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

A deformed analogue of Onsager's symmetry in the XXZ open spin chain

The XXZ open spin chain with general integrable boundary conditions is shown to possess a q-deformed analogue of the Onsager's algebra as fundamental non-abelian symmetry which ensures the integrability of the model. This symmetry implies the existence of a finite set of independent mutually commuting nonlocal operators which form an abelian subalgebra. The transfer matrix and local conserved quantities, for instance the Hamiltonian, are expressed in terms of these nonlocal operators. It follows that Onsager's original approach of the planar Ising model can be extended to the XXZ open spin chain.Comment: 12 pages; LaTeX file with amssymb; v2: typos corrected, clarifications in the text; v3: minor changes in references, version to appear in JSTA

The Erd\H{o}s-Ko-Rado theorem for twisted Grassmann graphs

We present a "modern" approach to the Erd\H{o}s-Ko-Rado theorem for Q-polynomial distance-regular graphs and apply it to the twisted Grassmann graphs discovered in 2005 by van Dam and Koolen.Comment: 5 page

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

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

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