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At least 109 records · Page 6

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

Here, we outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships - however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.

59 BASIC BIOLOGICAL SCIENCES↗

Strategies for simultaneous strengthening and toughening via nanoscopic intracrystalline defects in a biogenic ceramic

While many organisms synthesize robust skeletal composites consisting of spatially discrete organic and mineral (ceramic) phases, the intrinsic mechanical properties of the mineral phases are poorly understood. Using the shell of the marine bivalve Atrina rigida as a model system, and through a combination of multiscale structural and mechanical characterization in conjunction with theoretical and computational modeling, we uncover the underlying mechanical roles of a ubiquitous structural motif in biogenic calcite, their nanoscopic intracrystalline defects. These nanoscopic defects not only suppress the soft yielding of pure calcite through the classical precipitation strengthening mechanism, but also enhance energy dissipation through controlled nano- and micro-fracture, where the defects’ size, geometry, orientation, and distribution facilitate and guide crack initialization and propagation. These nano- and micro-scale cracks are further confined by larger scale intercrystalline organic interfaces, enabling further improved damage tolerance.

36 MATERIALS SCIENCE↗

Wave interactions with continuous fractal layers

Many natural structures possess self-similar multiscales which can be characterized by power law spectra. Under appropriate conditions, knowledge of the strength of these scale sizes provides information on the physical processes which formed these objects. In this paper, we investigate wave interactions with continuous fractal layers which model geological and variegated structures. Since fractal characteristics of the layers are embedded in the scattered field, they can be retrieved under appropriate conditions. This inversion can be performed in either the frequency or the time domain as desired.

Kim, Y.↗

TPS Certification by Analysis: Model-Driven Characterization of Properties and Failure in Woven Thermal Protection Systems

Woven, ablative thermal protection system (TPS) materials provide a robust option for aggressive (re)entries and thus have been baselined for the upcoming Mars Sample Return (MSR) mission's Earth Entry System (EES). The reliability requirements for MSR-EES necessitate understanding of material property variability, which could be significant given the complex structure and anisotropic nature of properties in TPS weaves, as well as the response to potential impact with micrometeoroids or orbital debris during the EES re-entry. The TPS Certification by Analysis effort within the Entry Systems Modeling project seeks to provide computational models and analyses that support the certification against such material-based risks. For the present talk, focus will be given to the characterization of baseline woven TPS material properties and mechanical failure limits, which entails (1) use of computational techniques (e.g., machine learning) to interpret computed tomography images of the weave to generate representative structural models and (2) application of multiscale material modeling approaches to characterize thermomechanical and failure properties.

thermal protection systems↗

TPS Certification by Analysis: Model-Driven Characterization of Properties and Failure in Woven Thermal Protection Systems

Woven, ablative thermal protection system (TPS) materials provide a robust option for aggressive (re)entries and thus have been baselined for the upcoming Mars Sample Return (MSR) mission’s Earth Entry System (EES). The reliability requirements for MSR-EES necessitate understanding of material property variability, which could be significant given the complex structure and anisotropic nature of properties in TPS weaves, as well as the response to potential impact with micrometeoroids or orbital debris during the EES re-entry. The TPS Certification by Analysis effort within the Entry Systems Modeling project seeks to provide computational models and analyses that support the certification against such material-based risks. For the present talk, focus will be given to the characterization of baseline woven TPS material properties and mechanical failure limits, which entails (1) use of computational techniques (e.g., machine learning) to interpret computed tomography images of the weave to generate representative structural models and (2) application of multiscale material modeling approaches to characterize thermomechanical and failure properties.

