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At least 109 records · Page 6

Continued Verification of MOOSE Structural Mechanics Tools for Modeling Core Bowing Phenomena in Fast Reactors

Under the U.S. Department of Energy Office of Nuclear Energy’s Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism whereby increased power (which leads to temperature and flux gradients) influences the core to bow into less reactive configurations when the restraint system is properly designed. The phenomenon includes a complex interplay of radiation transport, duct temperature calculations involving fluid flow and heat transfer, and thermo-mechanical responses to the induced temperature and flux gradients. Structural material properties are also important to determining inelastic response to longer term flux gradients which cause irradiation creep and swelling. While core bowing provides a strong negative reactivity feedback when the restraint system is designed properly, it also results in additional forces between assemblies which increase the loads required to extricate them during refueling or control rod movement. Therefore, the restraint system must be designed with these tradeoffs in mind. The first stage of the work, which commenced in FY21 and continues through FY22, assesses thermo-mechanical modeling tools for producing core bowing predictions consistent with conventional tools. The Multiphysics Object Oriented Simulation Environment (MOOSE) Tensor Mechanics and Contact Modules are employed. This status report describes work on additional thermo-mechanical benchmark verification problems with increased complexity from the examples demonstrated in FY21. Several benchmark verification examples were selected from the IAEA verification and validation report. These examples involve clusters of ducts representative of a sector of a hexagonal reactor core which bow into each other and cause contact and load pad elevations, as well as single ducts subjected to irradiation fields undergoing swelling and subsequent bowing. The MOOSE-based results were compared to both IAEA benchmark participants’ results, analytic equations as available, and NUBOW-3D, a beam model code developed by Argonne National Laboratory. In every case, the MOOSE results agreed with other simulations results, providing additional verification basis of the tools for this particular physics application.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

We report crystal structures of the antibacterial lasso peptides microcin J25 (MccJ25) and capistruin (Cap) bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). Both peptides bind within the RNAP secondary channel, through which NTP substrates enter the RNAP active site, and sterically block trigger-loop folding, which is essential for efficient catalysis by the RNAP. MccJ25 binds deep within the secondary channel in a manner expected to interfere with NTP substrate binding, explaining the partial competitive mechanism of inhibition with respect to NTPs found previously [Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH (2004) Mol Cell 14:739–751]. The Cap binding determinant on RNAP overlaps, but is not identical to, that of MccJ25. Cap binds further from the RNAP active site and does not sterically interfere with NTP binding, and we show that Cap inhibition is partially noncompetitive with respect to NTPs. This work lays the groundwork for structure determination of other lasso peptides that target the bacterial RNAP and provides a structural foundation to guide lasso peptide antimicrobial engineering approaches.

59 BASIC BIOLOGICAL SCIENCES↗

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallelize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet -- and perhaps will never -- be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Farhat, Charbel↗

Lunar regolith and structure mechanics

The topics are presented in viewgraph form and include the following: modeling of regolith-structure interaction in extraterrestrial constructed facilities; densification of lunar soil simulant; and vibration assisted penetration of lunar soil simulant.

Barnes, Frank↗

Compatibility Conditions of Structural Mechanics

The theory of elasticity has camouflaged a deficiency in the compatibility formulation since 1860. In structures the ad hoc compatibility conditions through virtual "cuts" and closing "gaps" are not parallel to the strain formulation in elasticity. This deficiency in the compatibility conditions has prevented the development of a direct stress determination method in structures and in elasticity. We have addressed this deficiency and attempted to unify the theory of compatibility. This work has led to the development of the integrated force method for structures and the completed Beltrami-Michell formulation for elasticity. The improved accuracy observed in the solution of numerical examples by the integrated force method can be attributed to the compliance of the compatibility conditions. Using the compatibility conditions allows mapping of variables and facile movement among different structural analysis formulations. This paper reviews and illustrates the requirement of compatibility in structures and in elasticity. It also describes the generation of the conditions and quantifies the benefits of their use. The traditional analysis methods and available solutions (which have been obtained bypassing the missed conditions) should be verified for compliance of the compatibility conditions.

Patnaik, Surya N.↗

Two-dimensional silica: Structural, mechanical properties, and strain-induced band gap tuning

Two-dimensional silica is of rising interests not only for its practical applications as insulating layers in nanoelectronics, but also as a model material to understand crystals and glasses. In this study, we examine structural and electronic properties of hexagonal and haeckelite phases of silica bilayers by performing first-principles calculations. We find that the corner-sharing SiO{sub 4} tetrahedrons in these two phases are locally similar. The robustness and resilience of these tetrahedrons under mechanical perturbation allow effective strain engineering of the electronic structures with band gaps covering a very wide range, from of that for insulators, to wide-, and even narrow-gap semiconductors. These findings suggest that the flexible 2D silica holds great promises in developing nanoelectronic devices with strain-tunable performance, and lay the ground for the understanding of crystalline and vitreous phases in 2D, where bilayer silica provides an ideal test-bed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Applications of artificial neural nets in structural mechanics

A brief introduction to the fundamental of Neural Nets is given, followed by two applications in structural optimization. In the first case, the feasibility of simulating with neural nets the many structural analyses performed during optimization iterations was studied. In the second case, the concept of using neural nets to capture design expertise was studied.

