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DOE OSTI2021

Rapid 3D nanoscale coherent imaging via physics-aware deep learning

Phase retrieval, the problem of recovering lost phase information from measured intensity alone, is an inverse problem that is widely faced in various imaging modalities ranging from astronomy to nanoscale imaging. The current process of phase recovery is iterative in nature. As a result, the image formation is time consuming and computationally expensive, precluding real-time imaging. Here, we use 3D nanoscale X-ray imaging as a representative example to develop a deep learning model to address this phase retrieval problem. We introduce 3D-CDI-NN, a deep convolutional neural network and differential programing framework trained to predict 3D structure and strain, solely from input 3D X-ray coherent scattering data. Our networks are designed to be “physics-aware” in multiple aspects; in that the physics of the X-ray scattering process is explicitly enforced in the training of the network, and the training data are drawn from atomistic simulations that are representative of the physics of the material. We further refine the neural network prediction through a physics-based optimization procedure to enable maximum accuracy at lowest computational cost. 3D-CDI-NN can invert a 3D coherent diffraction pattern to real-space structure and strain hundreds of times faster than traditional iterative phase retrieval methods. Our integrated machine learning and differential programing solution to the phase retrieval problem is broadly applicable across inverse problems in other application areas.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2018

A Computer Model to Study the Response of Energetic Materials to a Range of Dynamic Loads

Over the past decade we developed a model to enable computer simulation of the mechanical and subsequent energetic response of explosives and propellants to mechanical insults such as impacts, perforations, drops, and falls. The model is embedded in computer simulation programs that solve the non-linear, large deformation equations of compressible solid and fluid flow in space and time. It is implemented as a user-defined model, which returns the updated stress tensor and composition that result from the simulation supplied strain tensor change. Although it is multi-phase, in that gas and solid species are present, it is single-velocity, in that the gas does not flow through the porous solid. More than 70 time-dependent variables are made available for additional analyses and plotting. The model encompasses a broad range of possible responses: mechanical damage with no energetic response, and a continuous spectrum of degrees of violence including delayed and prompt detonation. This work describes the basic workings of the model.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Cosmology and fundamental physics with the Euclid satellite

Euclid is a European Space Agency medium-class mission selected for launch in 2020 within the cosmic vision 2015–2025 program. The main goal of Euclid is to understand the origin of the accelerated expansion of the universe. Euclid will explore the expansion history of the universe and the evolution of cosmic structures by measuring shapes and red-shifts of galaxies as well as the distribution of clusters of galaxies over a large fraction of the sky. Although the main driver for Euclid is the nature of dark energy, Euclid science covers a vast range of topics, from cosmology to galaxy evolution to planetary research. In this review we focus on cosmology and fundamental physics, with a strong emphasis on science beyond the current standard models. We discuss five broad topics: dark energy and modified gravity, dark matter, initial conditions, basic assumptions and questions of methodology in the data analysis. This review has been planned and carried out within Euclid’s Theory Working Group and is meant to provide a guide to the scientific themes that will underlie the activity of the group during the preparation of the Euclid mission.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Shape optimization under uncertainty for rotor blades of horizontal axis wind turbines

We present a computational framework for the shape optimization of a Horizontal-Axis Wind Turbine (HAWT) rotor blade under uncertainty. Our framework integrates aerodynamic simulations based on the blade element method which utilizes reduced order models of the blade structure and wind load with design sensitivity analysis and nonlinear programming. The wind velocity is modeled as a stochastic process to account for variations in time and space. An additional stochastic process accounts for uncertainties in the structural material properties. The uncertainty propagation is based on a non-intrusive polynomial chaos expansion that allows accurate estimation of stochastic performance metrics such as generated power and structural compliance. Sensitivities of cost and constraint functions with respect to shape parameters namely twist angles are computed with an efficient scheme to enable gradient based optimization. To demonstrate the effect of uncertainty, designs obtained from optimization under uncertainty are compared to those obtained from deterministic optimization.

