cctbx news (open access)

cctbx news

The 'Computational Crystallography Toolbox' (cctbx, http://cctbx.sourceforge.net/) is the open-source component of the Phenix project (http://www.phenix-online.org/). Most recent cctbx developments are geared towards supporting new features of the phenix.refine application. Thus, the open-source mmtbx (macromolecular toolbox) module is currently being most rapidly developed. In this article we give an overview of some of the recent developments. However, the main theme of this article is the presentation of a light-weight example command-line application that was specifically developed for this newsletter: sequence alignment and superposition of two molecules read from files in PDB format. This involves parameter input based on the Phil module presented in Newsletter No. 5, fast reading of the PDB files with the new iotbx.pdb.input class, simple sequence alignment using the new mmtbx.alignment module, and use of the Kearsley (1989) superposition algorithm to find the least-squares solution for superposing C-alpha positions. The major steps are introduced individually, followed by a presentation of the complete application. The example application is deliberately limited in functionality to make it concise enough for this article. The main goal is to show how the open-source components are typically combined into an application. Even though the example is quite specific to macromolecular crystallography, we believe it …
Date: November 22, 2006
Creator: Grosse-Kunstleve, Ralf W.; Zwart, Peter H.; Afonine, Pavel V.; Ioerger, Thomas R. & Adams, Paul D.
Object Type: Article
System: The UNT Digital Library
ALE3D Simulations of Gap Closure and Surface Ignition for Cookoff Modeling (open access)

ALE3D Simulations of Gap Closure and Surface Ignition for Cookoff Modeling

We are developing ALE3D models to describe the thermal, chemical and mechanical behavior during the heating, ignition and explosive phases of various cookoff phenomena. The candidate models and numerical strategies are being evaluated using benchmark cookoff experiments. ALE3D is a three-dimensional computer code capable of solving the model equations in a coupled fashion through all the phases of the cookoff in a single calculation. For the cookoff experiments, we are interested in representing behavior on widely varying timescales. We have used an implicit hydrodynamics option during the heating phase and an explicit solution method during the explosive phase. To complicate the modeling problem, high heat fluxes cause rapid temperature increases in boundary layers and lead to the formation of gaps between energetic and structural materials and ignition on surfaces. The initially solid energetic and structural materials react to produce gases, which fill the gaps. These materials can also melt and flow. Since an implicit solution method is used, simple no-strength materials models can no longer be used for liquids and gases. In this paper, we discuss and demonstrate choices of materials models for solid/liquid/gas mixtures to be used in conjunction with the implicit solution method. In addition, results are given …
Date: June 22, 2006
Creator: Howard, W. M.; McClelland, M. A. & Nichols, A. L.
Object Type: Article
System: The UNT Digital Library
FY04&05 LDRD Final Report Fission Fragment Sputtering (open access)

FY04&05 LDRD Final Report Fission Fragment Sputtering

Fission fragments born within the first 7 {micro}m of the surface of U metal can eject a thousand or more atoms per fission event. Existing data in the literature show that the sputtering yield ranges from 10 to 10,000 atoms per fission event near the surface, but nothing definitive is known about the energy of the sputtered clusters. Experimental packages were constructed allowing the neutron irradiation of natural uranium foils to investigate the amount of material removed per fission event and the kinetic energy distribution of the sputtered atoms. Samples were irradiated but were never analyzed after irradiation. Similar experiments were attempted in a non-radioactive environment using accelerator driven ions in place of fission induced fragments. These experiments showed that tracks produced parallel to the surface (and not perpendicular to the surface) are the primary source of the resulting particulate ejecta. Modeling studies were conducted in parallel with the experimental work. Because the reactor irradiation experiments were not analyzed, data on the energy of the resulting particulate ejecta was not obtained. However, some data was found in the literature on self sputtering of {sup 252}Cf that was used to estimate the velocity and hence the energy of the ejected particulates. …
Date: February 22, 2006
Creator: Ebbinghaus, B.; Trelenberg, T.; Meier, T.; Felter, T.; Sturgeon, J.; Kuboda, A. et al.
Object Type: Report
System: The UNT Digital Library
Uranium-lead isotope systematics of Mars inferred from the basaltic shergottite QUE 94201 (open access)

Uranium-lead isotope systematics of Mars inferred from the basaltic shergottite QUE 94201

