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At least 1,315 records · Page 73

Locality-Aware Scheduling for Scalable Heterogeneous Environments

Heterogeneous computing promise boost performance of scientific applications by allowing massively parallel execution of computational tasks. However, manually managing extremely heterogeneous, multi-device systems is complicated and may result in sub-optimal performance. Specifically, data management is an extremely challenging problem on multi-device systems. In this work, we introduce two locality-aware schedulers for the Minos Computing Library (MCL), an asynchronous, task-based programming model and runtime for extremely heterogeneous systems. The first scheduler implements a pure locality-aware algorithm to maximize data reuse, though it might incur in ”hot-spots” that limit system utilization. The second scheduler mitigates this drawback by dynamically targeting between locality-awareness and system utilization based on the current workload and available computing devices. Our results show that locality-awareness greatly benefit applications that exhibit data reuse, providing up to 6.9x and 7.9x over the original MCL scheduler and equivalent OpenCL implementations, respectively. Moreover, our schedulers introduce negligible overhead compared with the original MCL scheduler and achieve similar performance for applications that don’t benefit from data locality.

Architecture, co-design, Task-based programming mo↗

HiSPoD : a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

Here, a high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here, HiSPoD , a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. With HiSPoD , researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

36 MATERIALS SCIENCE↗

Operation and Dynamic Control of Hybrid Power Systems

Poster describing the planned startup process of a solid oxide gas turbine hybrid power system to be constructed at a 20 kW scale. The work is part of the ARPA-E project award to NETL under the INTEGRATE program.

Harun, Nor Farida↗

Nevada National Security Site: Site-Directed Research and Development (SDRD) Fiscal Year 2015 Annual Report

This report presents results of multiple research projects, new and ongoing, funded under the Site-Directed Research and Development Program for the Nevada National Security Site during federal fiscal year 2015. The Site's legacy capabilities in remote sensing combined with new paradigms for emergency response and consequence management help drive the need to develop advanced aerial sensor platforms. Likewise, dynamic materials science is a critical area of scientific research for which basic physics issues are still unresolved. New methods of characterizing materials in extreme states are vitally needed, and these efforts are paving the way with new knowledge. Projects selected in FY 2015 for the Exploratory Research portfolio exhibit a strong balance of NNSS mission relevance. Geoscience, seismology, and techniques for detecting underground nuclear events are still essential focus areas. Many of the project reports in the second major section of this annual report are ongoing continuations in multi-year lifecycles. Diagnostic techniques for stockpile and nuclear security science figured prominently as well, with a few key efforts coming to fruition, such as phase transition detection. In other areas, modeling efforts toward better understanding plasma focus physics has also started to pay dividends for major program needs.

42 ENGINEERING↗

NWChem: scalable parallel computational chemistry

NWChem is a general purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient computational chemistry code with high parallel scalability. NWChem is a modern, open source, computational chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This code design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in computational chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose computational chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.

99 GENERAL AND MISCELLANEOUS↗

Bioimaging Science Program: 2022 Principal Investigator Meetings Proceedings

The mission of the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program’s Bioimaging Science Program (BSP) is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. The extended goal of dynamic imaging is to functionally connect cellular components and interdependent organisms. Information about the time and place of chemical reactions in situ can identify causal relationships between biological activators and downstream effectors. BSP held its annual PI meeting virtually February 28–March 1. Contributing investigators are convened to review progress and current state-of-the-art bioimaging research. Holding the 2022 BSP meeting as part of the broader Genomic Science Program (GSP) PI meeting allowed researchers to interact with the extended GSP community. This convergence provided a platform for networking and exchange of ideas with experts in other technologies and in target BSP application areas, helping to forge new multidisciplinary collaborations among investigators from the sister programmatic areas within BER’s Biological Systems Science Division. An important highlight of the BSP meeting was the keynote presentation by Nobel Laureate Dr. Joachim Frank on Time-Resolved Macromolecular Imaging using Cryo-EM. He discussed microfluidic mixing and fast freezing to capture nonequilibrium intermediate states during molecular binding and conformational changes. The action of molecular machines can be captured at nanometer resolution and millisecond discrimination. BSP PIs made presentations describing their research focus and progress in plenary sessions on bioimaging science and on quantum-enabled bioimaging science research projects. BSP research at universities and DOE laboratories is presented in this report. A final discussion of the BSP was organized by meeting plenary session chairs, who prepared the following Executive Summary of current BSP research, research challenges, future opportunities, and potential ideas for expanding the BSP’s impact and interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Large Scale DD Simulation Results for Crystal Plasticity Parameters in Fe-Cr And Fe-Ni Systems

