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DOE OSTI2013

Thermodynamic and kinetic characterization of hydroxyethylamine β-secretase-1 inhibitors

Highlights: •Kinetic and thermodynamic characterization of 10 hydroxyethylamine BACE-1 inhibitors. •Equilibrium binding of inhibitors was enthalpy driven for BACE-1. •Negative entropy of binding was observed towards BACE-1, but not Cathepsin-D. •Structural analysis demonstrates ligand binding induces a major conformational change. •Structural analysis and SPR analysis corroborate induced fit and negative entropy of binding. -- Abstract: Alzheimer’s disease (AD) is a devastating neurodegenerative disease affecting millions of people. β-Secretase-1 (BACE-1), an enzyme involved in the processing of the amyloid precursor protein (APP) to form Aβ, is a well validated target for AD. Herein, the authors characterize 10 randomly selected hydroxyethylamine (HEA) BACE-1 inhibitors in terms of their association and dissociation rate constants and thermodynamics of binding using surface plasmon resonance (SPR). Rate constants of association (k{sub a}) measured at 25 °C ranged from a low of 2.42 × 10{sup 4} M{sup −1} s{sup −1} to the highest value of 8.3 × 10{sup 5} M{sup −1} s{sup −1}. Rate constants of dissociation (k{sub d}) ranged from 1.09 × 10{sup −4} s{sup −1} (corresponding to a residence time of close to three hours), to the fastest of 0.028 s{sup −1}. Three compounds were selected for further thermodynamic analysis where it was shown that equilibrium binding was enthalpy driven while unfavorable entropy of binding was observed. Structural analysis revealed that upon ligand binding, the BACE-1flap folds down over the bound ligand causing an induced fit. The maximal difference between alpha carbon positions in the open and closed conformations of the flap was over 5 Å. Thus the negative entropy of binding determined using SPR analysis was consistent with an induced fit observed by structural analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Bim-to-fea Conversion Program

The purpose of this program is to enable interoperability between BIM-based architectural design software (i.e., Revit, ArchiCAD, AVEVA E3D) to structural analysis software (i.e., SAP2000). The program takes in BIM building model data via the IFC file format, automatically transforms the architectural coordination entities (structural beams, columns, slabs, walls) to structural analysis entities (i.e., finite element space frames and shells), automatically adjusts the connectivity of the structural analysis entities, and finally exports the structural analysis entities as a structural analysis model contained within a new IFC file. For example, a 3D building in Revit can be exported to an IFC file, run through this BIM-to-FEA program, then the exported IFC can be inputted into SAP2000.

Crowder, Nicholas [Idaho National Laboratory (INL)↗

DOE OSTI2024

Improving and Automating Building Model Data Exchange

There are many instances throughout a project’s lifecycle where there arises a need for quick and accurate risk assessment of building designs. For example, an unexpected design change during construction may necessitate structural engineers to perform a seismic risk assessment on analytical models of the updated building design using high fidelity structural analysis software, such as ANSYS or Abaqus. However, the efficiency of such workflows often depends upon the interoperability of architectural design software and structural analysis software. When the quality of this interoperability is lacking or even non-existent, the efficiency of virtual engineering workflows is hampered, which increases project costs. A McGraw Hill industry survey of professional users of Building Information Modeling (BIM) technologies found that there is high demand for BIM interoperability for structural analysis, but that the value/difficulty ratio is currently too low for practical use. There have been efforts by the academic community to facilitate model data exchange between the architectural design and structural analysis domains, but such solutions have not been widely adopted by industry, face technical challenges, and oftentimes are limited in applicability for users of various BIM software. Therefore, INL is developing capabilities to improve, automate, and generalize model data exchange between architectural BIM software (e.g., Revit) and structural analysis software (e.g., SAP2000, ANSYS). The goal is to help expedite and automate as much of the pre-processing step for creating analytical models in finite element analysis software as reasonably as possible. Such a "BIM-to-FEA" conversion tool should provide direct benefit to end-users through accuracy, automation, quick turn-around, and wide applicability. To generalize the application of this BIM-to-FEA conversion tool and increase its useability among the many different commercial BIM software currently used by industry, the program is being developed with the concept of openBIM. OpenBIM is the application of non-proprietary, open data standards that allow for BIM model data exchange in a format that is accessible, retainable, and useable for all users. The most widely used open, non-proprietary data exchange format for BIM is the Industry Foundation Classes (IFC) schema. IFC is developed by buildingSMART international and is ISO certified (ISO 16739-1:2018). The BIM-to-FEA conversion tool is being developed for compatibility with typical commercial building designs of steel framed structures. The tool is currently capable of importing architectural BIM data of framed building structures, recognizing and extracting the aspects of the model that are required for structural analysis, adjusting the connectivity of frame members, and finally exporting to an analytical model stored in the IFC format. The exported IFC analytical model can then be imported into various openBIM compliant software, such as SAP2000. Such capabilities have already been tested on commercial software, as shown above, and continue to be improved. Work is underway to test the conversion on various commercial BIM software, develop a user-friendly interface, incorporate the program into the broader DeepLynx data warehouse project being developed by INL, and to eventually open-source the tool for the benefit of the community. Future development of the tool envisions the ability for efficient iterative risk assessment of generative building designs, all within a workflow utilizing open-source tools. One such open-source tool will be MOOSE, an advanced finite element analysis tool developed at INL. The conversion tool will also branch out from typical commercial building designs and will aim to incorporate nuclear construction. The aim will be to convert both structural and non-structural components of nuclear facilities, such as curved concrete containment structures and piping systems, respectively.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Limit Load and Buckling Analysis for Assessing Hanford Single-Shell Tank Dome Structural Integrity - 12278

