48,097 research outputs found
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 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
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