The development of viable nuclear energy source depends on ensuring structural materials integrity. Structural materials in nuclear reactors will operate in harsh radiation conditions coupled with high level hydrogen and helium production, as well as formation of high density of point defects and defect clusters, and thus will experience severe degradation of mechanical properties. Therefore, the main objective of this work is to develop a capability that predicts aging behavior and in-service lifetime of nuclear reactor components and, thus provide an instrumental tool for tailoring materials design and development for application in future nuclear reactor technologies. Towards this end goal, the long term effort is to develop a physically based multiscale modeling hierarchy, validated and verified, to address outstanding questions regarding the effects of irradiation on materials microstructure and mechanical properties during extended service in the fission and fusion environments. The focus of the current investigation is on modern steels for use in nuclear reactors including high strength ferritic-martensitic steels (Fe-Cr-Ni alloys). The effort is to develop a predicative capability for the influence of irradiation on mechanical behavior. Irradiation hardening is related to structural information crossing different length scales, such as composition, dislocation, and crystal orientation distribution. To predict effective hardening, the influence factors along different length scales should be considered. Therefore, a hierarchical upscaling methodology is implemented in this work in which relevant information is passed between models at three scales, namely, from molecular dynamics to dislocation dynamics to dislocation-based crystal plasticity. The molecular dynamics (MD) was used to predict the dislocation mobility in body centered cubic (bcc) Fe and its Ni and Cr alloys. The results are then passed on to dislocation dynamics to predict the critical resolved shear stress (CRSS) from the evolution of local dislocation and defects. In this report the focus is on the results obtained from large scale dislocation dynamics simulations. The effect of defect density, materials structure was investigated, and evolution laws are obtained. These results will form the bases for the development of evolution and hardening laws for a dislocation-based crystal plasticity framework. The hierarchical upscaling method being developed in this project can provide a guidance tool to evaluate performance of structural materials for next-generation nuclear reactors. Combined with other tools developed in the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the models developed will have more impact in improving the reliability of current reactors and affordability of new reactors.

36 MATERIALS SCIENCE↗

Programmable simulations of molecules and materials with reconfigurable quantum processors

Simulations of quantum chemistry and quantum materials are believed to be among the most important applications of quantum information processors. However, realizing practical quantum advantage for such problems is challenging because of the prohibitive computational cost of programming typical problems into quantum hardware. Here we introduce a simulation framework for strongly correlated quantum systems represented by model spin Hamiltonians that uses reconfigurable qubit architectures to simulate real-time dynamics in a programmable way. Our approach also introduces an algorithm for extracting chemically relevant spectral properties via classical co-processing of quantum measurement results. We develop a digital–analogue simulation toolbox for efficient Hamiltonian time evolution using digital Floquet engineering and hardware-optimized multi-qubit operations to accurately realize complex spin–spin interactions. As an example, we propose an implementation based on Rydberg atom arrays. In addition, we show how detailed spectral information can be extracted from the dynamics through snapshot measurements and single-ancilla control, enabling the evaluation of excitation energies and finite-temperature susceptibilities from a single dataset. To illustrate the approach, we show how to use the method to compute key properties of a polynuclear transition-metal catalyst and two-dimensional magnetic materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

Dynamics of Organophosphate‐Induced Structural Changes in Acetylcholinesterase Revealed by Time‐Resolved Small‐Angle X‐Ray Scattering and Inelastic Neutron Scattering