Uranium-lead ratios (commonly represented as {sup 238}U/{sup 204}Pb = {mu}) calculated for the sources of martian basalts preserve a record of petrogenetic processes that operated during early planetary differentiation and formation of martian geochemical reservoirs. To better define the range of {mu} values represented by the source regions of martian basalts, we completed U-Pb elemental and isotopic analyses on whole rock, mineral and leachate fractions from the martian meteorite Queen Alexandra Range 94201 (QUE 94201). The whole rock and silicate mineral fractions have unradiogenic Pb isotopic compositions that define a narrow range ({sup 206}Pb/{sup 204}Pb = 11.16-11.61). In contrast, the Pb isotopic compositions of weak HCl leachates are more variable and radiogenic. The intersection of the QUE 94201 data array with terrestrial Pb in {sup 206}Pb/{sup 204}Pb-{sup 207}Pb/{sup 204}Pb-{sup 208}Pb/{sup 204}Pb compositional space is consistent with varying amounts of terrestrial contamination in these fractions. We calculate that only 1-7% contamination is present in the purified silicate mineral and whole rock fractions, whereas the HCl leachates contain up to 86% terrestrial contamination. Despite the contamination, we are able to use the U-Pb data to determine the initial {sup 206}Pb/{sup 204}Pb of QUE 94201 (11.086 {+-} 0.008) and calculate the {mu} value …
Date: December 22, 2006
Creator: Gaffney, A M; Borg, L E & Connelly, J N
Object Type: Article
System: The UNT Digital Library
Atomic Force Microscope (AFM) measurements and analysis on Tinsley AIA-1000-003 primary substrate (open access)

Atomic Force Microscope (AFM) measurements and analysis on Tinsley AIA-1000-003 primary substrate

None
Date: February 22, 2006
Creator: Soufli, R; Baker, S L & Robinson, J C
Object Type: Report
System: The UNT Digital Library
Softwood Lumber Imports from Canada: Issues and Events (open access)

Softwood Lumber Imports from Canada: Issues and Events

This report provides a concise historical account of the dispute over softwood lumber imports from Canada, summarizes the subsidy and injury evidence, and discusses current issues and events.
Date: March 22, 2006
Creator: Gorte, Ross W. & Grimmett, Jeanne J.
Object Type: Report
System: The UNT Digital Library
Texas Attorney General Opinion: GA-0402 (open access)

Texas Attorney General Opinion: GA-0402

Document issued by the Office of the Attorney General of Texas in Austin, Texas, providing an interpretation of Texas law. It provides the opinion of the Texas Attorney General, Greg Abbott, regarding a legal question submitted for clarification; Whether an elected constable is prohibited from simultaneously serving as a full-time deputy sheriff (RQ 0383-GA)
Date: February 22, 2006
Creator: Texas. Attorney-General's Office.
Object Type: Text
System: The Portal to Texas History
Texas Attorney General Opinion: GA-0494 (open access)

Texas Attorney General Opinion: GA-0494

Document issued by the Office of the Attorney General of Texas in Austin, Texas, providing an interpretation of Texas law. It provides the opinion of the Texas Attorney General, Greg Abbott, regarding a legal question submitted for clarification: Whether Education Code sections 44.031 and 44.033 apply to real and personal property lease-purchase contracts authorized under Local Government Code sections 271.004 and 271.005 (RQ-0500-GA)
Date: December 22, 2006
Creator: Texas. Attorney-General's Office.
Object Type: Text
System: The Portal to Texas History
Texas Attorney General Opinion: GA-0495 (open access)

Texas Attorney General Opinion: GA-0495

Document issued by the Office of the Attorney General of Texas in Austin, Texas, providing an interpretation of Texas law. It provides the opinion of the Texas Attorney General, Greg Abbott, regarding a legal question submitted for clarification: Whether the Texas Department of Insurance is prohibited from disclosing the identities of companies writing commercial property insurance along the Texas coast (RQ-0502-GA)
Date: December 22, 2006
Creator: Texas. Attorney-General's Office.
Object Type: Text
System: The Portal to Texas History
Texas Attorney General Opinion: GA-0496 (open access)

Texas Attorney General Opinion: GA-0496

Document issued by the Office of the Attorney General of Texas in Austin, Texas, providing an interpretation of Texas law. It provides the opinion of the Texas Attorney General, Greg Abbott, regarding a legal question submitted for clarification: Education Code section 11.168 and its effect on an independent school district’s authority to build or pay for infrastructure for new schools within the district (RQ-0503-GA)
Date: December 22, 2006
Creator: Texas. Attorney-General's Office.
Object Type: Text
System: The Portal to Texas History
Texas Attorney General Opinion: GA-0497 (open access)

Texas Attorney General Opinion: GA-0497

Document issued by the Office of the Attorney General of Texas in Austin, Texas, providing an interpretation of Texas law. It provides the opinion of the Texas Attorney General, Greg Abbott, regarding a legal question submitted for clarification: Whether the 2006 Qualified Allocation Plan of the Texas Department of Housing and Community Affairs complies with Government Code section 2306.671(b) (RQ-0515-GA)
Date: December 22, 2006
Creator: Texas. Attorney-General's Office.
Object Type: Text
System: The Portal to Texas History
Iraq: Elections, Government, and Constitution (open access)

