depend on the tail twist mode. The hemispherically asymmetric earthward plasma flows are suggested to be a manifestation of an asymmetric Dungey cycle in a twisted magnetotail. The role of tailward flows deserve further investigation.

Orientational Instability and Hysteresis Phenomena in a Ferronematic Liquid Crystal in a Magnetic Field

A magnetic-field-induced orientational structure in a ferronematic (FN) liquid crystal (LC) layer is studied within the continuum theory. The rotation angles of the director and the magnetization and the concentration of magnetic impurity corresponding to a supertwisted orientational structure of the suspension are calculated. It is shown that the deviation angle of the director from the direction of the external field has the hysteresis region in which the orientational structure of the FN changes stepwise from a state with a positive twist of the director to a state with a negative twist. A value of the magnetic field strength is found above which orientational bistability regions arise. It is shown that orientational instability under the rotation of the field most clearly manifests itself in FNs with strong anchoring of particles to the LC matrix. It is established that the effect of magnetic segregation responsible for the redistribution of magnetic particles in the layer leads to the expansion of the hysteresis region and to a decrease in the field at which orientational instability arises. It is shown that, in FNs with soft anchoring between magnetic and LC subsystems, there exist several response modes to a quasistatic rotation of the magnetic field.

Locally helical surfaces have bounded twisting

A topologically minimal surface may be isotoped into a normal form with respect to a fixed triangulation. If the intersection with each tetrahedron is simply connected, then the pieces of this normal form are triangles, quadrilaterals, and helicoids. Helical pieces can have any number of positive or negative twists. We show here that the net twisting of the helical pieces of any such surface in a given triangulated 3-manifold is bounded.

Aerodynamic performance evaluation of basic airfoils for an agricultural unmanned helicopter using wind tunnel test and CFD simulation

There is growing interest in unmanned aerial pesticide application, which is a new farming paradigm aimed at reducing labor and improving production stability. To alleviate the difficulties being experienced by operators and pilots, researchers are focusing on the lack of lift and are trying to enhance lift by improving rotor airfoil. In this study, with the objective of enhancing the rotor performance of agricultural unmanned helicopters, the performance of basic airfoils was evaluated in a wind tunnel and via computational fluid dynamics simulation. The lift and power characteristics of rotor blades were also evaluated. As airfoil design steps to improve the lift of unmanned helicopter, the characteristics of lift, drag, and power were analyzed via wind tunnel tests for the 400 mm section models of two airfoils, specifically a thick airfoil (V1505A) with blunt nose and a thin airfoil (V2008B) with drooping nose. The V1505A airfoil is appropriate for the inboard region, which requires stable aerodynamics at a high angle of attack. On the other hand, the V2008B airfoil is ideal for the outboard region of the rotor because it has a relatively high dynamic efficiency. Therefore, it is expected that a transitional airfoil blade with a negative twist angle can solve the problems of unmanned aerial pesticide application.

Molecular Dynamics of Double Stranded Xylo-Nucleic Acid.

Xylo-nucleic acid (XyloNA) is a synthetic analogue of ribo-nucleic acid (RNA), where the ribose sugar has been replaced by xylose. We present a molecular dynamics study of the conformational evolution of XyloNA double strand oligomers derived from A-RNA through the substitution of β-d-ribofuranose by β-d-xylofuranose and having lengths of 8, 16, and 29 base pairs, using a set of independent all-atom simulations performed at various time scales ranging from 55 to 100 ns, with one long 500 ns simulation of the 29-mer. In order to validate the robustness of XyloNA conformation, a set of simulations using various cutoff distances and solvation box dimensions has also been performed. These independent simulations reveal the uncoiling or elongation of the initial conformation to form an open ladder type transient state conformation and the subsequent formation of a highly flexible duplex with a tendency to coil in a left-handed fashion. The observed open ladder conformation is in line with recently obtained NMR data on the XyloNA 8-mer derived using 5'-d(GUGUACAC)-3'. The observed negative interbase pair twist leads to the observed highly flexible left-handed duplex, which is significantly less rigid than the stable left-handed dXyloNA duplex having a strong negative twist. A comparison between the xylo-analogues of DNA and RNA shows a clear distinction between the helical parameters, with implications for the pairing mechanism.