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At least 469 records · Page 26

Structural Evidence of Interanionic Hydrogen Bonding in Phosphoric Acid Solutions

Interanionic hydrogen bonding (IAHB) is a noncovalent interaction between like-charged ions that challenges conventional electrostatic understanding. This study provides direct structural evidence of IAHB in concentrated aqueous phosphoric acid (PA) solutions, which exhibit >60% dissociation under these conditions. Oxygen K-edge X-ray absorption fine structure spectroscopy, combined with electron affinity time-dependent density functional theory calculations, reveals the formation of stable, cyclic phosphate-phosphate IAHB dimers at PA concentrations ≥7 M. Extended X-ray absorption fine structure data show distinct long-range ordering consistent with these dimers, and near-edge X-ray absorption fine structure spectra confirm a concentration-dependent transition from monomeric to dimeric species. Energy decomposition analysis through density functional theory shows that the formation of solution-phase IAHB is energetically favored and is attributed to polarization of and the charge transfer between the two fragments driven by the surrounding solvent molecules, in addition to the permanent electrostatics. These findings offers crucial structural insights into the H-bonded networks in concentrated PA, highlighting the critical role of solvent in facilitating anion–anion association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Process-Parameter-Dependent Optical and Structural Properties of ZrO2MgO Mixed-Composite Films Evaporated from the solid Solution

The process-parameter-dependent optical and structural properties of ZrO2MgO mixed-composite material have been investigated. Optical properties were derived from spectrophotometric measurements. By use of atomic force microscopy, x-ray diffraction analysis, and energy-dispersive x-ray (EDX) analysis, the surface morphology, grain size distributions, crystallographic phases, and process-dependent material composition of films have been investigated. EDX analysis made evident the correlation between the oxygen enrichment in the films prepared at a high level of oxygen pressure and the very low refractive index. Since oxygen pressure can be dynamically varied during a deposition process, coatings constructed of suitable mixed-composite thin films can benefit from continuous modulation of the index of refraction. A step modulation approach is used to develop various multilayer-equivalent thin-film devices.

Sahoo, N. K.↗

Application and Certification of Comparative Vacuum Monitoring Sensors for Structural Health Monitoring of 737 Wing Box Fittings

Multi-site fatigue damage, hidden cracks in hard-to-reach locations, disbonded joints, erosion, impact, and corrosion are among the major flaws encountered in today's extensive fleet of aging aircraft and space vehicles. The use of in-situ sensors for real-time health monitoring of aircraft structures are a viable option to overcome inspection impediments stemming from accessibility limitations, complex geometries, and the location and depth of hidden damage. Reliable, structural health monitoring systems can automatically process data, assess structural condition, and signal the need for human intervention. Prevention of unexpected flaw growth and structural failure can be improved if on-board health monitoring systems are used to continuously assess structural integrity. Such systems are able to detect incipient damage before catastrophic failures occurs. Condition-based maintenance practices could be substituted for the current time-based maintenance approach. Other advantages of on-board distributed sensor systems are that they can eliminate costly, and potentially damaging, disassembly, improve sensitivity by producing optimum placement of sensors and decrease maintenance costs by eliminating more time- consuming manual inspections. This report presents a Sandia Labs-aviation industry effort to move SHM into routine use for aircraft maintenance. This program addressed formal SHM technology validation and certification issues so that the full spectrum of concerns, including design, deployment, performance and certification were appropriately considered. The Airworthiness Assurance NDI Validation Center (AANC) at Sandia Labs, in conjunction with Boeing, Delta Air Lines, Structural Monitoring Systems Ltd., Anodyne Electronics Manufacturing Corp. and the Federal Aviation Administration (FAA) carried out a certification program to formally introduce Comparative Vacuum Monitoring (CVM) as a structural health monitoring solution to a specific aircraft wing box application. Validation tasks were designed to address the SHM equipment, the health monitoring task, the resolution required, the sensor interrogation procedures, the conditions under which the monitoring will occur, the potential inspector population, adoption of CVM into an airline maintenance program and the document revisions necessary to allow for routine use of CVM as an alternate means of performing periodic structural inspects. To carry out the validation process, knowledge of aircraft maintenance practices was coupled with an unbiased, independent evaluation. Sandia Labs designed, implemented, and analyzed the results from a focused and statistically-relevant experimental effort to quantify the reliability of the CVM system applied to the Boeing 737 Wing Box fitting application. All factors that affect SHM sensitivity were included in this program: flaw size, shape, orientation and location relative to the sensors, as well as operational and environmental variables. Statistical methods were applied to performance data to derive Probability of Detection (POD) values for CVM sensors in a manner that agrees with current nondestructive inspection (NDI) validation requirements and also is acceptable to both the aviation industry and regulatory bodies. This report presents the use of several different statistical methods, some of them adapted from NDI performance assessments and some proposed to address the unique nature of damage detection via SHM systems, and discusses how they can converge to produce a confident quantification of SHM performance An important element in developing SHM validation processes is a clear understanding of the regulatory measures needed to adopt SHM solutions along with the knowledge of the structural and maintenance characteristics that may impact the operational performance of an SHM system. This report describes the major elements of an SHM validation approach and differentiates the SHM elements from those found in NDI validation. The activities conducted in this program demonstrated the feasibility of routine SHM usage in general and CVM in particular for the application selected. They also helped establish an optimum OEM-airline-regulator process and determined how to safely adopt SHM solutions. This formal SHM validation will allow aircraft manufacturers and airlines to confidently make informed decisions about the proper utilization of CVM technology. It will also streamline the regulatory actions and formal certification measures needed to assure the safe application of SHM solutions.