Iraq: Elections, Government, and Constitution

None
Date: May 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Research Tax Credit: Current Status, Legislative Proposals in the 109th Congress, and Policy Issues (open access)

Research Tax Credit: Current Status, Legislative Proposals in the 109th Congress, and Policy Issues

None
Date: September 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Taiwan: Recent Developments and U.S. Policy Choices (open access)

Taiwan: Recent Developments and U.S. Policy Choices

None
Date: September 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Syria: U.S. Relations and Bilateral Issues (open access)

Syria: U.S. Relations and Bilateral Issues

None
Date: June 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Middle East Free Trade Area: Progress Report (open access)

Middle East Free Trade Area: Progress Report

None
Date: June 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Defense Procurement: Full Funding Policy — Background, Issues, and Options for Congress (open access)

Defense Procurement: Full Funding Policy — Background, Issues, and Options for Congress

This report discusses the full funding policy, which is a federal budgeting rule that has been applied to Department of Defense (DOD) procurement programs since the 1950s. In recent years, some DOD weapons — specifically, certain Navy ships — have been procured with funding profiles that do not conform to the policy as it traditionally has been applied to DOD weapon procurement programs.
Date: February 22, 2006
Creator: O'Rourke, Ronald & Daggett, Stephen
Object Type: Report
System: The UNT Digital Library
Coast Guard Deepwater Program: Background, Oversight Issues, and Options for Congress (open access)

Coast Guard Deepwater Program: Background, Oversight Issues, and Options for Congress

This report discusses the Integrated Deepwater Systems (IDS) program, or Deepwater program for short, which is a $24-billion, 25-year project to replace and modernize the Coast Guard’s aging fleet of deepwater-capable ships and aircraft. It is the largest and most complex acquisition effort in Coast Guard history, encompassing 91 new cutters, 124 new small surface craft, and 244 new or converted airplanes, helicopters, and unmanned aerial vehicles (UAVs). The issue for Congress is whether to approve, reject, or modify the Administration’s annual funding requests and overall approach for the program.
Date: December 22, 2006
Creator: O'Rourke, Ronald
Object Type: Report
System: The UNT Digital Library
Net Neutrality: Background and Issues (open access)

Net Neutrality: Background and Issues

None
Date: December 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
Current Economic Conditions and Selected Forecasts (open access)

Current Economic Conditions and Selected Forecasts

This report provides information about the Current Economic Conditions and Selected Forecasts. U.S GDP growth has been positive for 18th consecutive quarters and the economy is in "expansion Phase".
Date: November 22, 2006
Creator: Makinen, Gail E.
Object Type: Report
System: The UNT Digital Library
Iraqi Civilian Deaths Estimates (open access)

Iraqi Civilian Deaths Estimates

None
Date: November 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
U.S. Foreign Aid to the Palestinians (open access)

U.S. Foreign Aid to the Palestinians

None
Date: December 22, 2006
Creator: unknown
Object Type: Report
System: The UNT Digital Library
The “Farm Bill” in Brief (open access)

The “Farm Bill” in Brief

Federal farm support, food assistance, agricultural trade, marketing, and rural development policies are governed by a variety of separate laws. Many of these laws periodically have been evaluated, revised, and renewed through an omnibus, multi-year farm bill. This report discusses the "farm bill" and it's components.
Date: March 22, 2006
Creator: Becker, Geoffrey S.
Object Type: Report
System: The UNT Digital Library
ALE3D Simulation and Measurement of Violence in a Fast Cookoff Experiment with LX-10 (open access)

ALE3D Simulation and Measurement of Violence in a Fast Cookoff Experiment with LX-10

We performed a computational and experimental analysis of fast cookoff of LX-10 (94.7% HMX, 5.3% Viton A) confined in a 2 kbar steel tube with reinforced end caps. A Scaled-Thermal-Explosion-eXperiment (STEX) was completed in which three radiant heaters were used to heat the vessel until ignition, resulting in a moderately violent explosion after 20.4 minutes. Thermocouple measurements showed tube temperatures as high as 340 C at ignition and LX-10 surface temperatures as high as 279 C, which is near the melting point of HMX. Three micro-power radar systems were used to measure mean fragment velocities of 840 m/s. Photonics Doppler Velocimeters (PDVs) showed a rapid acceleration of fragments over 80 {micro}s. A one-dimensional ALE3D cookoff model at the vessel midplane was used to simulate the heating, thermal expansion, LX-10 decomposition composition, and closing of the gap between the HE (High Explosive) and vessel wall. Although the ALE3D simulation terminated before ignition, the model provided a good representation of heat transfer through the case and across the dynamic gap to the explosive.
Date: November 22, 2006
Creator: McClelland, M. A.; Maienschein, J. L.; Howard, W. M. & Dehaven, M. R.
Object Type: Article
System: The UNT Digital Library