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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A mesoporous cationic thorium-organic framework that rapidly traps anionic persistent organic pollutants

Many environmental pollutants inherently exist in their anionic forms and are therefore highly mobile in natural water systems. Cationic framework materials that can capture those pollutants are highly desirable but scarcely reported. Here we present a mesoporous cationic thorium-based MOF (SCU-8) containing channels with a large inner diameter of 2.2 nm and possessing a high surface area of 1360 m 2 g –1 . The anion-exchange properties of SCU-8 were explored with many anions including small oxo anions like ReO 4 – and Cr 2 O 7 2– as well as anionic organic dyes like methyl blue and the persistent organic pollutant, perfluorooctane sulfonate (PFOS). Both fast uptake kinetics and great sorption selectivity toward PFOS are observed. The underlying sorption mechanism was probed using quantum mechanical and molecular dynamics simulations. These computational results reveal that PFOS anions are immobilized in SCU-8 by driving forces including electrostatic interactions, hydrogen bonds, hydrophobic interactions, and van der Waals interactions at different adsorption stages.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2012

Guidance on the Use of Hand-Held Survey Meters for radiological Triage: Time-Dependent Detector Count Rates Corresponding to 50, 250, and 500 mSv Effective Dose for Adult Males and Adult Females

In June 2006, the Radiation Studies Branch of the Centers for Disease Control and Prevention held a workshop to explore rapid methods of facilitating radiological triage of large numbers of potentially contaminated individuals following detonation of a radiological dispersal device. Two options were discussed. The first was the use of traditional gamma cameras in nuclear medicine departments operated as makeshift wholebody counters. Guidance on this approach is currently available from the CDC. This approach would be feasible if a manageable number of individuals were involved, transportation to the relevant hospitals was quickly provided, and the medical staff at each facility had been previously trained in this non-traditional use of their radiopharmaceutical imaging devices. If, however, substantially larger numbers of individuals (100 s to 1,000 s) needed radiological screening, other options must be given to first responders, first receivers, and health physicists providing medical management. In this study, the second option of the workshop was investigated by the use of commercially available portable survey meters (either NaI or GM based) for assessing potential ranges of effective dose (G50, 50Y250, 250Y500, and 9500 mSv). Two hybrid computational phantoms were used to model an adult male and an adult female subject internally contaminated with 241Am, 60Cs, 137Cs, 131I, or 192Ir following an acute inhalation or ingestion intake. As a function of time following the exposure, the net count rates corresponding to committed effective doses of 50, 250, and 500 mSv were estimated via Monte Carlo radiation transport simulation for each of four different detector types, positions, and screening distances. Measured net count rates can be compared to these values, and an assignment of one of four possible effective dose ranges could be made. The method implicitly assumes that all external contamination has been removed prior to screening and that the measurements be conducted in a low background, and possibly mobile, facility positioned at the triage location. Net count rate data are provided in both tabular and graphical format within a series of eight handbooks available at the CDC website (http://www.bt.cdc.gov/radiation/clinicians/evaluation).

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

A phase-field study of stainless-steel oxidation from high-temperature carbon dioxide exposure

An electrochemical phase-field model has been developed to investigate the oxidation mechanisms of the 21-2N valve stainless steel alloy exposed to carbon dioxide at 973 K. Three oxide phases observed in oxidation experiments are included in the model: Mn 3 O 4 , Cr 2 O 3 , and MnCr 2 O 4 . Local charge neutrality and the conserved current condition are assumed to include the impact of the electric potential on oxidation, though it is found to be negligible when the system is electrically isolated. The sensitivity of the oxidation processes to the values of the diffusion mobilities is examined, and the oxidation rate is calibrated against experimental data by modifying the sensitive mobilities. We find that both inward oxygen and outward metal diffusion are important for oxidation. Furthermore, by investigating the impact of the order of the initial oxide layers, we find that Cr 2 O 3 serves as a barrier to outward Mn diffusion. Moreover, controlling the initial oxide layer order can be used to limit oxidation.

