Gravity and solidity in four great ape species (Gorilla gorilla, Pongo pygmaeus, Pan troglodytes, Pan paniscus): Vertical and horizontal variations of the table task.

Three experiments modeled after infant studies were run on four great ape species (Gorilla gorilla, Pongo pygmaeus, Pan troglodytes, Pan paniscus) to investigate their reasoning about solidity and gravity constraints. The aims were: (a) to find out if great apes are subject to gravity biased search or display sensitivity for object solidity, (b) to check for species differences, and (c) to assess if a gravity hypothesis or more parsimonious explanations best account for failures observed. Results indicate that great apes, unlike monkeys, show no reliable gravity bias, that ape species slightly differ in terms of their performance, and that the errors made are best explained by a gravity account. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Rational design and selection of bivalent peptide ligands of thrombin incorporating P4-P1 tetrapeptide sequences: from good substrates to potent inhibitors

The tetrapeptide Phe-Asn-Pro-Arg is a structurally optimized sequence for binding to the active site of thrombin. By conjugating this tetrapeptide or some variants to a C-terminal fragment of hirudin, we were able to generate a series of new bivalent inhibitors of thrombin containing only genetically encodable natural amino acids. We found that synergistic binding to both the active site and an exosite of thrombin can be enhanced through substitutions of amino acid residues at the P3 and P3' sites of the active-site directed sequence, Phe(P4)-Xaa(P3)-Pro(P2)-Arg(P1)-Pro(P1')-Gln(P2')-Yaa(P3'). Complementary to rational design, a phage library was constructed to explore further the residue requirements at the P4, P3 and P3' sites for bivalent and optimized two-site binding. Very significantly, panning of the phage library has led to thrombin-inhibitory peptides possessing strong anti-clotting activities in the low nanomolar range and yet interfering only partially the catalytic active site of thrombin. Modes of action of the newly discovered bivalent inhibitors are rationalized in light of the allosteric properties of thrombin, especially the interplay between the proteolytic action and regulatory binding occurring at thrombin surfaces remote from the catalytic active site.     

An adaptive geometry parametrization for aerodynamic shape optimization

An adaptive geometry parametrization is presented to represent aerodynamic configurations during shape optimization. This geometry parametrization technique is constructed by integrating the classical B-spline formulation with a knot insertion algorithm. It is capable of inserting control points into a given parametrization without modifying the geometry. Taking advantage of this technique, a shape optimization problem can be solved as a sequence of optimizations from the basic parametrization to more refined parametrizations. Additional control points are inserted based on criteria incorporating sensitivity analysis and geometric constraints. Example problems involving airfoil optimization and induced drag minimization demonstrate the effectiveness of the proposed approach in comparison to uniformly refined parametrizations.     

Opportunistic Software Systems Development: Making Systems from What's Available

Despite all the difficulties encountered in each incarnation of software reuse, we persist along the path of trying to figure out how we're going to create systems that meet the ever-increasing demand for capability and, with it, complexity and sheer size. Opportunistic software systems development is a reality today and for the foreseeable future, as the five articles in IEEE Software 's November/December 2008 special issue on OSSD demonstrate. This special issue aims to gather together insights into the viability, or perhaps the inevitability, of OSSD and to bring forward the most effective practices known today. Another goal is to point the way to what needs to be done to make OSSD more accessible to all practitioners. The editors hope to help the software community realize the importance of this new trend and the many aspects of it that have yet to be conquered.     

Alpha-helical regions of the protein molecule as organic nanotubes

An α-helical region of protein molecule was considered in a model of nanotube. The molecule is in conditions of quantum excitations. Such model corresponds to a one-dimensional molecular nanocrystal with three molecules in an elementary cell at the presence of excitation. For the analysis of different types of conformational response of the α-helical area of the protein molecule on excitation, the nonlinear response of this area to the intramolecular quantum excitation caused by hydrolysis of adenosine triphosphate (ATP) is taken into account. It has been established that in the simplest case, three types of excitation are realized. As estimates show, each of them ‘serves’ different kinds of protein. The symmetrical type of excitation, most likely, is realized in the reduction of traversal-striped skeletal muscles. It has the highest excitation energy. This well protects from casual actions. Antisymmetric excitations have intermediate energy (between symmetrical and asymmetrical). They, most likely, are realized in membranous and nucleic proteins. It is shown that the conformational response of the α-helical region of the protein is (in angstroms) a quantity of order N _c /5, where N _c is the number of spiral turns. For the number of turns typical in this case: N _c  ~ 10, displacement compounds are a quantity of order 2 Å. It qualitatively corresponds to observable values. Asymmetrical excitations have the lowest energy. Therefore, most likely, they are realized in enzymatic proteins. It was shown that at this type of excitation, the bending of the α-helix is formally directed to the opposite side with respect to the antisymmetric excitations. Also, it has a greater value than the antisymmetric case for N _c  ≤ 14 and smaller for N _c  > 14.