42 ENGINEERING↗

Microstructural Evolution and Mechanical Properties of LP-DED NASA HR-1 – A Hydrogen Resistant AM Superalloy for Space Propulsion Applications

The National Aeronautics and Space Administration (NASA) has actively pursued metal additive manufacturing (AM) technologies for spaceflight applications since the late 2000s. AM offers transformative advantages in cost, schedule, part consolidation, and design flexibility. Among the various AM techniques, laser powder directed energy deposition (LP-DED) is particularly well suited for fabricating complex geometries with fine feature resolution. In propulsion systems that utilize high-pressure gaseous hydrogen—such as liquid hydrogen rocket engines—hydrogen environment embrittlement (HEE) presents a serious threat to material performance 1,2 . Mechanical property degradation under these conditions can compromise component reliability, especially under cyclic loading. To address this challenge, NASA developed NASA HR-1 (Hydrogen Resistant-1) as a solution for liquid rocket engine components operating in hydrogen-rich environments, using the LP-DED technique 3-9 . A key component in a liquid rocket engine is the exhaust nozzle, which is typically regeneratively cooled (regen) due to the high heat flux. NASA HR-1 was specifically developed for regen nozzle applications using hydrogen as a propellant, providing resistance to HEE, a critical issue for many materials. The AM version of NASA HR-1 was also formulated to achieve high ultimate tensile strength, along with high yield strength and ductility in this environment 5,6 . Low-cycle fatigue (LCF) is another important consideration in nozzle design, as components are expected to endure multiple starts and missions. Additionally, the LP-DED version of the alloy exhibits improved thermal conductivity compared to its wrought counterpart, which benefits nozzle cooling. Overall, NASA HR-1 offers an excellent balance of high strength, HEE resistance, LCF performance, thermal conductivity, and ductility to meet the demanding requirements of channel-cooled nozzles and other components used with hydrogen and other propellants. The LP-DED–processed NASA HR-1 requires several post-processing heat treatment steps to achieve the material properties desirable for its intended application 6 . These steps include stress relief, homogenization, solution annealing, and aging for precipitation hardening. The stress relief treatment mitigates residual stresses accumulated during the LP-DED process and minimizes the potential for distortion. Homogenization, a common step for AM materials, reduces elemental segregation and promotes recrystallization to develop a more equiaxed grain structure. The subsequent solution annealing treatment heats the part to a solid solution temperature to dissolve the undesirable η-phase that forms during cooling from homogenization, followed by rapid cooling to retain an η-phase–free microstructure. Finally, aging promotes precipitation of the strengthening γ′ phase in the alloy. The integration of compositional design and optimized thermal processing enables high-quality LP-DED NASA HR-1 components with excellent microstructural and mechanical stability. Improved chemical and microstructure homogeneity enhances ductility and fatigue resistance—both critical for safe and reliable operation in high-pressure hydrogen environments. NASA has successfully fabricated and hot-fire tested multiple subscale and full-scale channel wall nozzles using LP-DED NASA HR-1 5,6, 9-14 . These efforts included process refinements to support thin-wall construction and various channel geometries. Throughout development, several key observations emerged. After homogenization, the as-built columnar grain structure transforms into a fully equiaxed microstructure. However, subsequent treatments—such as solution annealing and aging—result in changes that are more difficult to track. The grain structure remains largely unchanged, and the γ′ precipitates, typically 5–10 nm in diameter, are beyond the resolution of scanning electron microscopy (SEM). While transmission electron microscopy (TEM) can resolve these fine precipitates, TEM sample preparation is time-consuming and difficult for LP-DED material. As an alternative, differential scanning calorimetry (DSC) offers a useful, qualitative approach to monitor precipitate evolution throughout different stages of heat treatment. The overall goal is to improve the understanding of how heat treatment affects the microstructure and mechanical performance of LP-DED NASA HR-1. This paper presents heat treatment design considerations, microstructural characterization, mechanical testing – including tensile and LCF testing in both air and hydrogen environments.