Organophosphates (OPs), the active compounds in nerve agents and insecticides such as paraoxon (POX), exert their toxic effects by irreversibly inhibiting acetylcholinesterase (AChE). Currently available antidotes for OP toxicity can reactivate AChE, but reactivation rates are slow which can lead to irreversible nervous system damage or death. We hypothesize that better antidotes with accelerated reactivation rates can be developed by understanding the structural dynamics of OP‐AChE conjugates. Previous steady‐state small‐angle X‐ray scattering (SAXS) experiments showed that POX and certain other OPs induce quaternary structural changes in human AChE (hAChE) that were reversible by oxime antidotes. To characterize the dynamics of these OP‐induced structural changes we have used time‐resolved SAXS (TR‐SAXS) and inelastic neutron scattering (INS). Stopped‐flow TR‐SAXS experiments were performed at BL‐4 at the Stanford Synchrotron Radiation Lightsource by mixing a molar excess of POX (500 μM) with hAChE (50 μM). Scattering data were collected every 20 msec during the first 1000 msec after mixing. Changes in the solution structure of hAChE during this period occurred with k obs = 0.13(±0.01) s −1 . This rate of structural change is comparable to the rate of hAChE inactivation observed using biochemical assays. INS data were collected at the Cold Neutron Chopper Spectrometer at the Spallation Neutron Source at Oakridge National Laboratory using 100 mg samples of hAChE and POX‐hAChE that were lyophilized and rehydrated in D 2 O. INS data collected at 120 K (to prevent translational motions) were used to compare the vibrational density states of native and POX‐conjugated hAChE. The POX‐conjugated hAChE exhibited an increased number of vibrational states, particularly those associated with regional motions such as loop dynamics, whereas global collective motions remained unchanged. Molecular dynamics simulations were used to simulate the vibrational spectra and identify the region(s) in hAChE that contributed to the differences in the INS experimental data. In aggregate, these studies provide experimental evidence for OP conjugate‐induced changes in hAChE dynamics that has to be considered in the design of antidotes for OP poisoning that have improved efficacy and patient outcomes. Support or Funding Information This work was supported by the CounterACT Program, National Institutes of Health Office of the Director, Grant 1U01NS083451 from NINDS, and by grants to SSRL and ORNL from the U.S. Department of Energy, and the National Institutes of Health. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Blumenthal, Donald K.↗

Programmer-guided reliability for extreme-scale applications

We present “programmer-guided reliability” (PGR) as a systematic conceptual approach to address the expected rise in soft errors in coming extreme-scale systems at the application level. The approach involves instrumentation of the application with code to detect data corruption errors. The location and nature of these error detectors are at the discretion of the programmer, who uses their knowledge and experience with the problem domain, the application, the solution algorithms, etc., to determine the most vulnerable areas of the code and the most appropriate ways to detect data corruption. To illustrate the approach, we provide examples of error detectors from four different benchmark-scale applications. We also describe a simple control framework that allows for runtime configuration of the error detectors without recompilation of the application, as well as dynamic reconfiguration during the execution of the application. Lastly, we discuss a number of future directions building on the basic PGR approach, including the incorporation of some general error detectors into the programming environment in order to make them more easily usable by the programmer.

97 MATHEMATICS AND COMPUTING↗

CROCUS Urban Fluxes of CO₂, H₂O, and Turbulence at University of Illinois Chicago

As of May 12, 2026 this dataset is currently being versioned to include data up to April 2026. Once the versioning process is complete, new data files will be available for access. The dataset metadata will also be updated to reflect the data availability of the new data being versioned. This dataset was collected at the UIC Plant Research Laboratory in Chicago, Illinois, as part of the Community Research on Climate and Urban Science (CROCUS) Urban Integrated Field Laboratory (UIFL) project, led by Argonne National Laboratory. The site provides continuous atmospheric flux measurements, focusing on CO₂, H₂O, and heat and momentum transport in an urban setting. The data is processed at 30 minutes interval using the Eddy Covariance method and includes quality control and diagnostic data generated by EddyPro software. The data is stored in the netCDF files following CF conventions. The UIC Plant Research Laboratory is located near major highways and urban infrastructure, including buildings and parking areas. The surrounding landscape consists of a mix of turf, plants, trees, and impervious surfaces such as concrete and asphalt, making it ideal for studying urban at for studies on urban sustainability, air quality, and the effects of urbanization on atmospheric processes on urban climate dynamics, air quality, and surface-atmosphere exchanges within the city of Chicago. This dataset is funded by the U.S. Department of Energy’s Office of Science, Biological and Environmental Research (BER) program.

54 ENVIRONMENTAL SCIENCES↗

Physics Flash Fall 2020

The Fall 2020 edition of Physics Flash includes article briefs on: Patrick Younk, Fusing concepts, technology to past performance of nuclear explosives; LANL inertial confinement fusion programs aims to develop burning plasma for weapons science; Lab's high energy nuclear physics explored at international conference; and, Novel study reveals new details on the impact of thermal interfaces in dynamic compression experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Risk-Informed ATF and FLEX Analysis for an Enhanced Resilient BWR Under Design-Basis and Beyond-Design-Basis Accidents