36 MATERIALS SCIENCE↗
DOE OSTI2015

SU-E-I-12: Flexible Geometry Computed Tomography

Purpose: The concept separates the mechanical connection between the radiation source and detector. This design allows the trajectory and orientation of the radiation source/detector to be customized to the object that is being imaged. This is in contrast to the formulaic rotation-translation image acquisition of conventional computed tomography(CT).Background/significance:CT devices that image a full range of: anatomy, patient populations, and imaging procedures are large. The root cause of the expanding size of comprehensive CT is due to the commitment to helical geometry that is hardwired into the image reconstruction. FGCT extends the application of alternative reconstruction techniques, i.e. tomosynthesis, by separating the two main components— radiation source and detector— and allow for 6 degrees of freedom motion for radiation source, detector, or both. The image acquisition geometry is then tailored to how the patient/object is positioned. This provides greater flexibility on the position and location that the patient/object is being imaged. Additionally, removing the need of a rotating gantry reduces the footprint so that CT is more mobile and more available to move to where the patient/object is at, instead of the other way around. Methods: As proof-of-principle, a reconstruction algorithm is designed to produce FGCT images. Using simulated detector data, voxels intersecting a line drawn between the radiation source and an individual detector are traced and modified using the detector signal. The detector signal is modified to compensate for changes in the source to detector distance. Adjacent voxels are modified in proportion to the detector signal, providing a simple image filter. Results: Image-quality from the proposed FGCT reconstruction technique is proving to be a challenge, producing hardily recognizable images from limited projections angles. Conclusion: Preliminary assessment of the reconstruction technique demonstrates the inevitable tradeoff of producing meaningful image-quality verses the practicality of how to obtain sufficient image data.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2012

A DNA-Inspired Encryption Methodology for Secure, Mobile Ad Hoc Networks

Users are pushing for greater physical mobility with their network and Internet access. Mobile ad hoc networks (MANET) can provide an efficient mobile network architecture, but security is a key concern. A figure summarizes differences in the state of network security for MANET and fixed networks. MANETs require the ability to distinguish trusted peers, and tolerate the ingress/egress of nodes on an unscheduled basis. Because the networks by their very nature are mobile and self-organizing, use of a Public Key Infra structure (PKI), X.509 certificates, RSA, and nonce ex changes becomes problematic if the ideal of MANET is to be achieved. Molecular biology models such as DNA evolution can provide a basis for a proprietary security architecture that achieves high degrees of diffusion and confusion, and resistance to cryptanalysis. A proprietary encryption mechanism was developed that uses the principles of DNA replication and steganography (hidden word cryptography) for confidentiality and authentication. The foundation of the approach includes organization of coded words and messages using base pairs organized into genes, an expandable genome consisting of DNA-based chromosome keys, and a DNA-based message encoding, replication, and evolution and fitness. In evolutionary computing, a fitness algorithm determines whether candidate solutions, in this case encrypted messages, are sufficiently encrypted to be transmitted. The technology provides a mechanism for confidential electronic traffic over a MANET without a PKI for authenticating users.

Shaw, Harry↗
DOE OSTI2013

Affinity+: Semi-Structured Brainstorming on Large Displays

Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

large display, natural user interface, ubiquitous ↗
DOE OSTI2026

Measurements of the electron energy distribution function in partially magnetized low temperature plasmas

While Langmuir probes (LPs) are relatively simple and inexpensive plasma diagnostics for the electron density, temperature, and the electron energy distribution function (EEDF), the interpretation of the measured current–voltage (I–V) characteristic is complicated considerably by the presence of a magnetic field. In regimes where the electron gyroradius is comparable to the probe radius, the electron flux to the probe surface is retarded by reduced mobility across field lines and can no longer be described by a thermal model. Predicting the current collected by the probe in these regimes requires accurate estimates of the plasma diffusion coefficients, which are usually difficult to obtain. In this work, we measure electron energy distribution functions in E×B plasmas with magnetized electrons and non-magnetized ions in argon and krypton gases, using both a LP and laser Thomson scattering (LTS) at various magnetic fields. Using the LTS measurements to provide a robust benchmark for comparison, we compare existing theories describing the flux to the probe under magnetized conditions. We find that even when the electron gyroradius associated with the effective electron temperature is small compared to the probe radius, the EEDF computed using classical probe theory is still robust at energies higher than the energy at which the gyroradius becomes larger than the probe size. For plasmas that are not strongly non-Maxwellian, we formulate a method to extract robust density and temperature measurements using physics-informed fitting techniques to analyze EEDFs computed using classical theory.

