Anisotropic Bending Research Articles

NuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.

Effects of anisotropic bending stiffness of gas diffusion layers on the performance of polymer electrolyte membrane fuel cells with bipolar plates employing different channel depths

The effects of the anisotropic bending stiffness of gas diffusion layers (GDLs) on the performance of polymer electrolyte membrane fuel cells with metallic bipolar plates (MBPs), having different channel depths, are investigated. The current–voltage performance of fuel cells with 90° GDLs, whose directions of higher stiffness are perpendicular to the direction of the major flow field, is generally higher than that of cells with 0° GDLs, whose directions of higher stiffness are parallel to the direction of the major flow field. In the shallowest channel, the air pressure drop (ΔP) values of the 90° GDL cells are clearly lower than those of the 0° GDL cells, indicating less intrusion of the 90° GDL into the MBP channels. However, no significant difference appears between the air ΔP values of 0° and 90° GDL cells employing deeper channels. In comparison with other cells employing deeper channels, a dramatic increase in the high-frequency resistance of both the 0° and 90° GDL cells with the shallowest channel is unexpectedly observed, presumably due to the exceptional increase in the hydrogen and air pressure, which may cause more deformation and poor contact status of the GDLs in the cell. The cross-sectional images of GDLs upon compression indicate that the difference of blocked channel area between 0° and 90° GDL cells is much larger in the case of the shallowest channel, resulting in the observed air ΔP, whereas it is substantially negligible for the deepest channel.

Glass phase in anisotropic surface model for membranes

A Finsler geometric surface model for membranes is studied by using the Monte Carlo simulation technique on connection-fixed triangle lattices with sphere topology. An in-plane three-dimensional unit vector σ is assumed to be the in-plane tilt variable of the surface. The interaction with σ is described by the XY-model Hamiltonian. Since this variable σ is considered as a vector field on the surface, a Finsler metric is defined by using σ. We find that the model has three different phases. They change from the para-magnetic phase to the ferromagnetic and to the glass phases when the strength of the XY interaction increases. Both the para-magnetic and the glass phases are characterized by random configuration of σ; the variable σ randomly fluctuates in the para-magnetic phase while it is randomly frozen in the glass phase. We also find that the surface becomes spherical in both phases. On the contrary, in the ferro-magnetic phase the surface shape becomes tubular or discotic due to the anisotropic bending rigidity and surface tension coefficient, which are dynamically generated by ordered configurations of σ.

Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest

The tumor suppressor protein p53 exhibits high affinity to the response elements regulating cell cycle arrest genes (CCA-sites), but relatively low affinity to the sites associated with apoptosis (Apo-sites). This in vivo tendency cannot be explained solely by the p53-DNA binding constants measured in vitro. Since p53 can bind nucleosomal DNA, we sought to understand if the two groups of p53 sites differ in their accessibility when embedded in nucleosomes. To this aim, we analyzed the sequence-dependent bending anisotropy of human genomic DNA containing p53 sites. For the 20 CCA-sites, we calculated rotational positioning patterns predicting that most of the sites are exposed on the nucleosomal surface. This is consistent with experimentally observed positioning of human nucleosomes. Remarkably, the sequence-dependent DNA anisotropy of both the p53 sites and flanking DNA work in concert producing strong positioning signals. By contrast, both the predicted and observed rotational settings of the 38 Apo-sites in nucleosomes suggest that many of these sites are buried inside, thus preventing immediate p53 recognition and delaying gene induction. The distinct chromatin organization of the CCA response elements appears to be one of the key factors facilitating p53-DNA binding and subsequent activation of genes associated with cell cycle arrest.

Effects of anisotropic bending stiffness of gas diffusion layer on the MEA degradation of polymer electrolyte membrane fuel cells by wet/dry gas

The effects of anisotropic bending stiffness of a gas diffusion layer (GDL) on membrane electrode assembly (MEA) degradation were investigated. We prepared GDLs with a fiber direction perpendicular to the major flow (i.e., “90° GDL”) and with a fiber direction parallel to the major flow (i.e., “0° GDL”). To analyze the mechanical durability as a function of GDL anisotropy, we examined cell performances such as the I–V characteristics and impedances and the hydrogen crossover characteristics during wet/dry cycles. The results showed that the 90° GDL fuel cell is superior to the 0° GDL fuel cell in terms of higher I–V performance, lower resistance at high frequency, and lower hydrogen crossover through the MEA. Mechanical degradation of the 0° GDL was investigated using scanning electron microscopy (SEM).