This report documents the activities performed by the Idaho National Laboratory (INL) during fiscal year (FY) 2020 for the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program, Risk-Informed System Analysis (RISA) Pathway, Enhanced Resilient Plant (ERP) Systems research. The purpose of the RISA Pathway research and development is to support plant owner-operator decisions with the aim to improve the economics, reliability, and maintain the high levels of safety of current nuclear power plants over periods of extended plant operations. The concept of ERP refers to the combinations of accident-tolerant fuel (ATF), optimal use of diverse and flexible coping strategy (FLEX), enhancements to plant components and systems, and the incorporation of augmented or new passive cooling systems, as well as improved fuel cycle efficiency. The objective of the ERP research effort is to use the RISA methods and toolkit in industry applications, including methods development and early demonstration of technologies, in order to enhance existing reactors’ safety features (both active and passive) and to substantially reduce operating costs through risk-informed approaches to plant design modifications to the plant and their characterization. One main focus of the FY 2020 efforts documented in this report was to extend the analyses conducted in FYs 2018 and 2019 for a pressurized water reactor (PWR) to a boiling water reactor (BWR). The same analysis process, risk analysis approaches, and analysis tools as in the previous work for PWR were used for a generic BWR with near-term ATF cladding (i.e., Iron-Chromium-Aluminum [FeCrAl] cladding and Chromium [Cr]-coated cladding) designs under the postulated station blackout (SBO) and medium loss-of-coolant (MLOCA) accident scenarios. In addition, a FLEX model was developed and incorporated into a generic BWR probabilistic risk assessment (PRA) model using the INL-developed software tool, Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE), to assess the risk impact from FLEX. The other main focus of the FY 2020 efforts was to advance analysis methods, including developing dynamic approach for FLEX human reliability analysis (HRA) using the INL-developed software tool, Event Modeling Risk Assessment using Linked Diagrams (EMRALD), as well as developing a multicriterion benefit evaluation (MCBE) method for evaluating costs and benefits of safety enhancements in nuclear power plants (NPPs). As a case study, the MCBE method was applied to evaluate the costs and benefits brought by FLEX implementation.

99 GENERAL AND MISCELLANEOUS↗

Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C

Drainage structures are used to capture stormwater runoff in streets and highways in urban environments. These drainage structures, which typically consist of catch basins with grates, inlets, or combination grates/inlets, collect stormwater runoff and discharge through buried conveyance systems. They are strategically placed for public safety in curb and gutter systems to provide efficient drainage of water from roadways and thus reduce the risk of hydroplaning. The performance of drainage structures is measured in terms of hydraulic efficiency, which is defined as the percentage of flow captured by the basin as compared to the total flow drainage to the structure. Understanding of the performance of these drainage structures helps designers properly space inlets to promote an economic design that ensures the safety of the traveling public. The current design methodology used to determine drainage structure follows guidelines established in the current Michigan Department of Transportation (MDOT) Drainage Manual (2006). The guidelines in the MDOT Drainage Manual were modeled after the Federal Highway Administration’s (FHWA) Hydraulic Engineering Circular 22 “Urban Drainage Design” (HEC-22). HEC-22 includes empirically derived equations to calculate the interception capacity of drainage structures for several commonly used grate configurations, such as the parallel bar, curved vane and tilt bar grates, which are based on a research study performed by Burgi et al. in the 1970s. MDOT uses several drainage structures to capture runoff that are detailed as Standard Plans. Many of these drainage structures utilize sinusoidal type grates that are not described in HEC-22. Physical modeling of these structures has been limited, posing the need to have them analyzed to verify their capture efficiency. Current MDOT practice is to assume a similar sized reticuline grate, as described in HEC-22, for capture efficiencies. Until recently, evaluating the hydraulic performance of drainage structures was limited to physical modeling in a hydraulics laboratory. With advances in engineering software and computing power, computational fluid dynamics (CFD) modeling has become a more cost-effective alternative. The Federal Highway Administration (FHWA) provides states the option to evaluate their drainage structures using CFD through the Transportation Pooled Fund Program. This study, “Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C,” was carried out using the pooled fund. MDOT’s Cover C was chosen as the first test candidate, given its similar sinusoidal pattern to other MDOT grates, but it is typically used for high-volume, higher speed applications. A similar version, Cover CX, is used on interstate highways but does not have traverse bars for bicycle safety. Additional grates may be considered for evaluation in the future.