The U.S. Department of Energy, Office of River Protection has commissioned a structural analysis of record for the Hanford single shell tanks to assess their structural integrity. The analysis used finite element techniques to predict the tank response to the historical thermal and operating loads. The analysis also addressed the potential tank response to a postulated design basis earthquake. The combined response to static and seismic loads was then evaluated against the design requirements of American Concrete Institute standard, ACI-349-06, for nuclear safety-related concrete structures. Further analysis was conducted to estimate the plastic limit load and the elastic-plastic buckling capacity of the tanks. The limit load and buckling analyses estimate the margin between the applied loads and the limiting load capacities of the tank structure. The potential for additional dome loads from waste retrieval equipment and the addition of large dome penetrations to accommodate retrieval equipment has generated additional interest in the limit load and buckling analyses. This paper summarizes the structural analysis methods that were used to evaluate the limit load and buckling of the single shell tanks. This paper summarizes the structural analysis methods that were used to evaluate the limit load and buckling limit states of the underground single shell tanks at the Hanford site. The limit loads were calculated using nonlinear finite element models that capture the progressive deformation and damage to the concrete as it approaches the limit load. Both uniform and concentrated loads over the tank dome were considered, and the analysis shows how adding a penetration in the center of the tank would affect the limit loads. For uniform surface loads, the penetration does not affect the limit load because concrete crushing and rebar yielding initiates first at the top of the wall, away from the penetration. For concentrated loads, crushing initiates at the center of the dome, so the penetration does reduce the concentrated limit load somewhat. However, the safety factors comparing the limit loads to the maximum allowable applied loads remain well above the required value of 3.0. The buckling analysis method accounts for the geometric imperfections, concrete creep, cracking and reinforcements, and concrete plasticity in determining the allowable buckling load limits. The method was demonstrated in this paper for the evaluation of a tank before and after a penetration is added in the dome center. Finite element buckling models were used to accurately calculate the linear critical buckling loads. The models showed that adding the penetration reduces the linear critical buckling load by only 2.5%. Bounding cases also showed that the possible range of soil support on the walls does not significantly affect the dome buckling loads. Buckling models of the full 360 deg. dome also showed that the dome is more resistant to buckling when the load is offset than when it is positioned over the center. These limit load and buckling analysis methods are being used at the Hanford site to assess the tank loads that can be safely applied during future waste retrieval activities. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2012

Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp)

Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp), which is also known as 3D polymerase (3D pol ). In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3D pol using a combination of different computational tools. Model structures of BRBV 3D pol were verified for their stereochemical quality and accuracy. The BRBV 3D pol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P), nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3D pol (PDB, 1U09 and 2E9Z). The closest proximity of BRBV and FMDV 3D pol as compared to human rhinovirus type 16 (HRV-16) and rabbit hemorrhagic disease virus (RHDV) 3D pols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD) between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3D pol compared to FMDV 3D pol , indicate that despite a very high homology to FMDV 3D pol , BRBV 3D pol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the design of structure-function interventions and identification of molecular targets for drug design applicable to Aphthovirus RdRps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Advanced Seismic Fragility Modeling using Nonlinear Soil-Structure Interaction Analysis