42 ENGINEERING↗

DOE OSTI2026

The porosity surrounding carbides and second phase stringers in monolithic U-10Mo fuel plate after irradiation

Post-irradiation microstructure characterization plays an important role in qualifying the low-enriched uranium (LEU) monolithic U-10 wt%Mo plate-type fuel for United States high-performance research reactors (USHPRRs) program. Inhomogeneous features resulting from manufacturing and irradiation processes, including carbides, second phase stringers, and extensive void spaces caused by the combining of small porosities, may increase the risk of heat concentration in local regions of the fuel plate over the operating conditions. In this study, characteristics of carbides, stringers, and porosity after multiple levels of irradiation at varying fission densities were studied by electron microscopes to decipher the morphology of pores and the porosity evolution in U-10 wt%Mo. For carbides, the result shows that porosities start forming on UMo grain boundaries, then on UMo/carbides interfaces as the burn-up going higher. However, the porosities surrounding carbides grow larger than the ones on UMo grain boundaries. The porosities around the uranium carbides could interconnect to form larger void space. The study revealed that the void spaces larger than 5 µm were found around uranium carbides after high burnup, while no evidence was observed to support the similar voids formed near second phase stringers even though the size of the stringers (> 50 µm) was much larger than uranium carbides (< 20 µm). The evolution of porosities suggests that the formation of second phase stringers may not create more significant porosities compared to regular uranium carbides regions during fuel operating conditions.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2015

SU-E-T-637: Proton Aperture Quality Assurance Using Computed Tomography

Purpose: To develop an automated algorithm for aperture quality assurance for double scattering proton radiotherapy. Methods: Anterior-Posterior scout images were acquired on a CT scanner for five brass apertures (2 large, 3 small) with 120 kVp and 10mA. A semi-automated algorithm was developed for the QA process. The input includes a user selecting the scout image and the associated patient plan, field and aperture size. The program automatically thresholds the scout image. Next, a connectivity algorithm is used to determine the points associated with the central shape to obtain the contour. To compare with the plan contour, the program converts the detected and plan contours into polar coordinates, interpolates the data to a 1 degree spaced grid, and determines the differences in radial distance at each grid point. Results: The mean and maximum difference and the percentage of points with distance differences less than 1.25 mm (due to the divergent cut of the aperture) between the detected and plan field aperture contours were obtained. A repeatability coefficient was derived based on repeated scanning and processing of three of the apertures. The mean difference for five apertures was 0.44 +/−0.08 mm. The maximum difference in distance was 1.2 +/−0.23 mm for all apertures. The Repeatability Coefficient was +/−0.038 mm, indicating the technique is highly repeatable. The mean percent of points with distance less than 1.25 mm was 97.41 +/−0.35%. Conclusion: Automated CT scout image based proton aperture QA is feasible, saves time, and provides a quantitative metric for proton patient specific aperture QA.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Neutronic Safety Analysis of Pu-238 Production at Idaho National Laboratory

This analysis was completed to support the irradiation of plutonium fuel services (PFS) targets in the NEFT in the Advanced Test Reactor (ATR) as a part of the campaign to restart domestic production of plutonium-238 used in radioisotope power systems (RPS) by the National Aeronautical and Space Administration (NASA) and Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Nuclear Infrastructure Program (NE-3). Referred to as the PFS-ATR-GEN1-NEFT experiment, the assembly was designed to hold 46 PFS targets in the NEFT. The scope of this paper is to outline the MOPY method used to calculate the heat generation rates (HGRs), flux, fission density, and quantify the viability of the target design for Pu-238 production in ATR.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2017

Theory, Solution Methods, and Implementation of the HERMES Model

The HERMES (high explosive response to mechanical stimulus) model was developed over the past decade to enable computer simulation of the mechanical and subsequent energetic response of explosives and propellants to mechanical insults such as impacts, perforations, drops, and falls. The model is embedded in computer simulation programs that solve the non-linear, large deformation equations of compressible solid and fluid flow in space and time. It is implemented as a user-defined model, which returns the updated stress tensor and composition that result from the simulation supplied strain tensor change. Although it is multi-phase, in that gas and solid species are present, it is single-velocity, in that the gas does not flow through the porous solid. More than 70 time-dependent variables are made available for additional analyses and plotting. The model encompasses a broad range of possible responses: mechanical damage with no energetic response, and a continuous spectrum of degrees of violence including delayed and prompt detonation. This paper describes the basic workings of the model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Investing in Alternative Fuel Infrastructure: Insights for California from Stakeholder Interviews: Preprint

