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At least 1,297 records · Page 72

Three-dimensional structure-guided evolution of a ribosome with tethered subunits

We report RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comprehensive and fair comparison of two neural operators (with practical extensions) based on $\mathrm{FAIR}$ data

Neural operators can learn nonlinear mappings between function spaces and offer a new simulation paradigm for real-time prediction of complex dynamics for realistic diverse applications as well as for system identification in science and engineering. Herein, we investigate the performance of two neural operators, which have shown promising results so far, and we develop new practical extensions that will make them more accurate and robust and importantly more suitable for industrial-complexity applications. The first neural operator, DeepONet, was published in 2019 (Lu et al., 2019), and its original architecture was based on the universal approximation theorem of Chen & Chen (1995). The second one, named Fourier Neural Operator or FNO, was published in 2020, and it is based on parameterizing the integral kernel in the Fourier space. DeepONet is represented by a summation of products of neural networks (NNs), corresponding to the branch NN for the input function and the trunk NN for the output function; both NNs are general architectures, e.g., the branch NN can be replaced with a CNN or a ResNet. According to Kovachki et al. (2021), FNO in its continuous form can be viewed conceptually as a DeepONet with a specific architecture of the branch NN and a trunk NN represented by a trigonometric basis. In order to compare FNO with DeepONet computationally for realistic setups, we develop several extensions of FNO that can deal with complex geometric domains as well as mappings where the input and output function spaces are of different dimensions. We also develop an extended DeepONet with special features that provide inductive bias and accelerate training, and we present a faster implementation of DeepONet with cost comparable to the computational cost of FNO, which is based on the Fast Fourier Transform. Here we consider 16 different benchmarks to demonstrate the relative performance of the two neural operators, including instability wave analysis in hypersonic boundary layers, prediction of the vorticity field of a flapping airfoil, porous media simulations in complex-geometry domains, etc. We follow the guiding principles of FAIR (Findability, Accessibility, Interoperability, and Reusability) for scientific data management and stewardship. The performance of DeepONet and FNO is comparable for relatively simple settings, but for complex geometries the performance of FNO deteriorates greatly. We also compare theoretically the two neural operators and obtain similar error estimates for DeepONet and FNO under the same regularity assumptions.

42 ENGINEERING↗

Automatically adaptive stabilized finite elements and continuation analysis for compaction banding in geomaterials

Under compressive creep, viscoplastic solids experiencing internal mass transfer processes can accommodate singular cnoidal wave solutions as material instabilities at the stationary wave limit. These instabilities appear when the loading rate is significantly faster than the material's capacity to diffusive internal perturbations, leading to localized failure features (e.g., cracks and compaction bands). These cnoidal waves, generally found in fluids, have strong nonlinearities that produce periodic patterns. Due to the singular nature of the solutions, the applicability of the theory is currently limited. Additionally, practical simulation tools require proper regularization to overcome the challenges that singularity induces. We focus on the numerical treatment of the governing equation using a nonlinear approach building on a recent adaptive stabilized finite element method. This automatic refinement method provides an error estimate that drives mesh adaptivity, a crucial feature for the problem at hand. We compare the performance of this adaptive strategy against analytical and standard finite element solutions. We then investigate the sensitivity of the diffusivity ratio, the parameter controlling the process, and identify multiple possible solutions with several stress peaks. We also show the evolution of the spacing between peaks for all solutions as a function of that parameter.

42 ENGINEERING↗

A continuum damage mechanics (CDM) based Wilshire model for creep deformation, damage, and rupture prediction

In this report, a new constitutive model is derived that combines the Wilshire equations with continuum damage mechanics (CDM) to enable the long-term prediction of creep deformation, damage, and rupture. The Wilshire equations have been demonstrated to accurately extrapolate the stress-rupture, minimum-creep-strain-rate, and time-to-strain of various alloys across decade of life. Recently, the time-to-creep-strain equation has been rearranged to predict creep deformation curves; however, the resulting equation is difficult to calibrate and does not track damage. The CDM-based Sinh constitutive model accurately predicts creep deformation, damage, and stress-rupture for a variety of alloys; however, it lacks an explicit description of stress and temperature co-dependence which limits interpolation and extrapolation ability. In this study, the Wilshire and the CDM-based Sinh equations are combined to create the “WCS” model. The WCS model combines the best features of each model while eliminating their deficiencies. Experimental data for alloy P91 is gathered and the WCS model is calibrated to the data. The WCS model accurately predicts the stress rupture, minimum-creep-strain-rate, creep deformation, and damage of alloy P91 across the experimental stress and temperature range as well as consistency in parametric simulations.