The goal of this effort is to compare the seismic fragilities of a nuclear power plant system obtained by a traditional seismic probabilistic risk assessment (SPRA) and an advanced SPRA that utilizes Nonlinear Soil-Structure Interaction (NLSSI) analysis. Soil-structure interaction (SSI) response analysis for a traditional SPRA involves the linear analysis, which ignores geometric nonlinearities (i.e., soil and structure are glued together and the soil material undergoes tension when the structure uplifts). The NLSSI analysis will consider geometric nonlinearities.

31274, LWRS↗

DOE OSTI2022

University of Missouri Research Reactor (MURR) Design Demonstration Element End Fitting Structural Rigidity Analysis

The primary objective of this work is to assess the extent to which the stiffness (measured by means of maximum displacement) of the end fittings in the DDE contributes to the stiffness of the entire element, and how it compares to the equivalent stiffness of the end fittings in the LEU element. Structural analysis of both the LEU element and the DDE were performed using COMSOL 5.3a finite element software. Supporting combs are used on the leading and trailing edges of fuel plates for both the LEU element and the DDE. Therefore, simulations with and without combs are performed as two bounding boundary conditions on the leading edge of the fuel plates. Three types of loads are analyzed in this work: the hydraulic load due to the channel flow disparity-induced pressure differential, the thermal load due to the thermal expansion of the fuel plates, and a point load equal in magnitude to the LEU element’s weight.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2015

Advanced Seismic Fragility Modeling using Nonlinear Soil-Structure Interaction Analysis

31274, LWRS↗

DOE OSTI2017

A reversible phase transition for sodium insertion in anatase TiO 2

Anatase TiO 2 is a potential negative electrode for sodium-ion batteries. The sodium storage mechanism is, however, still under debate, yet its comprehension is required to optimize the electrochemical properties. To clarify the sodium storage mechanism occurring in anatase, we have used both electrochemical and chemical routes from which we obtained similar trends. During the first discharge, an irreversible plateau region is observed which corresponds to the insertion of Na+ within the interstitial sites of anatase and is accompanied by a drastic loss of the long-range order as revealed by X-ray diffraction, high resolution of high angle annular dark-field scanning transmission electron microscope (HAADF-STEM), and pair distribution function (PDF) analysis. Further structural analysis of the total scattering data indicates that the sodiated phase displays a layered-like rhombohedral R3m structure built from the stacking of Ti and Na slabs. Because of the initial 3D network of anatase, the reduced phase shows strong disorder due to cationic intermixing between the Ti and Na slabs and the refined chemical formula is (Na 0.43 Ti 0.57 ) 3a 0.22 Na 0.39 Ti 0.39 ) 3b O 2 , where refers to vacancy. The presence of high valence Ti ions in the Na layers induces a contraction of the c-parameter as compared to the ordered phase. Upon desodiation, the structure further amorphized and the local structure probed by PDF is shown to be similar to the anatase TiO 2 , suggesting that the 3D network is recovered. The reversible sodium insertion/deinsertion is thus attributed to the rhombohedral active phase formed during the first discharge, and an oxidized phase featuring the local structure of anatase. Due to the amorphous nature of the two phases, the potential-composition curves are characterized by a sloping curve. Lastly, a comparison between the intercalation of lithium and sodium into anatase TiO 2 performed by DFT calculations confirmed that, for the sodiated phase, the rhombohedral structure is more stable than the tetragonal phase observed during the lithiation of nanoparticles.