Development of Saddle-Shaped Coils Using Coated Conductors for Accelerator Magnets

A project to develop fundamental technologies for accelerator magnets using high-T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> superconductors is currently underway. The primary applications in this project are fixed field alternating gradient (FFAG) accelerators for carbon cancer therapy systems and accelerator-driven subcritical reactors. One of the challenging issues in this study is to accomplish the complicated coil shape required for the accelerator magnets using YBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> (YBCO) coated conductors. An asymmetric, three-dimensional winding structure has been designed for the main ring of an FFAG accelerator, but the anisotropic bending flexibility of coated conductors is constrained because of their tape-like shape. To demonstrate a suitable winding technology for a three-dimensional coil using coated conductors, a prototype winding machine with a two-axis motion mechanism was constructed. Based on the present design of the FFAG magnet, a saddle-shaped coil wound on a curved surface with a radius of 700 mm was designed. A 100-turn coil was wound by the winding machine using an approximately 90 m length of 3 mm-wide YBCO coated conductor made by the IBAD-MOCVD method. The coil was impregnated with epoxy resin, and the voltage-current ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> ) characteristics were evaluated in a liquid nitrogen environment. From the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> characteristics in an electric field region of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> V/cm, an index value of above 20 was obtained, which means that the superconducting properties were not degraded.

Effect of fiber angle orientation on a laminated composite single-lap adhesive joint

In the case of composite laminates with lap joints, one of the factors acting on the bonded joint behavior is the stacking sequence, most of research presented in the literature do not separate global effects (membrane and bending stiffness modification) and local effect (ply orientation near the adhesive layer). This study deals with the characterization of such effects in the case of single-lap joints of carbon/epoxy laminates. In order to isolate the local effects, specific quasi-isotropic quasi-homogeneous stacking sequences are used. When the stiffness properties are maintained constant, strength variations of more than 30% are observed with respect to remoteness position of 0°-ply orientation. Tests performed with a symmetric laminate with bending anisotropy show that the bending stiffness also plays an important role in the joint behavior. Fracture behavior of delamination occurs between these plies and also depends on an out-of-plane position of 0°-ply laminate near the adhesive layer.

Bio-mechanical Properties of Novel Bi-layer Collagen-Elastin Scaffolds for Heart Valve Tissue Engineering

Collagen and elastin are two major components of the extracellular matrix of heart valves. This work examines bi-layer scaffolds made of collagen and elastin for potential use in the tissue engineering of heart valves, by investigating the effects of the layered structure on the mechanical and biological properties. The scaffolds showed anisotropic bending moduli depending on the loading directions (lower when with curvature than against curvature), which mimicked the characteristic behaviour of the native heart valves. The interaction of cardiosphere-drived cells with the scaffolds was characterized by scanning electron microscopy and multiphoton microscopy, and an asymmetrical cell distribution was observed. The bi-layer scaffolds have represented a forwarding step to the tri-layer scaffolds that more closely resemble the native heart valves.

Failure mechanisms of sandwich composites with orthotropic integrated woven corrugated cores: Experiments

To enhance the skin–core debonding resistance of sandwich composites, a new integrated woven corrugated sandwich composite (IWCSC) was designed and fabricated. Quasi-static compression, shearing and three-point bending tests were carried out to reveal the mechanical property and the failure mechanism of the IWCSC. In compression, gradual core crushing and contacting with the skin induced ductile load–displacement curves featured by a long deformation plateau. The anisotropic core structure leads to orthotropic anti-shearing resistances in the warp and weft directions. The difference is even at the level of a magnitude. IWCSC is an anisotropic bending dominated light weight material. Anisotropy of the core structure leads to different failure mechanisms of IWCSC panels in bending. Bended in the warp direction failure mode of the beam is core shearing while in the weft direction is indentation. High skin–core debonding resistance has been testified by the experiments. Behaviors of IWCSC panels were predicted and the predictions are close to the tested data.