Increased interest in the use of alternative transportation fuels, such as natural gas, hydrogen, and electricity, is being driven by heightened concern about the climate impacts of gasoline and diesel emissions and our dependence on finite oil resources. A key barrier to widespread adoption of low- and zero-emission passenger vehicles is the availability of refueling infrastructure. Recalling the 'chicken and egg' conundrum, limited adoption of alternative fuel vehicles increases the perceived risk of investments in refueling infrastructure, while lack of refueling infrastructure inhibits vehicle adoption. In this paper, we present the results of a study of the perceived risks and barriers to investment in alternative fuels infrastructure, based on interviews with industry experts and stakeholders. We cover barriers to infrastructure development for three alternative fuels for passenger vehicles: compressed natural gas, hydrogen, and electricity. As an early-mover in zero emission passenger vehicles, California provides the early market experience necessary to map the alternative fuel infrastructure business space. Results and insights identified in this study can be used to inform investment decisions, formulate incentive programs, and guide deployment plans for alternative fueling infrastructure in the U.S. and elsewhere.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Exploring the Nucleon Structure via Deep Electroproduction Processes

Understanding the internal structure of the nucleon is a fundamental goal of modern physics, which aims at a comprehensive framework describing the internal dynamics of quarks and gluons. Among other structure functions, Generalized Parton Distributions (GPDs) offer a powerful framework for describing the nucleon dynamics by correlating the longitudinal momentum and the transverse position of its internal partons. Such a correlation provides a three-dimensional picture of the nucleon and enables access to fundamental properties, including the internal pressure distributions and the parton’s angular momentum contribution to the nucleon's total spin, thereby playing a central role in resolving the nucleon spin puzzle. At the Thomas Jefferson National Facility (JLab), polarized electron beam experiments allow for probing GPDs through the measurement of hard exclusive processes. Among the cleanest experimental channels, we find the electro-production of a real photon through the Deeply Virtual Compton Scattering (DVCS) mechanism. The first data-taking period of the CLAS12 program, taking place in 2018, allowed for unique DVCS Beam Spin Asymmetry (BSA) measurements in the phase space covered by a 10.6 GeV polarized electron beam impinging on an unpolarized liquid hydrogen target. Although detecting all final-state particles ensures exclusivity of the process, conservation laws indicate that it is not mandatory. I adopt an approach omitting the direct detection of the recoil proton, providing a simplified yet effective event selection strategy that boosts statistics and gives access to a larger phase space sensitive to the underlying GPD dynamics through BSA and cross section measurements. The Double DVCS (DDVCS) process promises a dedicated mapping of GPDs. Contributing to the electro-production of a lepton pair cross-section, the DDVCS reaction extends DVCS by allowing the final-state photon to be virtual, enriching the kinematic phase space and providing unique access to the internal correlations encoded by GPDs. A feasibility study is conducted to assess the potential of future DDVCS measurements at Jefferson Lab and the future Electron-Ion Collider (EIC). While Jefferson Lab will provide DDVCS measurements in the valence region through the SoLID$\mu$ and $\mu$CLAS12 experimental projects, in the long term, the EIC will provide complementary measurements in the sea region, both accessing unprecedented information about GPDs in a phase space region otherwise inaccessible. Taken together, these investigations demonstrate both the current capabilities and future opportunities for probing GPDs through exclusive processes. The experimental analysis of DVCS at CLAS12 provides precise measurements within an established framework, while the phenomenological study of DDVCS opens the door to richer and more comprehensive explorations with future detectors and facilities.

Alvarado, Juan [Université Paris-Saclay: Gif-sur-Y↗

DOE OSTI2020

A fully unprivileged CernVM-FS

The CernVM File System provides the software and container distribution backbone for most High Energy and Nuclear Physics experiments. It is implemented as a file system in user-space (Fuse) module, which permits its execution without any elevated privileges. Yet, mounting the file system in the first place is handled by a privileged suid helper program that is installed by the Fuse package on most systems. The privileged nature of the mount system call is a serious hindrance to running CernVM-FS on opportunistic resource and supercomputers. Fortunately, recent developments in the Linux kernel and in the Fuse user-space libraries enabled fully unprivileged mounting for Fuse file systems (as of RHEL 8), or at least outsourcing the privileged mount system call to a custom, external process. This opens the door to several, very appealing new ways to use CernVM-FS, such as a generally usable “super pilot” consisting of the pilot code bundled with Singularity and CernVM-FS, or the on-demand instantiation of unprivileged, ephemeral containers to publish new CernVM-FS content from anywhere. In this contribution, we discuss the integration of these new Linux features with CernVM-FS and show some of its most promising, new applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