Justin B. Haskins↗

Permeation of CO 2 and N 2 through glassy poly(dimethyl phenylene) oxide under steady- and presteady-state conditions

Glassy polymers are often used for gas separations because of their high selectivity. Although the dual-mode permeation model correctly fits their sorption and permeation isotherms, its physical interpretation is disputed, and it does not describe permeation far from steady state, a condition expected when separations involve intermittent renewable energy sources. To develop a more comprehensive permeation model, we combine experiment, molecular dynamics, and multiscale reaction–diffusion modeling to characterize the time-dependent permeation of N 2 and CO 2 through a glassy poly(dimethyl phenylene oxide) membrane, a model system. Simulations of experimental time-dependent permeation data for both gases in the presteady-state and steady-state regimes show that both single- and dual-mode reaction–diffusion models reproduce the experimental observations, and that sorbed gas concentrations lag the external pressure rise. The results point to environment-sensitive diffusion coefficients as a vital characteristic of transport in glassy polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comprehensive characterization of irradiation induced defects in ceria: Impact of point defects on vibrational and optical properties

Validation of multiscale microstructure evolution models can be improved when standard microstructure characterization tools are coupled with methods sensitive to individual point defects. We demonstrate how electronic and vibrational properties of defects revealed by optical absorption and Raman spectroscopies can be used to compliment transmission electron microscopy (TEM) and x-ray diffraction (XRD) in the characterization of microstructure evolution in ceria under non-equilibrium conditions. Experimental manifestation of non-equilibrium conditions was realized by exposing cerium dioxide (CeO2) to energetic protons at elevated temperature. Two sintered polycrystalline CeO2 samples were bombarded with protons accelerated to a few MeVs. These irradiation conditions produced a microstructure with resolvable extended defects and a significant concentration of point defects. A rate theory (RT) model was parametrized using the results of TEM, XRD, and thermal conductivity measurements to infer point defect concentrations. An abundance of cerium sublattice defects suggested by the RT model is supported by Raman spectroscopy measurements, which show peak shift and broadening of the intrinsic T2g peak and emergence of new defect peaks. Additionally, spectroscopic ellipsometry measurements performed in lieu of optical absorption reveals the presence of Ce3+ ions associated with oxygen vacancies. This work lays the foundation for a coupled approach that considers a multimodal characterization of microstructures to guide and validate complex defect evolution models.

Chauhan, Vinay S.↗

Tuning Surface Adhesion Using Grayscale Electron-beam Lithography

Surface texturing of manufactured products tailors their properties, such as friction, adhesion, biocompatibility, or fluid interactions. However, advancements in this area are largely the result of trial-and-effort testing and generally lack a science-guided framework for determining the surface topography that will optimize performance. The present investigation explores grayscale electron-beam lithography as a means to create multiscale surface patterns to control surface performance. Here, we created and characterized a set of surface textures on a silicon wafer; the textures were superpositions of sine waves of varying wavelengths and amplitudes. First, the multiscale topography of the patterned surface was characterized, using profilometry and atomic force microscopy, to understand its fidelity to the designed-in pattern. The results of this analysis demonstrated how grayscale lithography accurately controlled the lateral size of features but was less precise on the vertical height of the surface, and also introduced inherent roughness below the scale of patterning. Second, a micromechanical tester was used to characterize the adhesion of the surfaces with large-scale polished silicon spheres. The results showed that adhesion could be tailored, with significant contribution from all of the designed-in length scales of topography. The strength of adhesion did not correlate with conventional roughness parameters but could be accurately modeled using simple numerical integration. Taken together, this investigation demonstrates the promise and challenges of grayscale e-beam lithography with multiscale patterns as a method for the tailoring of surface performance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improving the particle dry deposition scheme in the CMAQ photochemical modeling system