Superalloy↗

Advanced reliability methods for structural evaluation

Fast probability integration (FPI) methods, which can yield approximate solutions to such general structural reliability problems as the computation of the probabilities of complicated functions of random variables, are known to require one-tenth the computer time of Monte Carlo methods for a probability level of 0.001; lower probabilities yield even more dramatic differences. A strategy is presented in which a computer routine is run k times with selected perturbed values of the variables to obtain k solutions for a response variable Y. An approximating polynomial is fit to the k 'data' sets, and FPI methods are employed for this explicit form.

Wirsching, P. H.↗

Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra

Identifying molecular structure based on spectroscopic readings is a key task in a variety of chemical and biological applications. Common spectroscopy techniques, such as Infrared (IR) Spectroscopy and Mass Spectrometry (MS), provide detailed information on the structure of molecular compounds but nonetheless require expert-level knowledge to decode. Machine learning has emerged as a potential solution for automating structure prediction from chemical spectra; however, current approaches generally focus on single sensor modalities, neglecting to leverage the complementary information contained within differing spectra. In this paper, we introduce Peak2Patch, a novel approach to fusion-enhanced prediction of functional groups from IR and mass spectra. First, we perform a detailed comparison of backbone networks for encoding both sparse mass spectra and dense IR spectra and demonstrate the superior performance of transformer neural networks over current state-of-the-art convolutional neural networks. Second, we evaluate three broad categories of fusion: early (raw feature), middle (deep feature), and late (decision) fusion, demonstrating the potential of a deep feature fusion-based approach. Lastly, we present Peak2Patch, our attention-based fusion scheme, which leverages cross-attention to mix features between encoded tokens of the two modalities. We validate our approach on a publicly available multimodal spectroscopic data set of 790k simulated molecules, demonstrating a large improvement in functional group prediction over both the previous state-of-the-art and our own strong single-modal baselines.