Devin, E. G. [Princeton Plasma Physics Laboratory ↗
DOE OSTI2016

A multiscale restriction-smoothed basis method for high contrast porous media represented on unstructured grids

A wide variety of multiscale methods have been proposed in the literature to reduce runtime and provide better scaling for the solution of Poisson-type equations modeling flow in porous media. We present a new multiscale restricted-smoothed basis (MsRSB) method that is designed to be applicable to both rectilinear grids and unstructured grids. Like many other multiscale methods, MsRSB relies on a coarse partition of the underlying fine grid and a set of local prolongation operators (multiscale basis functions) that map unknowns associated with the fine grid cells to unknowns associated with blocks in the coarse partition. These mappings are constructed by restricted smoothing: Starting from a constant, a localized iterative scheme is applied directly to the fine-scale discretization to compute prolongation operators that are consistent with the local properties of the differential operators. The resulting method has three main advantages: First of all, both the coarse and the fine grid can have general polyhedral geometry and unstructured topology. This means that partitions and good prolongation operators can easily be constructed for complex models involving high media contrasts and unstructured cell connections introduced by faults, pinch-outs, erosion, local grid refinement, etc. In particular, the coarse partition can be adapted to geological or flow-field properties represented on cells or faces to improve accuracy. Secondly, the method is accurate and robust when compared to existing multiscale methods and does not need expensive recomputation of local basis functions to account for transient behavior: Dynamic mobility changes are incorporated by continuing to iterate a few extra steps on existing basis functions. This way, the cost of updating the prolongation operators becomes proportional to the amount of change in fluid mobility and one reduces the need for expensive, tolerance-based updates. Finally, since the MsRSB method is formulated on top of a cell-centered, conservative, finite-volume method, it is applicable to any flow model in which one can isolate a pressure equation. Herein, we only discuss single and two-phase incompressible models. Compressible flow, e.g., as modeled by the black-oil equations, is discussed in a separate paper.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Mobility Selective Ion Soft-Landing and Characterization Enabled Using Structures for Lossless Ion Manipulation

In this study, while conventional ion-soft landing uses the mass-to-charge (m/z) ratio to achieve molecular selection for deposition, here we demonstrate the use of Structures for Lossless Ion Manipulation (SLIM) for mobility-based ion selection and deposition. The dynamic rerouting capabilities of SLIM were leveraged to enable the rerouting of a selected range of mobilities to a different SLIM path (rather than MS) that terminated at a deposition surface. A selected mobility range from a phosphazene ion mixture was rerouted and deposited with a current pulse (~150 pA) resembling its mobility peak. In addition, from a mixture of tetra-alkyl ammonium (TAA) ions containing chain lengths of C5–C8, selected chains (C6, C7) were collected on a surface, reconstituted into solution-phase, and subsequently analyzed with a SLIM-qToF to obtain an IMS/MS spectrum, confirming the identity of the selected species. Further, this method was used to characterize triply charged tungsten-polyoxometalate anions, PW 12 O 40 3– (WPOM). The arrival time distribution of the IMS/MS showed multiple peaks associated with the triply charged anion (PW 12 O 40 3– ), of which a selected ATD was deposited and imaged using TEM. Additionally, the identity of the deposited WPOM was ascertained using energy-dispersive (EDS) spectroscopy. Further, we present theory and computations that reveal ion landing energies, the ability to modulate the energies, and deposition spot sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Fractonic coset construction for spontaneously broken translations