RAVEN User Manual

RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncertainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by input files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused toward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is interested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for an important process such as peak pressure in a pipe) is exceeded under certain conditions. The initial development of RAVEN has been focused on providing dynamic risk assessment capability to RELAP-7, currently under development at the INL and, likely, future replacement of the RELAP5-3D code. Most the capabilities that have been implemented having RELAP-7 as principal focus are easily deployable for other system codes. For this reason, several side activates are currently ongoing for coupling RAVEN with software such as RELAP5-3D, etc. The aim of this document is the explanation of the input requirements, focusing on the input structure.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

X-Ray Imaging and Spectroscopy Mission

The X-Ray Imaging and Spectroscopy Mission (XRISM) is a joint mission between the Japan Aerospace Exploration Agency (JAXA) and the National Aeronautics and Space Administration (NASA) in collaboration with the European Space Agency (ESA). In addition to the three space agencies, universities and research institutes from Japan, North America, and Europe have joined to contribute to developing satellite and onboard instruments, data-processing software, and the scientific observation program. XRISM is the successor to the ASTRO-H (Hitomi) mission, which ended prematurely in 2016. Its primary science goal is to examine astrophysical problems with precise, high-resolution X-ray spectroscopy. XRISM promises to discover new horizons in X-ray astronomy. It carries a 6 × 6 pixelized X-ray microcalorimeter on the focal plane of an X-ray mirror assembly (Resolve) and a co-aligned X-ray CCD camera (Xtend) that covers the same energy band over a large field of view. XRISM utilizes the Hitomi heritage, but all designs were reviewed. The attitude and orbit control system was improved in hardware and software. The spacecraft was launched from the JAXA Tanegashima Space Center on 2023 September 6 (UTC). During the in-orbit commissioning phase, the onboard components were activated. Although the gate valve protecting the Resolve sensor with a thin beryllium X-ray entrance window was not yet opened, scientific observation started in 2024 February with the planned performance verification observation program. The nominal observation program commenced with the following guest observation program beginning in 2024 September.

Astronomy and AstroPhysics↗

DOE OSTI2020

Double-Shell Tank Primary Bottom Visual Inspection Results - 20025

A pressing need for the Double-Shell Tank Integrity Program at Hanford is of the ability to inspect the bottom of the tanks. Though the DSTs' annulus spaces (the space between the internal and external tank walls) have been inspected visually since 1992 and with Ultrasonic Testing (UT) since 1996, inspections of the tank bottoms have been able to be conducted due to limitations of available technology, omitting about 40 percent of the tank surface below the maximum fill level from routine inspection. Visual inspections of the tank annulus have been conducted up to five times in some DSTs and portions of the annulus space for all of the DSTs has been inspected twice with UT. This region includes the walls of the primary tank and secondary liner along with accessible portions of the secondary liner bottom. Due to this lack of technology, the degradation of the primary tank bottom in Tank AY-102 was undetected until the tank leaked into its annulus space, confirmed in 2012. Since that time, WRPS has been working with the nondestructive examination community and the Pacific Northwest National Laboratory, to evaluate potential technologies to conduct these challenging remote inspections. Recent work has included the development, testing, and deployment of several remote visual inspection technologies to observe the condition of the primary tank bottom of the DSTs by leveraging air distribution slots in the refractory pad on which it rests. Robotic solutions to conduct this inspection were developed with a detailed understanding of the physical configuration and operational logistics. Understanding and subsequent communication of these details to vendors within the robotics and nondestructive examination community was a critical component to the successful production of these new tools. Throughout the FY16-FY18 years, vendors from nondestructive examination community were solicited for ideas to meet the tank bottom inspection challenge. Two tank bottom visual inspection solutions were then pursued to meet that challenge. Both tools were successfully deployed at Tank AP-107, and provided valuable visuals, never before obtained from the under tank environment of a double-shell tank. While there are minor opportunities for improvement identified with each system, general outcomes were overwhelmingly positive. Both systems were successfully able to navigate the refractory air slot pattern from the outer edge to the tank center and record video footage. The micro-crawler provided high quality and very stable footage through the air slot pattern, but took longer to deploy into the slots and traverse through them than the alternative system. The push-pull tethered camera was able to navigate all seven of its target air slots in a matter of a few hours, which included deployment, movement between slot entrances, and complete removal of the system from the annulus environment. Through these air slots, new information was gained about the tank bottom and refractory pad condition of tank AP-107, AP-106, AP-108, and AN-102. While some debris was noted in the air slots, including sand, chipped refractory, and construction materials, the refractory was found to be structurally stable and adequately supporting the primary tank bottom through the full diameter of the tank. Primary tank bottom steel exterior was found to be in good condition, free of ongoing or aggressive corrosion conditions. Looking toward the future, robotic access to and visual inspection of refractory air slots and the primary tank bottom steel has now proven viable. Incorporating periodic air slot inspections as a regular practice within the Double-Shell Tank Integrity Program is the next step, allowing trending of any changes in condition. As ultrasonic testing infrastructure was leveraged to complete the initial system deployments described in this report, it makes sense to adopt that same strategy for ongoing periodic examinations and deploy these primary tank bottom inspection tools alongside ultrasonic testing operations. Development of visual inspection tools to evaluate the primary tank bottom region of the double-shell tanks was planned as the first stage of inspection. Continued development of volumetric sensors and incorporation of these inspection tools into Hanford's ongoing Double-Shell Tank Integrity Program are the next steps, seeking to continuously expand understanding of asset integrity and remaining useful life. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Information Content of a Synergy of Ground-Based and Space-Based Infrared Sounders. Part I: Clear-Sky Environments