36 MATERIALS SCIENCE↗

DOE OSTI2019

NONLINEAR SOIL-STRUCTURE INTERACTION ANALYSIS USING CO-SIMULATION

Nonlinear soil-structure interaction (NLSSI) analysis methods are currently being developed at Idaho National Laboratory. Appendix B in ASCE (2016) includes a framework for performing NLSSI analysis. For NLSSI analysis to be widely implemented in industry, it is important to demonstrate that accurate response in dynamically loaded, nonlinear models can be achieved in an efficient manner. Both explicit and implicit dynamic solvers are applicable to NLSSI. When considering cpu time, an explicit dynamic solver is often desirable for large models with no features (e.g. small elements, stiff elements, or stiffness damping) that can drive the time step unreasonably small. An implicit dynamic solver may be desirable in models not well suited for an explicit solver. A further option is co-simulation where a portion of the model is run with an explicit dynamic solver and the rest of the model is run with an implicit dynamic solver. This study explores NLSSI examples where co-simulation could be the most cpu efficient modelling strategy.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2019

In situ analysis of the structural transformation of glassy carbon under compression at room temperature

Room temperature compression of graphitic materials leads to interesting superhard sp 3 rich phases which are sometimes transparent. In the case of graphite itself, the sp 3 rich phase is proposed to be monoclinic M-carbon; however, for disordered materials such as glassy carbon the nature of the transformation is unknown. We compress glassy carbon at room temperature in a diamond anvil cell, examine the structure in situ using x-ray diffraction, and interpret the findings with molecular dynamics modeling. Experiment and modeling both predict a two-stage transformation. First, the isotropic glassy carbon undergoes a reversible transformation to an oriented compressed graphitic structure. This is followed by a phase transformation at ~35 GPa to an unstable, disordered sp 3 rich structure that reverts on decompression to an oriented graphitic structure. Analysis of the simulated sp 3 rich material formed at high pressure reveals a noncrystalline structure with two different sp 3 bond lengths.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Controlled Shape Memory Behavior of a Smectic Main-Chain Liquid Crystalline Elastomer

Here, we describe how a smectic main-chain liquid crystalline elastomer (LCE), with controlled shape memory behavior, is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic carboxylic acid curing agent. Microstructures of the LCEs, including their liquid crystallinity and cross-linking density, are modified by adjusting the stoichiometric ratio of the reactants to tailor the thermomechanical properties and shape memory behavior of the material. Thermal and liquid crystalline properties of the LCEs, characterized using differential scanning calorimetry and dynamic mechanical analysis, and structural analysis, performed using small-angle and wide-angle X-ray scattering, show that liquid crystallinity, cross-linking density, and network rigidity are strongly affected by the stoichiometry of the curing reaction. With appropriate structural modifications it is possible to tune the thermal, dynamic mechanical, and thermomechanical properties as well as the shape memory and thermal degradation behavior of LCEs.

36 MATERIALS SCIENCE↗

DOE OSTI2020

A cross-sectional aeroelastic analysis and structural optimization tool for slender composite structures

A fully open-source available framework for the parametric cross-sectional analysis and design optimization of slender composite structures, such as helicopter or wind turbine blades, is presented. The framework—Structural Optimization and Aeroelastic Analysis (SONATA)—incorporates two structural solvers, the commercial tool VABS, and the novel open-source code ANBA4. SONATA also parameterizes the design inputs, postprocesses and visualizes the results, and generates the structural inputs to a variety of aeroelastic analysis tools. It is linked to the optimization library OpenMDAO. This work presents the methodology and explains the fundamental approaches of SONATA. Structural characteristics were successfully verified for both VABS and ANBA4 using box beam examples from literature, thereby verifying the parametric approach to generating the topology and mesh in a cross section as well as the solver integration. The framework was furthermore exercised by analyzing and evaluating a fully resolved highly flexible wind turbine blade. Computed structural characteristics correlated between VABS and ANBA4, including off-diagonal terms. Stresses, strains, and deformations were recovered from loads derived through coupling with aeroelastic analysis. The framework, therefore, proves effective in accurately analyzing and optimizing slender composite structures on a high-fidelity level that is close to a three-dimensional finite element model.

42 ENGINEERING↗

DOE OSTI2012

Limit Load and Buckling Analysis for Assessing Hanford Single-Shell Tank Dome Structural Integrity

The U.S. Department of Energy, Office of River Protection has commissioned a structural analysis of record (AOR) for the Hanford single shell tanks (SSTs) to assess their structural integrity. The analysis used finite element techniques to predict the tank response to the historical thermal and operating loads. The analysis also addressed the potential tank response to a postulated design basis earthquake. The combined response to static and seismic loads was then evaluated against the design requirements of American Concrete Institute (ACI) standard, ACI-349-06, for nuclear safety-related concrete structures. Further analysis was conducted to estimate the plastic limit load and the elastic-plastic buckling capacity of the tanks. The limit load and buckling analyses estimate the margin between the applied loads and the limiting load capacities of the tank structure. The potential for additional dome loads from waste retrieval equipment and the addition of large dome penetrations to accommodate retrieval equipment has generated additional interest in the limit load and buckling analyses. This paper summarizes the structural analysis methods that were used to evaluate the limit load and buckling of the single shell tanks.