We study the homogeneous breaking of spatial translation symmetry concomitantly with the spontaneous breaking of other internal and spacetime symmetries, including dilations. We use the symmetry-breaking pattern as the only input to derive, via the coset construction, general effective field theories for the symmetry-originated modes associated with Goldstone’s theorem, namely the Nambu-Goldstone candidates. Through explicit computations, we show that integrating out the explicit massive Nambu-Goldstone candidates or imposing symmetric constraints, namely the inverse Higgs constraints, to express massive modes in terms of the massless ones leads to physically distinct effective field theories. This sensitivity to the chosen method can be traced back to the homogeneous breaking of translations, the homogeneous aspect of the breaking induces a mixing between internal and spacetime symmetries at the level of the Lie algebra. This, in turn, leads to subtle discussions about the inverse Higgs constraints, in particular that they lead to a loss of generality in our specific examples. The derived general effective field theories also give rise to a broad class of theories exhibiting emergent enhanced shift symmetries, which constrain the mobility of the modes. The latter are referred to as fractonic modes. Published by the American Physical Society 2025

Chavda, Ameya (ORCID:0000000211731605)↗
NASA NTRS1989

On principles, methods and recent advances in studies towards a GPS-based control system for geodesy and geodynamics

Although Very Long Baseline Interferometry (VLBI) and Satellite Laser Ranging (SLR) are becoming increasingly important tools for geodynamic studies, their future role may well be fulfilled by using alternative techniques such as those utilizing the signals from the Global Positioning System (GPS). GPS, without the full implementation of the system, already offers a favorable combination of cost and accuracy and has consistently demonstrated the capability to provide high precision densification control in the regional and local areas of the VLBI and SLR networks. This report reviews VLBI and SLR vis-a-vis GPS and outlines the capabilities and limitations of each technique and how their complementary application can be of benefit to geodetic and geodynamic operations. It demonstrates, albeit with a limited data set, that dual-frequency GPS observations and interferometric type analysis techniques make possible the modelling of the GPS orbits for several days with an accuracy of a few meters. The use of VLBI or SLR sites as fiducial stations together with refinements in the orbit determination procedures can greatly reduce the systematic errors in the GPS satellite orbits used to compute the positions of non-fiducial locations. In general, repeatability and comparison with VLBI of the GPS determined locations are of the order of between 2 parts in 10 to the 7th power and 5 parts in 10 to the 8th power for baseline lengths less than 2000 km. This report is mainly a synthesis of problems, assumptions, methods and recent advances in the studies towards the establishment of a GPS-based system for geodesy and geodynamics and is one phase in the continuing effort for the development of such a system. To some, including the author, it seems reasonable to expect within the next few years that more evidence will show GPS to be as a powerful and reliable a tool as mobile VLBI and SLR are today, but largely more economical.

