Emergence of highly-designable protein-backbone conformations in an off-lattice model

Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino-acid sequences for which they represent the unique ground state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off-lattice model. The highly designable conformations of a chain of 23 amino acids are identified, and found to be remarkably insensitive to model parameters. While some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix-turn-helix motifs, others do not resemble known folds and may be candidates for novel fold design.Comment: 7 figure

Analysis of the Relationship Between Microstructure and Elastic Properties of the Cell Wall

A three-dimensional analysis of the relationship between the microstructure and the anisotropic elastic properties of the cell wall was made, using the theory of composite materials. In particular, the influence of the orientation of microfibrils in each layer, crossed helical structure, thickness of layers, and the spacing between the rectangular reinforced microfibrils to such properties were explored; spacing between microfibrils in each wall layer was found to be critical, and presence of crossed helices in the Sa layer and the S2 micro-fibril angles was found significant in relation to elastic properties. Numerical data of all elastic constants of the cell wall were evaluated for five hypothetical models that included the fibers of earlywood, latewood, and compression wood. Theoretical data of the axial Young's modulus of the wood fibers were compared with those values obtained from static tension tests and sonic tests by other investigators. The inadequacy of the technique used in the static tension tests of wood fibers was discussed, and a proper approach for such analysis was suggested

Damping of metallic wool with embedded rigid body motion amplifiers

The use of entangled metallic wires as vibrational dampers and shock isolators is of interest in a variety of applications. By taking advantage of the frictional contact between the contiguous wires, it has been shown that significant amounts of energy dissipation can be achieved. The amount of energy dissipation is highly dependent on many factors with one in particular being the excitation amplitude. When the excitation amplitude is low, a combination of the number of contact points, in which have relative motion, and the contact pressure are lessened often leading to a sacrifice in energy dissipation. In this paper, spherical metallic rigid bodies are embedded within metallic wool. These rigid bodies act as motion amplifiers in which, locally within the metallic wool, amplify the excitation amplitude leading to an increase in vibrational damping. Presented are experimental modal results from various metallic wool/embedded rigid body arrangements within a prismatic hollow aluminium tube. It is found that the incorporation of the embedded rigid bodies into the steel wool significantly improves the damping within the system. It is demonstrated that an increase in damping by 2328% has been achieved at only a 3.8% penalty in mass. It is found that the level of damping from the embedded rigid bodies depends not only on the excitation amplitude but their quantity and the accompanying steel wool configuration. A finite element procedure coupled with an analytical model is proposed which accounts for the strain energy produced within the steel wool to estimate the damping effect that this filler material has on the behaviour of the overall structure. The model treats the metallic wool/rigid sphere combination as a homogeneous equivalent solid with amplitude dependent damping properties, thereby reducing the complexities of the physics-based model while still providing an estimate of the vibrational damping while in the frequency domain

Experimental investigation and modeling of dynamic performance of wave springs

This paper investigates vibration suppression potentials for a novel frictional system - a wave spring. Two different types of wave springs, crest-to-crest and nested ones, were used in this work. Compared with nested wave springs, crest-to-crest wave springs have lower damping and a larger range for the linear stiffness due to a reduced level of contact. Dynamic compressive tests, subject to different static compression levels, are carried out to investigate the force-displacement hysteresis of individual wave springs. The stiffness is shown to increase up to 800% when the static compression is at 40%. The crest-to-crest wave spring is shown to provide loss factors up to 0.12 while nested ones as high as 0.80. Testing also showed that performance did not degrade between room temperature and 100°C. The effect of different spring materials, inner diameter and flat spring width are also evaluated

Photomechanical Investigation of Structural Behavior of Gyroscope Components. Task IV - Analysis of Initial Redesign of AB5-K8 GYROSCOPE

Photomechanics of structure and materials in redesigned AB5-K8 gyroscope component

Superconducting correlations in ultra-small metallic grains

To describe the crossover from the bulk BCS superconductivity to a fluctuation-dominated regime in ultrasmall metallic grains, new order parameters and correlation functions, such as ``parity gap'' and ``pair-mixing correlation function'', have been recently introduced. In this paper, we discuss the small-grain behaviour of the Penrose-Onsager-Yang off-diagonal long-range order (ODLRO) parameter in a pseudo-spin representation. Relations between the ODLRO parameter and those mentioned above are established through analytical and numerical calculations.Comment: 7 pages, 1 figur

Symmetry and designability for lattice protein models

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a two-dimensional lattice protein model based on hydrophobicity, we find that those native structures that are encoded by the largest number of different sequences have high symmetry. However only certain symmetries are enhanced, e.g. x/y-mirror symmetry and $180^o$ rotation, while others are suppressed. If it takes a large number of mutations to destabilize the native state of a protein, then, by definition, the state is highly designable. Hence, our findings imply that insensitivity to mutation implies high symmetry. It appears that the relationship between designability and symmetry results because protein substructures are also designable. Native protein folds may therefore be symmetric because they are composed of repeated designable substructures.Comment: 13 pages, 10 figure

Forest structure, stand composition, and climate-growth response in montane forests of Jiuzhaigou National Nature Reserve, China.

Montane forests of western China provide an opportunity to establish baseline studies for climate change. The region is being impacted by climate change, air pollution, and significant human impacts from tourism. We analyzed forest stand structure and climate-growth relationships from Jiuzhaigou National Nature Reserve in northwestern Sichuan province, along the eastern edge of the Tibetan plateau. We conducted a survey to characterize forest stand diversity and structure in plots occurring between 2050 and 3350 m in elevation. We also evaluated seedling and sapling recruitment and tree-ring data from four conifer species to assess: 1) whether the forest appears in transition toward increased hardwood composition; 2) if conifers appear stressed by recent climate change relative to hardwoods; and 3) how growth of four dominant species responds to recent climate. Our study is complicated by clear evidence of 20(th) century timber extraction. Focusing on regions lacking evidence of logging, we found a diverse suite of conifers (Pinus, Abies, Juniperus, Picea, and Larix) strongly dominate the forest overstory. We found population size structures for most conifer tree species to be consistent with self-replacement and not providing evidence of shifting composition toward hardwoods. Climate-growth analyses indicate increased growth with cool temperatures in summer and fall. Warmer temperatures during the growing season could negatively impact conifer growth, indicating possible seasonal climate water deficit as a constraint on growth. In contrast, however, we found little relationship to seasonal precipitation. Projected warming does not yet have a discernible signal on trends in tree growth rates, but slower growth with warmer growing season climates suggests reduced potential future forest growth

Interaction of Individual Skyrmions in Nanostructured Cubic Chiral Magnet

We report the direct evidence of field-dependent character of the interaction between individual magnetic skyrmions as well as between skyrmions and edges in B20-type FeGe nanostripes observed by means of high resolution Lorentz transmission electron microscopy. It is shown that above certain critical values of external magnetic field the character of such long-range skyrmion interactions change from attraction to repulsion. Experimentally measured equilibrium inter-skyrmion and skrymion-edge distances as function of applied magnetic field shows quantitative agreement with the results of micromagnetic simulations. Important role of demagnetizing fields and internal symmetry of three-dimensional magnetic skyrmions are discussed in details.Comment: accepted in PR

Exact solutions for a mean-field Abelian sandpile

We introduce a model for a sandpile, with N sites, critical height N and each site connected to every other site. It is thus a mean-field model in the spin-glass sense. We find an exact solution for the steady state probability distribution of avalanche sizes, and discuss its asymptotics for large N.Comment: 10 pages, LaTe