Design analysis of ductile failure in dovetail connections

The static plastic collapse of ductile dovetail structures is investigated by three analysis methods: slip-line field (SLF) theory based on a sheet drawing model, finite element limit analysis, and linear elastic finite element analysis with adapted pressure vessel design stress linearization and categorization methods. A range of angles and heights are considered in the investigation. Three experimental test cases are also presented. The limit analysis results are found to give the best comparison with the limited experimental results, indicating similar collapse loads and modes of ductile collapse. The SLF solution is found to give conservative but useful failure loads for small dovetail angles but, at angles greater than 30°, the solution is not generally conservative. The pressure vessel design by the analysis stress categorization procedure was adapted for dovetail analysis and was found to give reasonably conservative collapse loads in most cases. However, the procedure requires the designer to consider a number of different stress classification lines to ensure that a conservative collapse load is identified. It is concluded that the finite element limit analysis approach provides the best and most direct route to calculating the allowable load for the joint and is the preferred method when appropriate finite element analysis facilities are available

Solitons in the Yakushevich model of DNA beyond the contact approximation

The Yakushevich model of DNA torsion dynamics supports soliton solutions, which are supposed to be of special interest for DNA transcription. In the discussion of the model, one usually adopts the approximation $\ell_0 \to 0$, where $\ell_0$ is a parameter related to the equilibrium distance between bases in a Watson-Crick pair. Here we analyze the Yakushevich model without $\ell_0 \to 0$. The model still supports soliton solutions indexed by two winding numbers $(n,m)$; we discuss in detail the fundamental solitons, corresponding to winding numbers (1,0) and (0,1) respectively

Bubble statistics and positioning in superhelically stressed DNA

We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for superhelical DNA. The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length ($10^6-10^9$ base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of $10^2-10^3$ base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.Comment: to be appeared in Physical Review

Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.Comment: 8 pages, 9 figure

Folding the Carpenter's Tape: Boundary Layer Effects

Abstract The “carpenter’s measuring tape” is a thin spring-steel strip, preformed to a curved cross section of radius R, which is straight when being used for measuring. Under bending moments, it forms a localized hinge, in which the transverse curvature is suppressed, and the longitudinal radius r is approximately equal to R. Rimrott made a simple strain energy analysis of the hinge region for isotropic material, which predicted that r = R. Both experimental observations and finite element computations show that ξ = r/R > 1, where the value of ξ exceeds unity by up to 15%, depending on whether the tape is bent in “equal-sense” or “opposite-sense” curvature; ξ varies linearly with Poisson’s ratio in both cases. We make a minor change to Rimrott’s analysis by introducing a boundary layer, in order better to satisfy the physical conditions at the free edges; this successfully accounts for the observed behavior of the tape.Non

Thermodynamics of Twisted DNA with Solvent Interaction

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over $\sim 10^7 - 10^8$ base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.Comment: The Journal of Chemical Physics (2011) in pres

Vegetation structure influences foraging decisions in a declining grassland bird : the importance of fine-scale habitat and grazing regime

Funding: British Trust for Ornithology (BTO) Research Grant.Capsule: Whinchat Saxicola rubetra foraging behaviour was significantly influenced by habitat structure and grazing. Aims: To assess how foraging habitats selected by breeding Whinchats differed from wider territory attributes under contrasting grazing management in multiple upland areas in Scotland: principally sheep grazed, Red Deer grazed or ungrazed, and to identify how differing land use may limit suitable foraging areas. Methods: We compared fine-scale vegetation structure in patches chosen for foraging by Whinchats in contrasting grazing management regimes. Results: Whinchats were less likely to forage in patches with a greater cover of bracken and tall non-bracken vegetation, regardless of grazing regime. Grass cover influenced foraging behaviour in ungrazed habitats only, where Whinchats were less likely to forage in areas with high grass cover. Conclusion: Whinchats appear to require a mosaic or range of sward structures within breeding territories, highlighting the importance of establishing how vegetation structure influences breeding birds at different spatial scales. Our results suggest that suitable foraging patches were plentiful within grazed habitats but potentially limited in ungrazed habitats. Further work is needed to identify management regimes and interventions to maintain conditions suitable for breeding Whinchats that are compatible with other land use and conservation objectives.PostprintPeer reviewe

Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops

The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized DNA with lengths that are not integer multiples of the pitch take on nontrivial shapes that involve bending out of planes and formation of kinks. The effect of sequence inhomogeneity on the shape of DNA is addressed, and shown to enhance the geometrical features. These findings could shed some light on the role of DNA conformation in protein--DNA interactions

Multistability of free spontaneously-curved anisotropic strips

Multistable structures are objects with more than one stable conformation, exemplified by the simple switch. Continuum versions are often elastic composite plates or shells, such as the common measuring tape or the slap bracelet, both of which exhibit two stable configurations: rolled and unrolled. Here we consider the energy landscape of a general class of multistable anisotropic strips with spontaneous Gaussian curvature. We show that while strips with non-zero Gaussian curvature can be bistable, strips with positive spontaneous curvature are always bistable, independent of the elastic moduli, strips of spontaneous negative curvature are bistable only in the presence of spontaneous twist and when certain conditions on the relative stiffness of the strip in tension and shear are satisfied. Furthermore, anisotropic strips can become tristable when their bending rigidity is small. Our study complements and extends the theory of multistability in anisotropic shells and suggests new design criteria for these structures.Comment: 20 pages, 10 figure

Structural, mechanical and thermodynamic properties of a coarse-grained DNA model

We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective interactions are used to represent chain connectivity, excluded volume, base stacking and hydrogen bonding, naturally reproducing a range of DNA behaviour. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the torsional and stretching stiffness of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.Comment: 25 pages, 16 figure