Healing performance of Ti2AlC ceramic studied with in situ microcantilever bending

In situ microcantilever bending tests were carried out to evaluate the healing efficiency of pre-notched Ti2AlC ceramic after annealing at 1200 °C for 1.5 h. Microcantilevers of different orientations were fabricated with focused ion beam method at different locations, i.e. in a singular Ti2AlC grain, at a grain boundary or at the Ti2AlC–Al2O3 interface after healing. Ti2AlC microcantilever shows an anisotropic bending strength (ranging between 9.6 GPa and 4.6 GPa depending on the precise crystallographic orientations) that is closely related to the different atomic bonds in the layered structure. After healing, the Ti2AlC–Al2O3 microcantilevers exhibit almost the same strength of about 5.2 GPa, i.e. slightly higher than the cleavage strength (4.6 GPa) of the initial Ti2AlC microcantilevers. It suggests that the orientation of the matrix grain has no significant influence on the strength of healed microcantilevers. Furthermore, it turns out that the strength of the microcantilever with a healed grain boundary is at least twice the strength of the initial Ti2AlC cantilever with a grain boundary. It is concluded that the oxidation dominated self-healing mechanism of Ti2AlC ceramics can result in a perfect recovery of mechanical performance. The paper shows that the in situ microcantilever bending test provides a quantitative method for the evaluation of the strength of self-healing ceramics.

DNA information: from digital code to analogue structure

The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone-octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry.

Correlation between anisotropic bending stiffness of GDL and land/channel width ratio of polymer electrolyte membrane fuel cells

A correlation between anisotropic bending stiffness of a gas diffusion layer (GDL) and land/channel width ratios of metallic bipolar plates (MBPs) in polymer electrolyte membrane fuel cells has been systematically investigated. I–V performances of the fuel cells with 90° GDLs, whose directions of higher stiffness are perpendicular to the direction of the major flow field, are generally higher than those with 0° GDLs, whose directions of higher stiffness are parallel with the direction of the major flow field. However, the differences of I–V performances and high-frequency resistance values between 0° and 90° GDL cells gradually decrease with increasing land/channel width ratio, because of the reduced anisotropic stiffness effects of the GDLs due to the better support by the MBPs with wider lands. The cross-sectional images of GDLs upon compression indicate that the 0° GDL appears to be more deformed and intruded into channel than the 90° GDL under the narrowest lands, whereas both 0° and 90° GDLs show very little intrusion and deformation under the widest lands. The results clearly explain why some MBPs (i.e., narrower lands) exhibit strong effects of GDL’s anisotropic stiffness on cell performances, whereas other MBPs (i.e., wider lands) do not experience such effects.

Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.

Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models.

Formability of Ultrafine-Grained AA6016 Sheets Processed by Accumulative Roll Bonding

Aluminium alloy AA6016 was accumulative roll bonded up to eight cycles in order to produce an ultrafine-grained microstructure. The formability of these sheets was investigated by means of bending tests. Furthermore the influence of a local laser heat treatment at the bending edge is observed. The strength of the UFG samples is increased by a factor of around two compared to the conventionally grained T4 condition which also results in up to 50 % higher punch forces needed for bending of ARB processed samples. An anisotropic bending behaviour is observed. By applying a tailored laser heat treatment along the bending edge prior to the bending tests a local recrystallization and recovery at the deformation zone of the samples is achieved. Thus, ductility is increased locally whereby bending to an angle of 80° is possible with lower forming forces compared to the non-heat treated specimens. The results are compared to previous studies on mechanical properties and formability investigations of ARB processed AA6016.

Conformational collapse of surface-bound helical filaments

Chiral polymers are ubiquitous in nature and in the cellular context they are often found in association with membranes. Here we show that surface bound polymers with an intrinsic twist and anisotropic bending stiffness can exhibit a sharp continuous phase transition between states with very different effective persistence lengths as the binding affinity is increased. Above a critical value of the binding strength, determined solely by the torsional modulus and intrinsic twist rate, the filament can exist in a zero twist, surface bound state with a homogeneous stiffness. Below the critical binding strength, twist walls proliferate and function as weak or floppy joints that sharply reduce the effective persistence length that is measurable on long length scales. The existence of such dramatically different conformational states has implications for both biopolymer function in vivo and for experimental observations of such filaments in vitro.