Abstract Profiles of atmospheric temperature and water vapor from remotely sensed platforms provide critical observations within the temporal and spatial gaps of the radiosonde network. The 2017 National Academies of Science Decadal Survey highlighted that observations of the planetary boundary layer (PBL) from the current space-based observing system are not of the necessary accuracy or resolution for monitoring and predicting high-impact weather phenomena. One possible solution to improving observations of the PBL is supplementing the existing space-based observing system with a network of ground-based profilers. A synthetic information content study is developed utilizing profiles from the Atmospheric Radiation Measurement (ARM) program sites at the Southern Great Plains (SGP), east North Atlantic (ENA), and North Slope of Alaska (NSA) to assess the benefits, in terms of degrees of freedom (DOF), vertical resolution, and uncertainties, of a synergy between the ground-based Atmospheric Emitted Radiance Interferometer (AERI) with space-based hyperspectral infrared (IR) sounders. A combination of AERI with any of the three polar-orbiting IR sounders: the Atmospheric Infrared Sounder (AIRS), the Cross-track Infrared Sounder (CrIS), or the Infrared Atmospheric Sounding Interferometer (IASI), results in a DOF increase of 30%–40% in the surface-to-700-hPa layer compared to the space-based instrument alone. Introducing AERI measurements to the observing system also results in significant improvements to vertical resolution and uncertainties in the bottom 1000 m of the atmosphere compared to CrIS measurements alone. A synergy of CrIS and AERI exceeds the 1-km-vertical-resolution goal set by the Decadal Survey in the lowest 1000 m.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

The geometry of the modular bootstrap

Abstract We explore the geometry behind the modular bootstrap and its image in the space of Taylor coefficients of the torus partition function. In the first part, we identify the geometry as an intersection of planes with the convex hull of moment curves onR + ⊗ℤ, with boundaries characterized by the total positivity of generalized Hankel matrices. We phrase the Hankel constraints as a semi-definite program, which has several advantages, such as the validity of bounds irrespective of spin truncation. We derive bounds on the gap, twist-gap, and the space of Taylor coefficients themselves. We find that if the gap is above$$ {\Delta }_{\textrm{gap}}^{\ast } $$ ∆ gap ∗ , where$$ \frac{c-1}{12}<{\Delta}_{\textrm{gap}}^{\ast }<\frac{c}{12} $$ c − 1 12 < Δ gap ∗ < c 12 , all coefficients become bounded on both sides and kinks develop in the space. In the second part, we propose an analytic method of imposing the integrality condition for the degeneracy number in the spinless bootstrap, which leads to a non-convex geometry. We find that even at very low derivative order this condition rules out regions otherwise allowed by bootstraps at high derivative order.

Physics↗

DOE OSTI2017

Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini

R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. We investigated the space sampled by the disordered N-termini of R67 DHFR using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (Rg) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the Rg increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ~900 waters indicates the N-termini are well-hydrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