Delikaraoglou, Demitris↗
DOE OSTI2023

2023 SAGE-Camp Report

The 7 th Summer Physics Camp for Young Women was successfully held in person in 2023 from June 5 th to 16 th at the New Mexico School for the Arts in Santa Fe, NM at Hilo Intermediate School in Hawaii. This year’s camp was dedicated to the topic of Energy Security and was made possible thanks to the strong collaboration of Los Alamos, Sandia and Hawaii teams and the logistical and financial support of Los Alamos and Sandia National Laboratories, New Mexico Consortium, SAGE- Moore Foundation, LANL Foundation, ACS, IEE, APS four corners, N3B, Hawaii Museum of Science and Technology, New Mexico School for the Arts (NMSA) and Tech Source. The camp mobilized more than 120 volunteers who made the camp a success. The camp is free of charge to the students and included free lunch and snacks for the busy brains to have plenty of energy, also included all materials needed for the hands-on activities (like drone building, crystal structure, solar panels, wind turbine fabrication, soldering, coding etc) and also a stipend for students who attended for the full two weeks and for two educators and two student mentors in NM. The camp offered 32 high school students from New Mexico and 8 from Hawaii a unique opportunity to explore science topics and meet a broad range of role model professionals across STEM fields including astrophysics, cybersecurity, Energy fields, space science, engineering, biophysics, environmental science, robotics, computer science, nuclear engineering, radiological science, physics and chemistry. With nearly 120 volunteers who came mainly from Los Alamos National Laboratory (66%) and Sandia national laboratories (18%), two funded educators from NM, Dr. Weldon Beauchamp and Dr. Ellee Cook, and two educators from Hilo, Dr. Pascale Creek Pinner and LeAnn Ragasa, the camp was educationally sound and extremely varied. The collaboration with school educators is critical for the goal of this camp to not only impact students' lives but also improve STEM education in NM and Hawaii. The ultimate goal of the camp is to increase higher education aspirations of students, empower them to consider careers in STEM and learn more about the opportunities available to them in our local colleges and DOE National Laboratories. In addition, the camp also hired 2 past students as student mentors, Megan Odom and Elisea Jackson, who currently attend NMSA and were students at the camp in 2022 when it was virtual. The in-person camp which aims at empowering under-represented minorities in STEM in our community received more than 52 applications this year from all over NM and 8 applications from Hawaii. Our selection criteria are based on diversity, equity and inclusion, and students for whom the camp can be a life-changing opportunity are given a chance to attend the camp. During COVID, the camp was held virtually and gave the opportunity to students from remote areas in NM and Hawaii to attend from their homes. This year, fantastic families supported students everyday even when home was in remote areas in NM like Lea county, Sandoval county, Bernalillo or Mora county. The organizers hope next year they can offer a residential option for students from remote areas.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS1995

Techniques for Improving the Performance of Future EVA Maneuvering Systems

The Simplified Aid for EVA Rescue (SAFER) is a small propulsive backpack that was developed as an in-house effort at Johnson Space Center; it is a lightweight system which attaches to the underside of the Primary Life Support Subsystem (PLSS) backpack of the Extravehicular Mobility Unit (EMU). SAFER provides full six-axis control, as well as Automatic Attitude Hold (AAH), by means of a set of cold-gas nitrogen thrusters and a rate sensor-based control system. For compactness, a single hand controller is used, together with mode switching, to command all six axes. SAFER was successfully test-flown on the STS-64 mission in September 1994 as a Development Test Objective (DTO); development of an operational version is now proceeding. This version will be available for EVA self-rescue on the International Space Station and Mir, starting with the STS-86/Mir-7 mission in September 1997. The DTO SAFER was heavily instrumented, and produced in-flight data that was stored in a 12 MB computer memory on-board. This has allowed post-flight analysis to yield good estimates for the actual mass properties (moments and products of inertia and center of mass location) encountered on-orbit. By contrast, Manned Maneuvering Unit (MMU) post-flight results were generated mainly from analysis of video images, and so were not very accurate. The main goal of the research reported here was to use the detailed SAFER on-orbit mass properties data to optimize the design of future EVA maneuvering systems, with the aim being to improve flying qualities and/or reduce propellant consumption. The Automation, Robotics and Simulation Division Virtual Reality (VR) Laboratory proved to be a valuable research tool for such studies. A second objective of the grant was to generate an accurate dynamics model in support of the reflight of the DTO SAFER on STS-76/Mir-3. One complicating factor was the fact that a hand controller stowage box was added to the underside of SAFER on this flight; the position of this box was such that two of the SAFER jets plume it. A second complication was that the EVA astronaut will sometimes be transporting a massive experiment package. This will not only alter the overall mass properties significantly, but can itself also be plumed.