Berke, Laszlo↗

Applications of artificial neural nets in structural mechanics

A brief introduction to the fundamental of Neural Nets is given, followed by two applications in structural optimization. In the first case, the feasibility of simulating with neural nets the many structural analyses performed during optimization iterations was studied. In the second case, the concept of using neural nets to capture design expertise was studied.

Berke, L.↗

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics, part 2

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallellize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet and perhaps will never be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient than explicit codes when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Farhat, Charbel↗

Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery

Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD ( Mt NadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, Mt NadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect the structural elements that contribute to the interactions of the two Mt NadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type Mt NadD, we used a small molecule inhibitor of MtNadD with moderate affinity ( K i ~ 25 μM) and antimycobacterial activity (MIC 80 ) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of Mt NadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequential mechanism is consistent with the requirement of transition to catalytically competent (open) conformation hypothesized from structural modeling. A possible physiological significance of this mechanism is to enable the down-regulation of NAD synthesis under ATP-limiting dormancy conditions. Lastly, these findings point to a possible new strategy for designing inhibitors that lock the enzyme in the inactive over-closed conformation.

59 BASIC BIOLOGICAL SCIENCES↗

Thermal and mechanical structure of the upper mantle: A comparison between continental and oceanic models

Temperature, velocity, and viscosity profiles for coupled thermal and mechanical models of the upper mantle beneath continental shields and old ocean basins show that under the continents, both tectonic plates and the asthenosphere, are thicker than they are beneath the oceans. The minimum value of viscosity in the continental asthenosphere is about an order of magnitude larger than in the shear zone beneath oceans. The shear stress or drag underneath continental plates is also approximately an order of magnitude larger than the drag on oceanic plates. Effects of shear heating may account for flattening of ocean floor topography and heat flux in old ocean basins.

Froidevaux, C.↗

Computational structural mechanics and fluid dynamics: Advances and trends; Proceedings of the Symposium, Washington, DC, Oct. 17-19, 1988

Recent advances in computational structural and fluid dynamics are discussed in reviews and reports. Topics addressed include fluid-structure interaction and aeroelasticity, CFD techniques for reacting flows, micromechanics, stability and eigenproblems, probabilistic methods and chaotic dynamics, and perturbation and spectral methods. Consideration is given to finite-element, finite-volume, and boundary-element methods; adaptive methods; parallel processing machines and applications; and visualization, mesh generation, and AI interfaces.

Noor, Ahmed K.↗

Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins

Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here in this paper we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA “bridge” and identifies an interface, termed the “bridge interface,” that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells.

59 BASIC BIOLOGICAL SCIENCES↗

Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters

Abstract Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn 2+ status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn 2+ uptake and cell growth viability assays reveal a negative regulation of Zn 2+ uptake through sensing intracellular Zn 2+ status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Mechanism of an Efficacy Photoswitch Targeting the β 2 ‐adrenergic Receptor

The field of photopharmacology develops light-responsive drugs that can modulate protein activity, enabling precise and dynamic investigations of their roles in health and disease. Adrenergic receptors are prominent targets for this approach because they are prototypical G protein-coupled receptors with high clinical relevance in bronchial and cardiovascular diseases. Here, we employed the azobenzene-based compound photoazolol-1 in combination with time-resolved serial crystallography at X-ray free-electron lasers to resolve the molecular mechanisms by which photoswitchable β-blockers modulate activity of the β 2 -adrenoceptor (β 2 AR). Time-resolved structures of the receptor bound to trans-photoazolol-1 (pre-photoconversion), a strained intermediate in the nanosecond range, and the fully photoisomerized cis-photoazolol-1 reveal how isomerization of the azobenzene moiety induces distinct conformational changes within the orthosteric ligand binding pocket. Within seconds, light-excited photoazolol-1 adopts a new binding pose, altering interactions with extracellular loop 2 and shifting the positions of transmembrane helices 5, 6, and 7. Functional assays of β 2 AR in cellular membranes show that photoazolol-1 acts as an efficacy photoswitch, changing from an inverse agonist to a neutral antagonist upon isomerization without leaving the binding pocket. In combination, these findings suggest a molecular mechanism for activity modulation via efficacy photoswitches and provide a framework for designing ligands that exploit light-driven transitions within the binding pocket to achieve spatiotemporal control of receptor function.

G protein-coupled receptors↗

Structural mechanics of 3-D braided preforms for composites. IV - The 4-step tubular braiding

This paper presents the fundamentals of the 4-step 3D tubular braiding process and the structure of the preforms produced. Based on an idealized structural model, geometric relations between the structural parameters of the preform are analytically established. The effects of machine arrangement and operating conditions are discussed. Yarn retraction, yarn surface angle, outside diameter, and yarn volume fraction of the preform in terms of the pitch length, the inner diameter, and the machine arrangement are theoretically predicted and experimentally verified.

Hammad, M.↗

Parallel algorithms and archtectures for computational structural mechanics

The determination of the fundamental (lowest) natural vibration frequencies and associated mode shapes is a key step used to uncover and correct potential failures or problem areas in most complex structures. However, the computation time taken by finite element codes to evaluate these natural frequencies is significant, often the most computationally intensive part of structural analysis calculations. There is continuing need to reduce this computation time. This study addresses this need by developing methods for parallel computation.

Patrick, Merrell↗