Jacobson, Philip [Sandia National Laboratories (SN↗

Review of analytical studies on seismic fluid-structure interaction of base-supported cylindrical tanks

Analytical solutions for seismic fluid-structure interaction (FSI) of tanks are used by analysts and engineers for a number of purposes, including preliminary sizing, risk assessment, and verification of numerical models. Analytical solutions for seismic FSI of tanks were first developed in the 1930s and have been extended and/or modified in the following nine decades to accommodate different seismic inputs and boundary conditions. This report reviews published analytical solutions for rigid and flexible, base-supported, cylindrical tanks subjected to unidirectional horizontal motion of a small amplitude. The studies parsed the fluid-structure (FSI) response into an impulsive and a convective component, and addressed frequencies of lateral motions of the tank (i.e., impulsive frequencies), hydrodynamic pressures, frequencies of waves (i.e., convective frequencies), wave heights, and reactions at the base. The solutions were categorized into exact and approximate solutions based on the methodologies used. Herein, FSI responses are calculated and compared for a range of tank dimensions using the analytical solutions from the different studies. The responses presented here are normalized to be unitless, and can be used for tanks with different dimensions and mechanical properties, and subjected to different input motions. A sample steel water tank is analyzed using the normalized solutions for two earthquake ground motions with different frequency contents. Ignoring tank flexibility may significantly underestimate seismic responses of the tank and its contained fluid. The approximate solutions, which have been widely used for decades, may not be sufficiently accurate in the modern era. Calculation errors in the reviewed studies are identified and corrected, and differences are quantified for the sample tank.

42 ENGINEERING↗

Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns

Staphylococcus epidermidis and Staphylococcus aureus are highly problematic bacteria in hospital settings. A major challenge is their ability to form biofilms on abiotic or biotic surfaces. Biofilms are well-organized, multicellular bacterial aggregates that resist antibiotic treatment and often lead to recurrent infections. Bacterial cell wall-anchored (CWA) proteins are important players in biofilm formation and infection. Many have putative stalk-like regions or regions of low complexity near the cell wall-anchoring motif. Recent work demonstrated the strong propensity of the stalk region of S. epidermidis accumulation-associated protein (Aap) to remain highly extended under solution conditions that typically induce compaction. This behavior is consistent with the expected function of a stalk-like region that is covalently attached to the cell wall peptidoglycan and projects the adhesive domains of Aap away from the cell surface. In this study, we evaluate whether the ability to resist compaction is a common theme among stalk regions from various staphylococcal CWA proteins. Circular dichroism spectroscopy was used to examine secondary structure changes as a function of temperature and cosolvents along with sedimentation velocity analytical ultracentrifugation, size-exclusion chromatography, and SAXS to characterize structural characteristics in solution. All stalk regions tested are intrinsically disordered, lacking secondary structure beyond random coil and polyproline type II helix, and they all sample highly extended conformations. Remarkably, the Ser-Asp dipeptide repeat region of SdrC exhibited nearly identical behavior in solution when compared to the Aap Pro/Gly-rich region, despite highly divergent sequence patterns, indicating conservation of function by various distinct staphylococcal CWA protein stalk regions.

59 BASIC BIOLOGICAL SCIENCES↗

Materials constitutive models for nonlinear analysis of thermally cycled structures

Effects of inelastic materials models on computed stress-strain solutions for thermally loaded structures were studied by performing nonlinear (elastoplastic creep) and elastic structural analyses on a prismatic, double edge wedge specimen of IN 100 alloy that was subjected to thermal cycling in fluidized beds. Four incremental plasticity creep models (isotropic, kinematic, combined isotropic kinematic, and combined plus transient creep) were exercised for the problem by using the MARC nonlinear, finite element computer program. Maximum total strain ranges computed from the elastic and nonlinear analyses agreed within 5 percent. Mean cyclic stresses, inelastic strain ranges, and inelastic work were significantly affected by the choice of inelastic constitutive model. The computing time per cycle for the nonlinear analyses was more than five times that required for the elastic analysis.