Dry deposition of atmospheric aerosols in large-scale models is a critical, but highly uncertain, sink process with a strong dependence on particle size, meteorological conditions, and land surface properties. This study investigates the particle dry deposition scheme implemented in the standard Community Multiscale Air Quality (CMAQ) model v5.2.1, characterizes its underlying parameterized components with comparison to a similar scheme in a contemporary regional-scale model, and proposes two updated schemes that are then evaluated with available ambient particle deposition velocity (V d ) measurements. Both updated schemes reduce the surprisingly strong dependence of deposition velocity on the aerosol mode width, with one scheme further introducing a dependence on vegetation coverage that is broadly consistent with variability in observations between vegetated and non-vegetated surfaces. Compared to the base scheme, the updated scheme with vegetation dependence increases V d for submicron particles and decreases it for larger particles by an average of 37% and –66%, respectively. This scheme performs statistically better than the base scheme, reducing fractional biases by 56%–97% for vegetated land-use types and has roughly equivalent performance over water. The base and updated schemes are tested with three annual CMAQ (v5.2.1) simulations for the year 2011; predicted ambient aerosol concentrations are evaluated with routine monitoring network observations and predicted dry deposition fluxes are evaluated with data from the Clean Air Status and Trends Network (CASTNET). The updated scheme with vegetation dependence reduces negative fractional biases for PM 10 by 41% and positive fractional biases for PM 2.5 organic carbon by 15%. This scheme has been incorporated into the most recent publicly accessible versions of CMAQ (v5.3 and beyond) to replace the scheme used in previous versions of CMAQ (v4.5 through v5.2.1).

54 ENVIRONMENTAL SCIENCES↗

Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system

The soft corals (Cnidaria, Octocorallia), a diverse group of colonial marine invertebrates, can reversibly tune their body stiffness in response to external stimuli. This capability is attributed to their dynamic skeletal systems, which consist of thousands of mineralized skeletal elements, called sclerites, embedded within a gel-like matrix that swells/deswells and unjams/jams the sclerites, thus modulating skeletal stiffness. While sclerite morphology is widely used for species identification, its role in the mechanical performance of a soft coral’s skeletal system is largely unknown. Here, we investigated structure-jamming relationships in sclerite-based skeletal architectures using the red gorgonian octocoral Leptogorgia chilensis as a model system. The sclerites of L. chilensis exhibit a shaft-like geometry with two axial branches and two sets of triradiate side branches, which are aligned with the crystallographic symmetry of the constituent magnesium-containing calcite. By combining multiscale three-dimensional (3D) structural characterization, parametric geometrical modeling, 3D printing, mechanical testing, and discrete element simulations, we demonstrate how sclerite geometry achieves a balanced jamming performance in terms of stiffness, weight, strength, and fracture resistance in comparison to alternative geometries parametrically modified from the native sclerites (e.g., changes in the length and number of side branches). Here, we also found that these performance metrics are achieved through the effective interlocking among side and axial branches, which is further enhanced by the fractal-like microscopic spikes on the branch tips. The findings in this natural jamming system offer insights for designing synthetic mechanotunable material architectures for a wide range of applications, from soft robotics to mechanical dampeners.

36 MATERIALS SCIENCE↗

Computed Tomography Scans of Naturally Mineralized Fractures in Upper Wolfcamp Shale

Computed tomography scans of fractures in small samples of Wolfcamp Shale from the Permian Basin and a depth of approximately 10,400 feet that have been cemented through natural processes. These samples were CT scanned at NETL. The data sets compliment the manuscript by Hajirezaie et al entitled "Mineral characterization of a sealed fracture: A multiscale multimodal imaging study of a syntaxial vein"

Computed Tomography↗

Recognition and characterization of hierarchical interstellar structure. I - Correlation function

The problem of the quantitative description of multiscale structure in interstellar cloud complexes and gravitational collapse calculations is considered, emphasizing the recognition and characterization of hierarchical fragmentation structure. The response of the two-point correlation function to a variety of analytical models for density structure is discussed for simple clustering of pointlike clouds to more complex models involving clouds with a distribution of sizes and densities and hierarchical substructure. By expressing the density distribution as the superposition of individual clouds, it is shown that the correlation function generates two types of terms: those involving each cloud's density convolved with itself and those involving pairs of different clouds. Major distortion of the correlation function are introduced by the presence of any image features with size scales a significant fraction of the image size.

