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At least 37 records · Page 2

All sources NASA NTRS DOE OSTI

DOE OSTI2012

Effects of restraint on expansion due to delayed ettringite formation

Delayed ettringite formation (DEF) is a chemical reaction that causes expansion in civil engineering structures. The safety level of such damaged structures has to be reassessed. To do this, the mechanical conditions acting on DEF expansions have to be analysed and, in particular, the variation of strength with expansion and the effect of restraint on the DEF expansion. This paper highlights several points: DEF expansion is isotropic in stress-free conditions, compressive stresses decrease DEF expansion in the direction subjected to restraint and lead to cracks parallel to the restraint, and expansion measured in the stress-free direction of restrained specimens is not modified. Thus restraint causes a decrease of the volumetric expansion and DEF expansion under restraint is anisotropic. Moreover, the paper examines the correlation between DEF expansion and concrete damage, providing data that can be used for the quantification of the effect of stresses on DEF induced expansion.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Arginine off-kilter: guanidinium is not as planar as restraints denote

Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N ∊ —C ζ —N η1 and N ∊ —C ζ —N η2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the C δ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the C δ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix , that take into account the asymmetry of the group and the planar deviation of the C δ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

The refinement of biomolecular crystallographic models relies on geometric restraints to help address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here we present an integration of the full all-atom Amber molecular dynamics force field into Phenix crystallographic refinement, which enables a more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of non-bonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over twenty-two thousand protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better; clash scores and MolProbity scores are significantly improved; and the modelling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined with traditional geometry restraints. We find in general that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum mechanical representation of active sites and improved geometric restraints for simulated annealing. This document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr Word tools (available from http://journals.iucr.org/services/docxtemplate/ ) are installed when editing this document. The full Amber force field has been integrated into Phenix as an alternative refinement target. With a slight loss in speed, it achieves improved stereochemistry, fewer steric clashes and better hydrogen bonds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber -based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

Adrenocortical response in rats subjected to a stress of restraint by immobilization whether accompanied by hypothermia or not

The restraint associated with hypothermia which increases the adrenal activity in rats was investigated. In rats with nomothermia or light hypothermia, the plasma and adrenal corticosterone levels increase at least threefold whatever the duration of restraint. Their return to normal values depends on the duration of the restraint. Exposure to cold produces in free rats a light hypothermia with an increase of the plasma and adrenal corticosterone levels, and in restraint animals an important hypothermia which does not potentiate the stimulation of adrenocortical activity induced by the restraint alone.

Buchel, L.↗

NASA NTRS1994

M.E.366-J embodiment design project: Portable foot restraint

During space shuttle operations, astronauts require support to carry out tasks in the weightless environment. In the past, portable foot restraints (PFR) with orientations adjustable in pitch, roll, and yaw provided this support for payload bay operations. These foot restraints, however, were designed for specific tasks with a load limit of 111.2 Newtons. Since the original design, new applications for foot restraints have been identified. New designs for the foot restraints have been created to boost the operational work load to 444.8 Newtons and decrease setup times. What remains to be designed is an interface between the restraint system and the extravehicular mobility unit (EMU) boots. NASA provided a proposed locking device involving a spring-loaded mechanism. This locking mechanism must withstand loads of 1334.4 Newtons in any direction and weigh less than 222.4 Newtons. This paper develops an embodiment design for the interface between the PFR and the EMU boots. This involves design of the locking mechanism and a removable cleat that allows the boot to interface with this mechanism. The design team used the Paul Beitz engineering methodology to present the systematic development, structural analysis, and production considerations of the embodiment design. This methodology provides a basis for understanding the justification behind the decisions made in the design.

Heaton, Randall↗

NASA NTRS1990

Full body restraint system

A body restraint system (30) allows the user's body (10) to be in the zero gravity neutral posture. The system (30) includes a waist restraint (32) in the form of a curved, padded unit (34) containing a retractable belt (36) coiled on a spring loaded capstan (38) with a buckle (40) extending from front (42) of the unit (34). A second belt (44) is fastened around the user's waist (16). A clasp (46) is configured to engage the buckle (40). The waist restraint (32) is positioned near foot restraints (52). The foot restraints (52) have foot platforms (59) with pads (60) of a suitable two part attaching material, such as the fasteners available from Minnesota Mining and Manufacturing Company under the trademark Scotchmate Duallock. A mating pad (62) of the material is provided on soles (64) of cotton net shoes (66).

Ryder, Susan↗

NASA NTRS2000

Surgical Instrument Restraint in Weightlessness

Performing a surgical procedure during spaceflight will become more likely with longer duration missions in the near future. Minimal surgical capability has been present on previous missions as the definitive medical care time was short and the likelihood of surgical events too low to justify surgical hardware availability. Early demonstrations of surgical procedures in the weightlessness of parabolic flight indicated the need for careful logistical planning and restraint of surgical hardware. The consideration of human ergonomics also has more impact in weightlessness than in the conventionall-g environment. Three methods of surgical instrument restraint - a Minor Surgical Kit (MSK), a Surgical Restraint Scrub Suit (SRSS), and a Surgical Tray (ST) were evaluated in parabolic flight surgical procedures. The Minor Surgical Kit was easily stored, easily deployed, and demonstrated the best ability to facilitate a surgical procedure in weightlessness. Important factors in this surgical restraint system include excellent organization of supplies, ability to maintain sterility, accessibility while providing secure restraint, ability to dispose of sharp items and biological trash, and ergonomical efficiency.