Kaufman, A.↗

Structure of steady state accretion shocks with several cooling functions: Closed integral-form solution

We present, for the first time, a closed integral-form solution to the accretion shock structures for the case where the cooling is due to optically thin bremsstrahlung emission and a series of power-law cooling functions of density and temperature. Our results can provide useful checks on numerical calculations and simple accurate estimates for valuable parameters such as the shock height. For the case where the cooling rate j = (2/3)Arho(exp 2)(P/rho)(exp 1/2)(1 + epsilon (sub s)(P/P(sub s)(exp alpha)(rho(sub s)/rho)(exp beta)), we find that a substantial amount of the accretion energy is released at the base of the accretion shock in the form of bremsstrahlung radiation. This implies that for a cyclotron-dominated shock (qualitatively given by alpha = 2.0, beta = 3.85, and epsilon(sub s) is much greater than 1), bremsstrahlung cooling still plays a crucial role in determining the shock structure. Our results are shown to be consistent with detailed numerical calculations.

Wu, Kinwah↗

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

Weaver, D. L.↗

Local molecular environment drives speciation and reactivity of ion complexes in concentrated salt solution

The speciation and reactivity of aqueous salt solutions are important for a wide variety of applications. However, application of this information is inhibited by broad disagreement about composition, mechanisms, and structure in concentrated solutions especially. Here, neutron diffraction with isotopic substitution measurements on aqueous zinc chloride solutions are used to calibrate molecular dynamics simulations that include effective electronic polarization. This allows us to probe the origin of speciation and reactivity of zinc chloride-water ion complexes, ZnCl x (H 2 O) y 2-x (x ≤ 4 and y ≤ 6), by comparing the reactivity of species in concentrated (4.5 m) and dilute (0.01 m) conditions. Within the concentrated solution, it is found that the extended solvation environment is dominated by solvent-separated ion complexes whose presence increases the free energy of activation for interconversion of species while simultaneously enhancing their thermodynamic stability. This concentration-dependent reactivity and stability suggests that other reactions, such as the nucleation of solid phases, will also be affected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

User's Guide for GAA_JET_FV (v1): A Jet Noise Prediction Code Based on the Generalized Acoustic Analogy

This document is a user’s guide for the jet noise prediction code GAA_JET_FV, which can be used to make predictions of turbulent mixing noise in high-speed free jets (ie. in the absence of any solid surfaces) of arbitrary cross section. The code requires a Reynolds-averaged Navier-Stokes (RANS) solution for the mean flow and turbulence as input. A script is provided in the code package which can be used to interpolate structured or unstructured RANS solutions onto a structured grid suitable for the noise calculations. Output file formats for two commonly used RANS solvers are currently supported by this script. The document describes how the code can be obtained and installed on a user’s system. A simple test case is provided that can be run with minimal user knowledge of the code details. General instructions for running the interpolation script and the main code are given along with descriptions of the input and output data files and individual code modules. Several additional test cases are provided which allow the user to exercise additional features of the code. This document is Version 1, Revision 0 of the User’s Guide, which contains examples of round and non-axisymmetric unheated jet test cases. Future versions are planned which will include additional functionality for the code and more complex test cases.

Jet Noise↗

The local ordering of polar solvents around crystalline carbon nitride nanosheets in solution

The crystalline graphitic carbon nitride, poly-triazine imide (PTI) is highly unusual among layered materials since it is spontaneously soluble in aprotic, polar solvents including dimethylformamide (DMF). The PTI material consists of layers of carbon nitride intercalated with LiBr. When dissolved, the resulting solutions consist of dissolved, luminescent single to multilayer nanosheets of around 60–125 nm in diameter and Li+ and Br- ions originating from the intercalating salt. To understand this unique solubility, the structure of these solutions has been investigated by high-energy X-ray and neutron diffraction. Although the diffraction patterns are dominated by inter-solvent correlations there are clear differences between the X-ray diffraction data of the PTI solution and the solvent in the 4–6 Å -1 range, with real space differences persisting to at least 10 Å. Structural modelling using both neutron and X-ray datasets as a constraint reveal the formation of distinct, dense solvation shells surrounding the nanoparticles with a layer of Br - close to the PTI-solvent interface. This solvent ordering provides a configuration that is energetically favourable underpinning thermodynamically driven PTI dissolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines

The LINFLUX-AE computer code predicts flutter and forced responses of blades and vanes in turbomachines under subsonic, transonic, and supersonic flow conditions. The code solves the Euler equations of unsteady flow in a blade passage under the assumption that the blades vibrate harmonically at small amplitudes. The steady-state nonlinear Euler equations are solved by a separate program, then equations for unsteady flow components are obtained through linearization around the steady-state solution. A structural-dynamics analysis (see figure) is performed to determine the frequencies and mode shapes of blade vibrations, a preprocessor interpolates mode shapes from the structural-dynamics mesh onto the LINFLUX computational-fluid-dynamics mesh, and an interface code is used to convert the steady-state flow solution to a form required by LINFLUX. Then LINFLUX solves the linearized equations in the frequency domain to calculate the unsteady aerodynamic pressure distribution for a given vibration mode, frequency, and interblade phase angle. A post-processor uses the unsteady pressures to calculate generalized aerodynamic forces, response amplitudes, and eigenvalues (which determine the flutter frequency and damping). In comparison with the TURBO-AE aeroelastic-analysis code, which solves the equations in the time domain, LINFLUX-AE is 6 to 7 times faster.

Trudell, J. J.↗

Inertial dynamics of an interface with interfacial mass flux: Stability and flow fields’ structure, inertial stabilization mechanism, degeneracy of Landau’s solution, effect of energy fluctuations, and chemistry-induced instabilities

This work focuses on the long-standing problem of inertial dynamics of an interface with interfacial mass flux and reports new mechanisms for the interface stabilization and destabilization. The interface is a phase boundary separating fluids of different densities and having interfacial mass flux. To analyze the interface dynamics from a far field, we develop and apply the general matrix method to rigorously solve the boundary value problem involving the governing equations in the fluid bulk and the boundary conditions at the interface and at the outside boundaries of the domain. We find the fundamental solutions for the linearized system of equations and analyze the interplay of interface stability with flow fields’ structure by directly linking rigorous mathematical attributes to physical observables. We find that the interface is stable when the dynamics conserves the fluxes of mass, momentum, and energy; the stabilization is due to an inertial mechanism causing small oscillations of the interface velocity. In the classic Landau’s dynamics, the postulate of perfect constancy of the interface velocity leads to the development of Landau–Darrieus instability. This destabilization is also linked to the imbalance of the perturbed energy at the interface. The classic Landau’s solution is found to have degeneracy; lifting of the degeneracy may lead to singularity and self-similar dynamics. Our results compare well with traditional theories of combustion and propose new experiments to study the dynamics of the interface and the flow fields in combustible systems. We further conduct reactive molecular dynamics simulations to elucidate the complexity of chemical processes, to study the destabilizing effect of energy fluctuations on the interface stability, and to illustrate the chemistry-induced instabilities. In summary, we identify the extreme sensitivity of the interface dynamics to the interfacial boundary conditions, including the formal properties of fundamental solutions and the qualitative and quantitative properties of the flow fields. This provides new opportunities for studies, diagnostics, and control of multiphase flows in a broad range of processes in nature and technology.

42 ENGINEERING↗

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.

59 BASIC BIOLOGICAL SCIENCES↗

A Julia Framework for Graph-Structured Nonlinear Optimization

Graph theory provides a convenient framework for modeling and solving structured optimization problems. Under this framework, the modeler can arrange/assemble the components of an optimization model (variables, constraints, objective functions, and data) within nodes and edges of a graph, and this representation can be used to visualize, manipulate, and solve the problem. In this work, we present a Julia framework for modeling and solving graph-structured nonlinear optimization problems. Our framework integrates the modeling package Plasmo.jl (which facilitates the construction and manipulation of graph models) and the nonlinear optimization solver MadNLP.jl (which provides capabilities for exploiting graph structures to accelerate solution). We illustrate with a simple example how model construction and manipulation can be performed in an intuitive manner using Plasmo.jl and how the model structure can be exploited by MadNLP.jl. We also demonstrate the scalability of the framework by targeting a large-scale, stochastic gas network problem that contains over 1.7 million variables.

Cole, David↗