Houlahan, Padraig↗

Quantification of the Impact of Acidified Brine on Fracture-Matrix Transport in a Naturally Fractured Shale Using in Situ Imaging and Modeling

Understanding flow, transport, chemical reactions, and hydromechanical processes in fractured geologic materials is key for optimizing a range of subsurface processes including carbon dioxide and hydrogen storage, unconventional energy resource extraction, and geothermal energy recovery. Flow and transport processes in naturally fractured shale rocks have been challenging to characterize due to experimental complexity and the multiscale nature of quantifying continuum scale descriptions of mass exchange between micrometer-scale fractures and nanometer-scale pores. In this study, we use positron emission tomography (PET) to image the transport of a conservative tracer in a naturally fractured Wolfcamp shale core before and after the core was exposed to low pH brine conditions. Image-based experimental observations are interpreted by fitting an analytical transport model to fracture-containing voxels in the core. Results of this analysis indicate subtle increases in matrix diffusivity and a slightly more uniform fracture velocity distribution following exposure to low pH conditions. These observations are compared with a multicomponent one-dimensional reactive transport model that indicates the capacity for a 10% increase in porosity at the fracture-matrix interface as a result of the low pH brine exposure. This porosity change is the result of the dissolution of carbonate minerals in the shale matrix to low pH conditions. Further, this image-based workflow represents a new approach for quantifying spatially resolved fracture-matrix transport processes and provides a foundation for future work to better understand the role of coupled transport, reaction, and mechanical processes in naturally fractured rocks.

58 GEOSCIENCES↗

Summary of Methodology for Mitigating Risks Associated with Licensing and Qualifying AM Nuclear Materials

The US Department of Energy’s Advanced Materials and Manufacturing Technologies (AMMT) program focuses on accelerating the development, qualification, demonstration, and deployment of advanced materials and manufacturing technologies to enable reliable and economical nuclear energy. Laser powder bed fusion (LPBF) is one of the most popular additive manufacturing (AM) processes for fabricating components with intrinsically complex geometries. LPBF was extensively explored for nuclear applications under the previous Transformational Challenge Reactor program. Additionally, Oak Ridge National Laboratory developed and licensed the Peregrine software and larger digital platform that couples machine learning and in situ data collection during AM to detect anomalies and any evolved defects. The digital platform will be critical to (1) the qualification of AM components for nuclear applications that link location-specific data to macroscopic properties and (2) predict final component performance. Current in situ process monitoring tools are valuable for observing the formation of stochastic flaws, but additional data are needed to predict the resulting microstructures and associated material performance. Rapid cooling rates and large thermal gradients have caused large heterogeneities in the microstructure, which cause anisotropy in mechanical performance. The AMMT program is evaluating the best approaches for addressing these heterogeneities and their effect on component performance using a combination of multiscale modeling, enhanced in situ process monitoring, and high throughput experimental testing. This report summarizes strategies for mitigating the risks associated with qualifying AM components, including developing new sensing capabilities for in situ process monitoring and characterizing melt pool solidification and residual stresses to inform multiscale modeling efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Complete Development of Critical Capabilities for TRISO Fission Product Source Term Calculations and Quantify Mechanisms for Pd Penetration of SiC

Overall fission product (FP) release will be an important consideration for the licensing and deployment of advanced reactors utilizing tristructural isotropic (TRISO) fuels. This work focuses on enhancing and applying the BISON models needed to predict FP transport within TRISO particles and particle failure probability, both of which factor directly into release predictions. Specifically, this report details (1) the development of the models needed to predict palladium (Pd) conservation at the engineering scale and the application of those models to characterize Pd fluxes for input into a mechanistic multiscale model for Pd penetration; (2) the refinement of sorption mass transfer models and the development of models for trapping in porous layers, which were applied and compared to particle scans from AGR-2 to provide proof of concept for a method of particle-scale validation that may reduce uncertainties compared to compact-scale validation using data from integral effects tests; (3) the development of a failure-statistics-informed, mesh-independent methodology for applying smeared cracking, enabling further study of the localized multiphysics behaviors associated with cascading particle failure mechanisms; and (4) the preliminary characterization of those coupled multiphysics particle failure behaviors using smeared, nonretentive diffusivities to provide a baseline for future study and to guide ongoing engineering applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The Effect of Fiber Strength Stochastics and Local Fiber Volume Fraction on Multiscale Progressive Failure of Composites