42 ENGINEERING↗

Using an operator training simulator in the undergraduate chemical engineering curriculim

An operator training simulator (OTS) is to the chemical engineer what a flight simulator is to the aerospace engineer. The basis of an OTS is a high-fidelity dynamic model of a chemical process that allows an engineer to simulate start-up, shut-down, and normal operation. It can also be used to test the skill and ability of an engineer or operator to respond and control some unforeseen situation(s) through the use of programmed malfunctions. West Virginia University (WVU) is a member of the National Energy Technology Laboratory’s Regional University Alliance (NETL-RUA). Working through the NETL-RUA, the authors have spent the last four years collaborating on the development of a high-fidelity OTS for an Integrated Gasification Combined Cycle (IGCC) power plant with CO{sub 2} capture that is the cornerstone of the AVESTARTM (Advanced Virtual Energy Simulation Training And Research) Center with sister facilities at NETL and WVU in Morgantown, WV. This OTS is capable of real-time dynamic simulation of IGCC plant operation, including start-up, shut-down, and power demand load following. The dynamic simulator and its human machine interfaces (HMIs) are based on the DYNSIM and InTouch software, respectively, from Invensys Operations Management. The purpose of this presentation is to discuss the authors’ experiences in using this sophisticated dynamic simulation-based OTS as a hands-on teaching tool in the undergraduate chemical engineering curriculum. At present, the OTS has been used in two separate courses: a new process simulation course and a traditional process control course. In the process simulation course, concepts of steady-state and dynamic simulations were covered prior to exposing the students to the OTS. Moreover, digital logic and the concept of equipment requiring one or more permissive states to be enabled prior to successful operation were also covered. Students were briefed about start-up procedures and the importance of following a predetermined sequence of actions in order to start-up the plant successfully. Student experience with the dynamic simulator consisted of a six-hour training session in which the Claus sulfur capture unit of the IGCC plant was started up. The students were able to operate the simulator through the InTouch-based HMI displays and study and understand the underlying dynamic modeling approach used in the DYNSIM-based simulator. The concepts learned during the training sessions were further reinforced when students developed their own DYNSIM models for a chemical process and wrote a detailed start-up procedure. In the process control course, students learned how the plant responds dynamically to changes in the manipulated inputs, as well as how the control system impacts plant performance, stability, robustness and disturbance rejection characteristics. The OTS provided the opportunity to study the dynamics of complicated, “real-life” process plants consisting of hundreds of pieces of equipment. Students implemented ideal forcing functions, tracked the time-delay through the entire plant, studied the response of open-loop unstable systems, and learned “good practices” in control system design by taking into account the real-world events where significant deviations from the “ideal” or “expected” response can occur. The theory of closed-loop stability was reinforced by implementing limiting proportional gain for stability limits of real plants. Finally, students were divided into several groups where each group was tasked to control a section of the plant within a set of operating limits in the face of disturbances and simulated process faults. At the end of this test, they suggested ways to improve the control system performance based on the theory they learned in class and the hands-on experience they earned while working on the OTS.

97 MATHEMATICS AND COMPUTING↗

Numerical modeling of Joule heated ceramic melter

Computational fluid dynamics and heat transfer models of waste glass melters are being developed to support the vitrification campaign at the Waste Treatment and Immobilization Plant (WTP) as part of the United States nuclear waste stewardship and environmental protection programs. The WTP mission aims to achieve the stable and durable processing of vitrified waste in the safest, most efficient, and economical manner possible. Hanford’s tank waste is far more complex and varied than the waste treated by other vitrification facilities and both startup and long-term operational challenges are likely to be even greater than prior experience has shown. There are thousands of different waste compositions, which makes processing the waste a complex and challenging task. Models of test melters, pilot-scale, and full-scale melters have been developed to provide understanding and insight into the various physical and chemical phenomena occurring during vitrification. So the results of these modeling activities will be used to support the WTP operations to process legacy nuclear waste into a stable form for disposal.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Multi-channel probes to understand fission dynamics

Explaining the origin of the elements is a major outstanding question in nuclear astrophysics. Observed elemental abundance distribution shows strong nuclear physics effects. In conclusion, neutron-induced reactions are important for nuclear astrophysics and applied fields in nuclear energy and security. LANSCE has a program to address many of these questions directly with neutron beams on (near-)stable nuclei. Increasing demand for correlated data to test details of fission models poses additional challenges. Possibilities exist to extend existing experimental efforts to radioactive beam facilities. Kinematic focusing from using inverse kinematics has potential to circumvent some challenges associated with measuring correlations between fission output channels.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