SAGA: A project to automate the management of software production systems

The project to automate the management of software production systems is described. The SAGA system is a software environment that is designed to support most of the software development activities that occur in a software lifecycle. The system can be configured to support specific software development applications using given programming languages, tools, and methodologies. Meta-tools are provided to ease configuration. Several major components of the SAGA system are completed to prototype form. The construction methods are described

Central extension of the reflection equations and an analog of Miki's formula

Two different types of centrally extended quantum reflection algebras are introduced. Realizations in terms of the elements of the central extension of the Yang-Baxter algebra are exhibited. A coaction map is identified. For the special case of $U_q(\hat{sl_2})$, a realization in terms of elements satisfying the Zamolodchikov-Faddeev algebra - a `boundary' analog of Miki's formula - is also proposed, providing a free field realization of $O_q(\hat{sl_2})$ (q-Onsager) currents.Comment: 11 pages; two references added; to appear in J. Phys.

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement

Analyzing power measurements in high‐P2∥ p‐p elastic scattering

The analyzing power in 28 GeV/c proton/proton elastic scattering was measured at P2∥=5.95 and 6.56 (GeV/c)2 using a polarized proton target and an unpolarized proton beam at the Brookhaven National Laboratory AGS. Results indicate that the analyzing power, A, is rising sharply with P2∥.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87401/2/1123_1.pd

Adaptive response and enlargement of dynamic range

Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems.Comment: Corrected typos, minor text revision

From Quantum Affine Symmetry to Boundary Askey-Wilson Algebra and Reflection Equation

Within the quantum affine algebra representation theory we construct linear covariant operators that generate the Askey-Wilson algebra. It has the property of a coideal subalgebra, which can be interpreted as the boundary symmetry algebra of a model with quantum affine symmetry in the bulk. The generators of the Askey-Wilson algebra are implemented to construct an operator valued $K$- matrix, a solution of a spectral dependent reflection equation. We consider the open driven diffusive system where the Askey-Wilson algebra arises as a boundary symmetry and can be used for an exact solution of the model in the stationary state. We discuss the possibility of a solution beyond the stationary state on the basis of the proposed relation of the Askey-Wilson algebra to the reflection equation

High-Temperature Stress-Strain Behavior of MgO in Compression

Compressive stress-strain curves for several types of polycrystalline MgO specimens were correlated with those for single crystals and analyzed as a function of grain size and grain-boundary character at 1200 and 1400 C for several strain rates. The results for fully dense specimens were explained in terms of grain-boundary sliding and intergranular separation in addition to slip. The modification of grain-boundary nature concurrent with heat treatment for grain growth, caused by residual LUF, was associated with enhanced grain-boundary sliding and intergranular separation. For grain sizes <30 {micro}m, it was concluded that the von Miss criteria for ductility could be relaxed by the Occurrence of dislocation climb and, to a limited extent, by intergranular separation. Yield drop corresponding to dislocation multiplication occurred when grain-boundary sliding was initially promoted. Specimens with a liquid phase of adequate viscosity also indicated plasticity accompanied by high strength. Specimens with clean grain boundaries exhibited ductility and normal strain hardening with no intergranular separation

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users