36 MATERIALS SCIENCE↗

Coregistered positron emission particle tracking (PEPT) and X-ray computed tomography (CT) for engineering flow measurements

Increasingly, fully 3D experimental measurements of flow in complex engineering geometries are required to validate computational fluid dynamics models that support and inform reactor design and licensing. One barrier to such measurements is the complexity of typical reactor components and subsequent lack of optical access in these systems. To overcome this, the deployment of coregistered positron emission particle tracking (PEPT) and X-ray computed tomography (CT) is explored for flow measurement in reactor thermal hydraulic components and model (scaled) systems. Through this methodology, fully 3D flow information (via PEPT) and detailed internal geometry (via CT) are captured in opaque systems such as pipes, rod bundles, packed beds, etc. The reconstructed flow field and geometry can then be overlain to reveal detailed flow features around internal structures within a given test section. This is enabled through the use of a combined preclinical PET/CT scanner with overlapping PET and CT fields of view. Such measurements are useful for characterizing flow inside such intricate nuclear thermal hydraulic components as core geometries and heat exchangers, among others, and providing valuable 3D validation data for CFD models. In this work, basic tests of this 3D flow/geometry mapping are presented, and the implications of such measurements are discussed. Further, preliminary measurements are made with both point sources and flow in a simple pipe flow geometry to evaluate the capabilities of this technique. PEPT and CT features are coregistered with up to 0.1 mm precision, and pipe flow mean velocity and Reynolds stresses are reconstructed with similar accuracy to previous PEPT demonstrations. The utility of PEPT/CT is shown herein, and suggestions for future measurements are made.

3D flow measurement↗

Directed Self-Assembly of the Organic Semiconductor C8-BTBT-C8 in Anodic Aluminum Oxide Nanopores

Controlling the self-assembly of organic semiconductors at the nanoscale is critical for advancing high-performance electronic and photonic devices, yet it remains challenging due to their intrinsic anisotropic crystallization and sensitivity to processing conditions. Here, in this study, we demonstrate that cylindrical nanoconfinement within anodic aluminum oxide membranes provides a versatile platform to precisely tune the molecular orientation and phase behavior of the prototypical organic semiconductor 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT-C8). Combining temperature-dependent high-resolution synchrotron X-ray scattering with optical birefringence measurements, we uncover that confinement geometries (pore diameters 25–180 nm) and surface chemistry govern the emergence of distinct smectic A textures, featuring molecular layers either parallel or perpendicular to the pore axis. The competition between axial and radial smectic layering is modulated by pore size, surface hydrophilicity, and thermal history, enabling reversible control over domain orientations and transitions between liquid crystalline and crystalline states. Notably, nanoconfinement stabilizes the smectic phase over an expanded temperature range compared to bulk, while inducing complex multidomain configurations owing to geometric constraints and anchoring conditions. Our results elucidate fundamental mechanisms by which anisotropic nanoscale confinement directs the self-organization of highly conjugated organic molecules, with implications for optimizing directional charge transport and anisotropic optical responses in organic–inorganic hybrid nanoarchitectures. This study establishes nanoconfinement as a powerful strategy to engineer morphology and functional properties in organic semiconducting materials with nanoscale precision.

36 MATERIALS SCIENCE↗

A new woven composite constitutive model validated by shock wave experiments

In this paper, we present results of plate impact simulations of shock compressed woven glass fiber-reinforced plastic (GRP) performed using the Arbitrary Lagrangian–Eulerian three-dimensional finite element code. A hyperelastic large-strain-based empirical Continuum Damage Mechanics (CDM) formulation is employed to describe damage initiation and growth in the shock-compressed GRP. The model parameters calibration scheme utilizes the Velocity Interferometer System for Any Reflector normal particle velocity measurements at the free surface of the GRP target plates. The impact velocity in the experiments ranged from 8.5 to 418 m/s. The finite element model considered planar 0°/90° bidirectional plies with an individual ply thickness of 0.68 mm, stacked to reach a total laminate thickness of 6.8 mm. The anisotropic elastic strains were estimated from the experimentally determined tetragonal symmetry stiffness matrix for the GRP. The strain-based damage model captures several salient features observed in the measured free surface particle wave profiles, including the shock rise time, onset of Elastic—Elastic Cracking, and the shape of the nonlinear portion of the experimental particle velocity profiles. Furthermore, the CDM model predicts the dominant damage mode to be matrix microcracking due to shear and the associated bulk expansion (bulking) under the global compressive loading in the plate impact configuration.

