Introduction to Protein Structure Prediction

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated

Theorizing ideas and discourse in political science: intersubjectivity, neo-institutionalisms, and the power of ideas

Oscar Larsson’s (2015) essay condemns discursive institutionalism for the “sin” of subjectivism. In reality, however, discursive institutionalism emphasizes the intersubjective nature of ideas through its theorization of agents’ “background ideational abilities” and “foreground discursive abilities.” It also avoids relativism by means of Wittgenstein’s distinction between experiences of everyday life and pictures of the world. Contrary to Larsson, what truly separates post-structuralism from discursive institutionalism is the respective approaches’ theorization of the relationship of power to ideas, with discursive institutionalists mainly focused on persuasive power through ideas, while post-structuralists focus on the structural power in ideas or on coercive power over ideas

On the origin of second-peak splitting in the static structure factor of metallic glasses

It is proposed that the splitting of the second peak of the total static structure factor, S(k), of many metallic glasses is essentially the same feature as the indentation at kσ = (9/2)π in the function (sin k σ + α−1 sin kασ), caused by the coincidence of the fourth minimum of the second term with the third maximum of the first term when α ≈ 5/3. Together with the strong-weak relation of the split peak components of S(k), this feature indicates the splitting to be direct evidence for face-sharing of regular tetrahedra (α = 2√2/3) dominating the topological short range order; increasing the number of face-sharing tetrahedra in local structural units indeed increases the amount of peak splitting in S(k); a dense random packing of well defined identical structural units (DRPSU), with neighbouring units linked together by a shared icosahedron, is described in detail. The packing fraction in a homogeneous, isotropic 1078-atom model is 0.67, after static relaxation under a two-body Lennard-Jones potential.\ud \u

The 1985 Chile earthquake: Structural characteristics and damage statistics for the building inventory in Vina del Mar

The Chile earthquake of 3 March 1985 resulted in an effective peak acceleration of 0.36g in the coastal city of Vina del Mar. The city had an inventory of over 400 reinforced concrete buildings ranging in height from 5 to 23 stories. The observed behavior of the buildings is interpreted in relation to the physical characteristics of the structural systems.National Science Foundation Grant ECE 86-0378

Improving machine dynamics via geometry optimization

The central thesis of this paper is that the dynamic performance of machinery can be improved dramatically in certain cases through a systematic and meticulous evolutionary algorithm search through the space of all structural geometries permitted by manufacturing, cost and functional constraints. This is a cheap and elegant approach in scenarios where employing active control elements is impractical for reasons of cost and complexity. From an optimization perspective the challenge lies in the efficient, yet thorough global exploration of the multi-dimensional and multi-modal design spaces often yielded by such problems. Morevoer, the designs are often defined by a mixture of continuous and discrete variables - a task that evolutionary algorithms appear to be ideally suited for. In this article we discuss the specific case of the optimization of crop spraying machinery for improved uniformity of spray deposition, subject to structural weight and manufacturing constraints. Using a mixed variable evolutionary algorithm allowed us to optimize both shape and topology. Through this process we have managed to reduce the maximum roll angle of the sprayer by an order of magnitude , whilst allowing only relatively inexpensive changes to the baseline design. Further (though less dramatic) improvements were shown to be possible when we relaxed the cost constraint. We applied the same approach to the inverse problem of reducing the mass while maintaining an acceptable roll angle - a 2% improvement proved possible in this cas

Structural properties of disk galaxies. II. Intrinsic shape of bulges

(Abridged) The structural parameters of a magnitude-limited sample of 148 unbarred S0-Sb galaxies were analyzed to derive the intrinsic shape of their bulges. We developed a new method to derive the intrinsic shape of bulges based on the geometrical relationships between the apparent and intrinsic shapes of bulges and disks. The equatorial ellipticity and intrinsic flattening of bulges were obtained from the length of the apparent major and minor semi-axes of the bulge, twist angle between the apparent major axis of the bulge and the galaxy line of nodes, and galaxy inclination. We found that the intrinsic shape is well constrained for a subsample of 115 bulges with favorable viewing angles. A large fraction of them is characterized by an elliptical section (B/A<0.9). This fraction is 33%, 55%, and 43% if using their maximum, mean, or median equatorial ellipticity, respectively. Most are flattened along their polar axis (C<(A+B)/2). The distribution of triaxiality is strongly bimodal. This bimodality is driven by bulges with Sersic index n>2, or equivalently, by the bulges of galaxies with a bulge-to-total ratio B/T>0.3. In particular, bulges with n\leq2 and with B/T\leq0.3 show a larger fraction of oblate axisymmetric (or nearly axisymmetric) bulges, a smaller fraction of triaxial bulges, and fewer prolate axisymmetric (or nearly axisymmetric) bulges with respect to bulges with n>2 and with B/T>0.3, respectively. According to predictions of the numerical simulations of bulge formation, bulges with n\leq2, which show a high fraction of oblate axisymmetric (or nearly axisymmetric) shapes and have B/T\leq0.3, could be the result of dissipational minor mergers. Both major dissipational and dissipationless mergers seem to be required to explain the variety of shapes found for bulges with n>2 and B/T>0.3.Comment: 16 pages, 12 figures; accepted for publication in A&

Vibrational Modal Frequencies and Shapes of Two-Span Continuous Timber Flooring Systems

Based on classic vibrational bending theory on beams, this paper provides comprehensive analytical formulae for dynamic characteristics of two equal span continuous timber flooring systems, including frequency equations, modal frequencies, and modal shapes. Four practical boundary conditions are considered for end supports, including free, sliding, pinned, and fixed boundaries, and a total of sixteen combinations of flooring systems are created. The deductions of analytical formulae are also expanded to two unequal span continuous flooring systems with pinned end supports, and empirical equations for obtaining the fundamental frequency are proposed. The acquired analytical equations for vibrational characteristics can be applied for practical design of two-span continuous flooring systems. Two practical design examples are provided as well

Self-supporting structure design in additive manufacturing through explicit topology optimization

One of the challenging issues in additive manufacturing (AM) oriented topology optimization is how to design structures that are self-supportive in a manufacture process without introducing additional supporting materials. In the present contribution, it is intended to resolve this problem under an explicit topology optimization framework where optimal structural topology can be found by optimizing a set of explicit geometry parameters. Two solution approaches established based on the Moving Morphable Components (MMC) and Moving Morphable Voids (MMV) frameworks, respectively, are proposed and some theoretical issues associated with AM oriented topology optimization are also analyzed. Numerical examples provided demonstrate the effectiveness of the proposed methods.Comment: 81 pages, 45 figure