Campbell, Mark R.↗

DOE OSTI2020

Pipe restraint and shield

A pipe restraint assembly includes a restraint body configured to be removably attached to a portion of pipe. The portion of pipe is associated with a postulated pipe failure associated with a release of high pressure fluid. A plurality of apertures penetrate through the restraint body and are positioned proximate to a location of the postulated pipe failure. The apertures are configured to provide a number of passageways for the fluid to exit from the location of the postulated pipe failure and to be released outside of the restraint body. One or more restraint devices maintain the position of the apertures relative to the location of the postulated pipe failure.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2015

Programming new geometry restraints: Parallelity of atomic groups

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox ( cctbx ) are presented.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

A new default restraint library for the protein backbone in Phenix : a conformation-dependent geometry goes mainstream

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriarty et al. (2014), FEBS J. 281 , 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used by Phenix is described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Enhanced rigid-bond restraints

An extension is proposed to the rigid-bond description of atomic thermal motion in crystals. The rigid-bond model [Hirshfeld (1976 ▶). Acta Cryst. A32, 239–244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [Crystallographic Computing (1970 ▶), edited by F. R. Ahmed et al., pp. 167–181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution (e.g. 1.7 Å)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2012

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine . Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a φ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free .

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

The effects of restraint on uptake of radioactive sulfate in the salivary and gastric secretions of rats with pyloric ligation

The effects of restraint on the amount of nondialysable radioactive sulfate in the gastric wall and the gastric juice and saliva were investigated. It was found that restraint provokes a significant decrease in salivary radioactive sulfate. This, in turn, is responsible for the decrease of sulfate in the gastric contents observed under these conditions in rats with pyloric ligation. Esophageal ligation associated with this prevents passage of saliva and lowers the amount of radioactive sulfate in the gastric juice. Restraint causes then an increase in the amount of sulfate in the gastric juice, the value observed being very much lower than that of rats with a free esophagus. At the level of the gastric wall, the change observed during restraint does not reach a significant threshold.

Chayvialle, J. A.↗

NASA NTRS1992

Fixed Or Controlled-Movement Foot Restraint

Foot restraint gives user three options: holds user's feet in fixed position, allows them to slide sideways, or allows them to pivot independently about axis through ball of foot, as user chooses. Selects degree of restraint to suit task at hand. Movements to enter and leave foot restraint simple and direct. Simply forces each cleat lightly into space between rails until spring force of movable rail secures it. Body movements for sliding and rotation equally straightforward. Designed for use in absence of gravitation, restraint useful on Earth, underwater or in some hazardous locations where movements restricted.

Reilly, Gloria B.↗

NASA NTRS2006

Crew Restraint Design for the International Space Station

With permanent human presence onboard the International Space Station (ISS), crews will be living and working in microgravity, dealing with the challenges of a weightless environment. In addition, the confined nature of the spacecraft environment results in ergonomic challenges such as limited visibility and access to the activity areas, as well as prolonged periods of unnatural postures. Without optimum restraints, crewmembers may be handicapped for performing some of the on-orbit tasks. Currently, many of the tasks on ISS are performed with the crew restrained merely by hooking their arms or toes around handrails to steady themselves. This is adequate for some tasks, but not all. There have been some reports of discomfort/calluses on the top of the toes. In addition, this type of restraint is simply insufficient for tasks that require a large degree of stability. Glovebox design is a good example of a confined workstation concept requiring stability for successful use. They are widely used in industry, university, and government laboratories, as well as in the space environment, and are known to cause postural limitations and visual restrictions. Although there are numerous guidelines pertaining to ventilation, seals, and glove attachment, most of the data have been gathered in a 1-g environment, or are from studies that were conducted prior to the early 1980 s. Little is known about how best to restrain a crewmember using a glovebox in microgravity. Another ISS task that requires special consideration with respect to restraints is robotic teleoperation. The Robot Systems Technology Branch at the NASA Johnson Space Center is developing a humanoid robot astronaut, or Robonaut. It is being designed to perform extravehicular activities (EVAs) in the hazardous environment of space. An astronaut located inside the ISS will remotely operate Robonaut through a telepresence control system. Essentially, the robot mimics every move the operator makes. This requires the operator to be stable enough to prevent inadvertent movements, while allowing the flexibility to accomplish the controlled movements of the robot. Some type of special purpose restraint will be required to operate Robonaut and similar devices.

Norris, Lena↗

NASA NTRS2011

The Influence of Restraint Systems on Panel Behavior

When a panel is tested in uniaxial compression in a test machine, the boundary conditions are not quite the same as they would be if it were part of a complete structure. A restraint system may be used to simulate conditions found in a complete vehicle. Quantifying the quality of the restraint with only point-measurement devices can leave an inadequate characterization of the out-of-plane behavior. However, today s full-field displacement monitoring techniques allow for much more accurate views of the global panel deformation and strain, and therefore allow for a better understanding of panel behavior. In the current study, the behavior of a hat-stiffened and two rod-stiffened carbon-epoxy panels is considered. Panels were approximately 2 meters tall and 0.76 to 1.06 m wide. Unloaded edges were supported by knife edges and stiffeners were attached to a support structure at selected locations to restrain out-of-plane motion. A comparison is made between test results based on full-field measurements and analyses based on assumptions of boundary conditions of a completely rigid edge restraint and the absence of any edge restraint. Results indicate that motion at the restrained edges must be considered to obtain accurate test-analysis correlation.

Jegley, Dawn C.↗

DOE OSTI2014

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.

59 BASIC BIOLOGICAL SCIENCES↗