Williams, Trevor W.↗
DOE OSTI2013

Intelligent Software Agents: Sensor Integration and Response

Abstract In a post Macondo world the buzzwords are Integrity Management and Incident Response Management. The twin processes are not new but the opportunity to link the two is novel. Intelligent software agents can be used with sensor networks in distributed and centralized computing systems to enhance real-time monitoring of system integrity as well as manage the follow-on incident response to changing, and potentially hazardous, environmental conditions. The software components are embedded at the sensor network nodes in surveillance systems used for monitoring unusual events. When an event occurs, the software agents establish a new concept of operation at the sensing node, post the event status to a blackboard for software agents at other nodes to see , and then react quickly and efficiently to monitor the scale of the event. The technology addresses a current challenge in sensor networks that prevents a rapid and efficient response when a sensor measurement indicates that an event has occurred. By using intelligent software agents - which can be stationary or mobile, interact socially, and adapt to changing situations - the technology offers features that are particularly important when systems need to adapt to active circumstances. For example, when a release is detected, the local software agent collaborates with other agents at the node to exercise the appropriate operation, such as: targeted detection, increased detection frequency, decreased detection frequency for other non-alarming sensors, and determination of environmental conditions so that adjacent nodes can be informed that an event is occurring and when it will arrive. The software agents at the nodes can also post the data in a targeted manner, so that agents at other nodes and the command center can exercise appropriate operations to recalibrate the overall sensor network and associated intelligence systems. The paper describes the concepts and provides examples of real-world implementations including the Threat Detection and Analysis System (TDAS) at the International Port of Memphis and the Biological Warning and Incident Characterization System (BWIC) Environmental Monitoring (EM) Component. Technologies developed for these 24/7 operational systems have applications for improved real-time system integrity awareness as well as provide incident response (as needed) for production and field applications.

emergency response↗
DOE OSTI2018

Implementation of a dislocation-density based single-crystal model into a continuum shock hydrodynamics code

The dynamic thermomechanical responses of polycrystalline materials under shock loading are often dominated by the interaction of defects and interfaces. For example, within metals, a prescribed deformation associated with a shock wave may be accommodated by crystallographic slip, provided a sufficient population of mobile dislocations is available. However, if the deformation rate is large enough, there may be an insufficient number of freely mobile dislocations. In this case, additional dislocations may be nucleated, or alternate mechanisms (e.g. twinning, damage) activated in order to accommodate the deformation. Furthermore, direct numerical simulation at the mesoscale offers insight into these physical processes that can be invaluable to the development of macroscale constitutive theories, if the mesoscale models adequately represent the anisotropic nonlinear thermomechanical response of individual crystals and their interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

NEXT Generation Energy Technologies for Connected and Automated On-Road Vehicles (NEXTCAR Phase I & II)

The Ohio State University’s ARPA-E NEXTCAR project was a multi-phase, multi-year research, development, and demonstration program focused on improving the energy efficiency of connected and automated vehicles (CAVs). The team developed and validated advanced vehicle motion and powertrain control algorithms that coordinate propulsion and automation systems to optimize energy use. Key technologies included Dynamic Skip Fire engine control, predictive eco-driving functions such as Eco-Approach and Departure (Eco-AND) and Eco-Adaptive Cruise Control (Eco-ACC), and powertrain-agnostic optimization frameworks for hybrid, plug-in hybrid, and battery electric vehicles. The project successfully demonstrated up to 30% energy-efficiency improvement during real-world testing at the Transportation Research Center and the American Center for Mobility. The outcomes provide a foundation for scalable, cost-effective deployment of energy-optimized CAV technologies across the automotive industry.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
NASA NTRS1997

A Scalable Distributed Approach to Mobile Robot Vision

This paper documents our progress during the first year of work on our original proposal entitled 'A Scalable Distributed Approach to Mobile Robot Vision'. We are pursuing a strategy for real-time visual identification and tracking of complex objects which does not rely on specialized image-processing hardware. In this system perceptual schemas represent objects as a graph of primitive features. Distributed software agents identify and track these features, using variable-geometry image subwindows of limited size. Active control of imaging parameters and selective processing makes simultaneous real-time tracking of many primitive features tractable. Perceptual schemas operate independently from the tracking of primitive features, so that real-time tracking of a set of image features is not hurt by latency in recognition of the object that those features make up. The architecture allows semantically significant features to be tracked with limited expenditure of computational resources, and allows the visual computation to be distributed across a network of processors. Early experiments are described which demonstrate the usefulness of this formulation, followed by a brief overview of our more recent progress (after the first year).

Kuipers, Benjamin↗
DOE OSTI2015

From deep TLS validation to ensembles of atomic models built from elemental motions

Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