PACS

92C05

MCS

36.20.Ey     

Kinematic calibration of Orthoglide-type mechanisms from observation of parallel leg motions

The paper proposes a new calibration method for parallel manipulators that allows efficient identification of the joint offsets using observations of the manipulator leg parallelism with respect to the base surface. The method employs a simple and low-cost measuring system, which evaluates deviation of the leg location during motions that are assumed to preserve the leg parallelism for the nominal values of the manipulator parameters. Using the measured deviations, the developed algorithm estimates the joint offsets that are treated as the most essential parameters to be identified. The validity of the proposed calibration method and efficiency of the developed numerical algorithms are confirmed by experimental results. The sensitivity of the measurement methods and the calibration accuracy are also studied.     

Conservative and Stable Degree Preserving SBP Operators for Non-conforming Meshes

Non-conforming numerical approximations offer increased flexibility for applications that require high resolution in a localized area of the computational domain or near complex geometries. Two key properties for non-conforming methods to be applicable to real world applications are conservation and energy stability. The summation-by-parts (SBP) property, which certain finite-difference and discontinuous Galerkin methods have, finds success for the numerical approximation of hyperbolic conservation laws, because the proofs of energy stability and conservation can discretely mimic the continuous analysis of partial differential equations. In addition, SBP methods can be developed with high-order accuracy, which is useful for simulations that contain multiple spatial and temporal scales. However, existing non-conforming SBP schemes result in a reduction of the overall degree of the scheme, which leads to a reduction in the order of the solution error. This loss of degree is due to the particular interface coupling through a simultaneous-approximation-term (SAT). We present in this work a novel class of SBP–SAT operators that maintain conservation, energy stability, and have no loss of the degree of the scheme for non-conforming approximations. The new degree preserving discretizations require an ansatz that the norm matrix of the SBP operator is of a degree \(\ge 2p\), in contrast to, for example, existing finite difference SBP operators, where the norm matrix is \(2p-1\) accurate. We demonstrate the fundamental properties of the new scheme with rigorous mathematical analysis as well as numerical verification.     

Comparison of fast radiation-annealed and isothermally annealed 75As+-implanted layers on silicon wafers

An investigation of fast radiation annealing (FRA) of ⁷⁵As⁺ -implanted silicon is presented which explores the influence of the following factors on the properties of the implanted layers compared with those of the same material subjected to an isochronal anneal under isothermal furnace annealing (IFA) conditions: the FRA power density (effectively the average temperature of the wafer); the orientation of the implanted layer with respect to the FRA source (face up to the source or face down); the implant dose and energy; the time schedule for the anneal; the distance of the wafer from the source and from a water-cooled platen. All experiments are conducted in a normal laboratory environment without the benefit of clean air. The principle variables studied are the spreading resistance profile and the sheet resistance. Significant differences are observed between IFA and FRA material. The most dramatic is that diffusion in the face-up FRA material is significantly less than that in the face-down FRA material. No explanation has been obtained to date for this difference. Devices made from these layers were tested. Excellent device results have been obtained on both types of annealed material.     

Enhanced stiffness modeling of manipulators with passive joints

The paper presents a methodology to enhance the stiffness analysis of serial and parallel manipulators with passive joints. It directly takes into account the influence of external and internal loadings on the manipulator configuration and, consequently, on its Jacobians and Hessians. The main contributions of this paper are the introduction of a non-linear stiffness model for the manipulators with passive joints, a relevant numerical technique for computing the Cartesian stiffness and stability criteria for configurations of the kinematic chains. Within the developed technique, the manipulator elements are presented as pseudo-rigid bodies separated by multidimensional virtual springs and perfect passive joints. Simulation examples are presented that deal with parallel manipulators of the Ortholide family and demonstrate the ability of the developed methodology to describe non-linear behavior of the manipulator structure such as a sudden change of the elastic instability properties (buckling).