Chirality- and curvature-dependent bending stiffness of single layer graphene

An analytical molecular mechanics model is developed to relate the bending properties of a single layer graphene to its atomic structure. Explicit expression for the bending stiffness of graphene with arbitrary chirality is derived. The results show that the bending stiffness of graphene depends significantly on the chiral angle, especially when the bending curvature is large. Curvature can induce significant anisotropic bending properties of graphene. The present analytical results are helpful for understanding of chirality- and curvature-dependent bending properties of graphene and thus useful for potential applications of graphene as a bending component of nano devices.

A parallel implementation of a mixed-hybrid finite element method for anisotropic plate bending problems

The paper deals with a parallel implementation of a mixed-hybrid finite element method for anisotropic plate bending problems with different boundary conditions. The mixed-hybrid method gives a simultaneous approximation to bending/twisting moments and deflection fields in the interior of each triangle and traces of displacement field and its normal derivative on sides of each triangle. Efficient parallel implementation procedures have been developed and the results of numerical experiments with time, speed-up comparisons on some aniso-/ortho-/isotropic plates of practical and research interest are given.

Modal analysis of anisotropic plates using the boundary element method

A numerical formulation for analysis of dynamic problems of thin anisotropic plates bending is presented. The bending behavior follows Kirchhoff's hypothesis. The formulation is based on the direct boundary element method. The problem is simplified by using the elastostatic fundamental solution of an infinite plate. Domain integrals arising from inertial terms are transformed into boundary integrals using the dual reciprocity technique. Boundary integrals are discretized and evaluated numerically. Natural frequencies for free vibration are obtained and the respective mode shapes are shown. The accuracy of numerical results obtained is assured by comparison with analytical or finite element results.

Influence of anisotropic bending stiffness of gas diffusion layers on the degradation behavior of polymer electrolyte membrane fuel cells under freezing conditions

The effects of gas diffusion layer’s (GDL’s) anisotropic bending stiffness on the degradation behavior of polymer electrolyte membrane fuel cells have been investigated under freezing conditions. We have prepared GDL sheet samples such that the higher stiffness direction of GDL roll is aligned with the major flow field direction of a metallic bipolar plate at angles of 0° (parallel: ‘0° GDL’) and 90° (perpendicular: ‘90° GDL’). The I–V performances before and after 1000 temperature cycles between −10 and 1 °C of 90° GDL stack are higher than those of 0° GDL stack, and the voltages of 90° GDL stack are decreased slower than those of 0° GDL stack, indicating a higher durability of 90° GDL stack. Furthermore, the values and increasing rates of high-frequency resistance of 90° GDL stack are lower than those of 0° GDL stack. However, the H 2 and air pressure differences before and after 1000 temperature cycles of 90° GDL stack are very similar to those of 0° GDL stack. The surface of anode catalyst layer (CL) of membrane-electrode assembly (MEA) with catalyst-coated membrane type in 0° GDL stack appears to be more severely damaged than that in 90° GDL stack, especially under the channels, whereas the surfaces of cathode CLs of MEAs in both 0° and 90° GDL stacks are slightly damaged after 1000 temperature cycles.

1201 シェル構造の補剛模様の一設計手法(GS1-1 一般セッションI,GS1 一般セッション)

Corrugated sheets have been used in various applications where lightweight and high bending stiffness have been required. However, they have limited their usefulness due to their extreme anisotropic bending stiffness. I developed isotropic patterned shell structures which had the high second moment of area in arbitrary cross sectional dimensions in the previous report. FEM and experimental results indicated that the developed shell structures made the weight of sheets less than half under the equivalent bending stiffness condition. Until now, the optimal design to maximize their bending stiffness has not been made clear yet. In this paper, new patterned shell structures are created by improving conventional pattern of the previous report to increase the bending stiffness.