nuclear waste tank, structural evaluation, limit l↗

DOE OSTI2016

Synthesis and characterization of a new photoluminescent material (8-hydroxy quinoline) bis (2-2’bipyridine) lanthanum La(Bpy)2q

A new photoluminescence material, (8-hydroxy quinoline) bis (2-2’bipyridine) lanthanum has been synthesized and characterized by different techniques. The prepared material La(Bpy){sub 2}q was characterized for structural, thermal and photoluminescence analysis. Structural analysis of this material was done by Fourier transformed infrared spectroscopy (FTIR) and mass spectroscopy. Thermal analysis of this material was done by thermal gravimetric analysis (TGA) shows the thermal stability up to 190°C.Absorption and emission spectra of the material was measured by UV-visible spectroscopy and photoluminescence spectroscopy. Solution of this material La(Bpy){sub 2}q in ethanol showed absorption peak at 385nm, which may be attributed due to (π – π*) transitions. The photoluminescence spectra of La(Bpy){sub 2}q in ethanol solution showed intense peak at 490 nm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Enhancement in dielectric behavior of (Ni, Zn)Fe{sub 2}O{sub 4} ferrite

In present work, NiFe{sub 2}O{sub 4}(NFO), ZnFe{sub 2}O{sub 4} (ZFO) and Ni{sub 0.5}Zn{sub 0.5}Fe{sub 2}O{sub 4} (NZFO) are synthesized by microwave assisted co-precipitation route. Their structural properties are confirmed by X-ray diffraction and data is fitted through Reitveld refinement using Full-Prof software suite. After refinement, the systematic crystal structures of NFO, ZFO and NZFO compounds are generated using output .cif file by VESTA (Visualization for Electronic and Structural Analysis) program. Structural parameters obtained after refinement and unit cell construction, are systematically tabulated. Room temperature frequency dependence dielectric properties are studied. We found enhanced values of dielectric constant for NZFO than individual NFO and ZFO phases. For NZFO sample, greater electron exchange between Fe{sup 2+} and Fe{sup 3+} which enhances polarization and dielectric constant.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Synthesis and characterization of a new photoluminescent material tris (2-methyl-8-hydroxy quinoline) lanthanum La(mq){sub 3}

A new photoluminescence material, tris (2-methyl-8-hydroxy quinoline) lanthanum has been synthesized and characterized by different techniques. The prepared material La(mq){sub 3} was characterized for structural, thermal and photoluminescence analysis. Structural analysis of this material was done by fourier transformed infrared spectroscopy (FTIR) and mass spectroscopy. Thermal analysis of this material was done by thermal gravimetric analysis (TGA) shows the thermal stability up to 400°C. Absorption and emission spectra of the material was measured by UV-visible spectroscopy and photoluminescence spectroscopy. Solution of this material La(mq){sub 3} in ethanol showed absorption peak at 385 nm respectively which may be attributed due to (π – π*) transitions. The photoluminescence spectra of La(mq){sub 3} in ethanol solution showed intense peak at 430 nm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

A suite-level review of the neutron single-crystal diffraction instruments at Oak Ridge National Laboratory

The nascent suite of single-crystal neutron diffractometers at the Oak Ridge National Laboratory has no equal at any other neutron scattering facility worldwide and offers the potential to re-assert single-crystal diffraction using neutrons as a significant tool to study nuclear and magnetic structures of small unit cell crystals, nuclear structures of macromolecules, and diffuse scattering. Signature applications and features of single-crystal neutron diffraction are high resolution nuclear structure analysis, magnetic structure and spin density determinations, contrast variation (particularly D 2 O/H 2 O) for nuclear structural studies, lack of radiation damage when using crystals of biological molecules such as proteins, and the fidelity to measure nuclear and magnetic diffuse scattering with elastic discrimination.

47 OTHER INSTRUMENTATION↗