Continuous fiber unidirectional polymer matrix composites (PMCs) can exhibit significant local variations in fiber volume fraction as a result of processing conditions that can lead to further local differences in material properties and failure behavior. In this work, the coupled effects of both local variations in fiber volume fraction and the empirically-based statistical distribution of fiber strengths on the predicted longitudinal modulus and local tensile strength of a unidirectional AS4 carbon fiber/ Hercules 3502 epoxy composite were investigated using the special purpose NASA Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC); local effective composite properties were obtained by homogenizing the material behavior over repeating units cells (RUCs). The predicted effective longitudinal modulus was relatively insensitive to small (~8%) variations in local fiber volume fraction. The composite tensile strength, however, was highly dependent on the local distribution in fiber strengths. The RUC-averaged constitutive response can be used to characterize lower length scale material behavior within a multiscale analysis framework that couples the NASA code FEAMAC and the ABAQUS finite element solver. Such an approach can be effectively used to analyze the progressive failure of PMC structures whose failure initiates at the RUC level. Consideration of the effect of local variations in constituent properties and morphologies on progressive failure of PMCs is a central aspect of the application of Integrated Computational Materials Engineering (ICME) principles for composite materials.

multiscale analysis↗

Stochastic nonlinear analysis of unidirectional fiber composites using image-based microstructural uncertainty quantification

Here, we present a data-driven nonlinear uncertainty quantification and propagation framework to study the microstructure-induced stochastic performance of unidirectional (UD) carbon fiber reinforced polymer (CFRP) composites. The proposed approach integrates (1) microscopic image characterization, (2) stochastic microstructure reconstruction, and (3) efficient multiscale finite element simulations enabled by self-consistent clustering (SCA) analysis. To model the complex microstructural variability, the proposed UQ methods take the non-Gaussian uncertainty sources into account through a distribution-free sampling approach leveraging nonparametric and asymptotic statistical tools. A hierarchical conditional sampling strategy enables the simultaneous sampling of multiple sources of uncertainties. Our approach provides insights into the impact of microstructural variabilities, which are shown to have an increasing impact on the nonlinear responses of UD CFRP parts under progressive compression loading and ultimately on the failure rate over time. We discover that before CFRP parts start to fail, a characteristic time period emerges with distinctive uncertainty distributions specific to the microstructure variability and the probability of failure. Identifying the failure time period is crucial to the reliability prediction, which is an essential component of CFRP design.

36 MATERIALS SCIENCE↗

Ionic-content-driven restructuring of spirobisindane ionene networks: implications for mechanics, self-healing, and gas transport

Polymers of intrinsic microporosity (PIMs) offer exceptional gas permeability but remain brittle and susceptible to physical aging, limiting their durability in separation applications. Here, we introduce a reconfigurable microporous polymer network that uniquely integrates permanent PIM microporosity with autonomous, intrinsic self-healing driven by imidazolium-based ionic motifs. Spirobisindane units generate the intrinsic free-volume architecture, while an imidazolium-containing polyamide ionene supplies dynamic ionic and hydrogen-bonding interactions that reorganize under mild activation. Incorporation of imidazolium-based ionic liquids further tunes cohesion, mobility, and densification, enabling the network to relax, re-associate, and retain microporosity without structural collapse. Through a comprehensive multiscale approach combining spectroscopy, scattering, thermal and mechanical characterization with all-atom molecular dynamics and density functional theory calculations, we elucidate how ionic content, as a single control parameter that reshapes free-volume distributions, modulates local coordination environments, and governs relaxation and healing kinetics. At intermediate ionic loadings, the networks achieve rapid, repeatable self-healing while maintaining CO$_2$ selectivity, demonstrating an optimal balance between segmental mobility and structural integrity. By establishing how hierarchical ionic interactions couple structure, dynamics, and transport in microporous ionene networks, this work provides generalizable design rules for adaptive soft-matter systems that require simultaneous mechanical resilience, reconfigurability, and selective gas transport.

36 MATERIALS SCIENCE↗