42 ENGINEERING↗

Formation of Nano- and Micro-Scale Surface Features Induced by Long-Range Femtosecond Filament Laser Ablation

In this work, we study the characteristics of femtosecond-filament-laser–matter interactions and laser-induced periodic surface structures (LIPSS) at a beam-propagation distance up to 55 m. The quantification of the periodicity of filament-induced self-organized surface structures was accomplished by SEM and AFM measurements combined with the use of discrete two-dimensional fast Fourier transform (2D-FFT) analysis, at different filament propagation distances. The results show that the size of the nano-scale surface features increased with ongoing laser filament processing and, further, periodic ripples started to form in the ablation-spot center after irradiation with five spatially overlapping pulses. The effective number of irradiating filament pulses per spot area affected the developing surface texture, with the period of the low spatial frequency LIPSS reducing notably at a high pulse number. The high regularity of the filament-induced ripples was verified by the demonstration of the angle-of-incidence-dependent diffraction of sunlight. This work underlines the potential of long-range femtosecond filamentation for energy delivery at remote distances, with suppressed diffraction and long depth focus, which can be used in biomimetic laser surface engineering and remote-sensing applications.

36 MATERIALS SCIENCE↗

The Event Detection System in the NEXT-White Detector

This article describes the event detection system of the NEXT-White detector, a 5 kg high pressure xenon TPC with electroluminescent amplification, located in the Laboratorio Subterráneo de Canfranc (LSC), Spain. The detector is based on a plane of photomultipliers (PMTs) for energy measurements and a silicon photomultiplier (SiPM) tracking plane for offline topological event filtering. The event detection system, based on the SRS-ATCA data acquisition system developed in the framework of the CERN RD51 collaboration, has been designed to detect multiple events based on online PMT signal energy measurements and a coincidence-detection algorithm. Implemented on FPGA, the system has been successfully running and evolving during NEXT-White operation. The event detection system brings some relevant and new functionalities in the field. A distributed double event processor has been implemented to detect simultaneously two different types of events thus allowing simultaneous calibration and physics runs. This special feature provides constant monitoring of the detector conditions, being especially relevant to the lifetime and geometrical map computations which are needed to correct high-energy physics events. Other features, like primary scintillation event rejection, or a double buffer associated with the type of event being searched, help reduce the unnecessary data throughput thus minimizing dead time and improving trigger efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-Kernel Adaptive Support Vector Machine for Scalable Predictive Maintenance

Application of data-driven solutions across an industry is challenging, since the data are often stored locally, and increasing privacy and security concerns restrict access to the data. In addition, it is highly unlikely that all potential data patterns are captured in a single data source. Because it is highly unlikely that all potential data patterns are captured in a single data source, machine learning (ML) models developed from a single source cannot be robust enough. An alternative is to train the ML model at each source and develop a distributed knowledge discovery and aggregation approach to build global knowledge. In this paper, we develop and demonstrate a distributed ML model, federated transfer learning (FTL), using a multi-kernel-based adaptive support vector machine (MK-A-SVM). For federated learning (FL), the multi-kernel (MK) approach enables feature-specific model aggregation under data heterogeneity; whereas for transfer learning (TL) the adaptive model enables utilization of an aggregated model from a different task. The proposed approach is validated using nuclear power plant (NPP) vertical motor-driven pump data to predict the health condition of vertical motor-driven pumps as an anomaly detection. The efficiency of the proposed approach is also quantified and compared with neural network.

42 ENGINEERING↗

Structural plasticity enables evolution and innovation of RuBisCO assemblies

Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.

59 BASIC BIOLOGICAL SCIENCES↗

A high fidelity and user-friendly equation-oriented optimization model for carbon capture using a novel water-lean solvent

Research Triangle Institute (RTI) International and SLB have developed a novel water-lean solvent technology for carbon capture, demonstrating low specific reboiler duty (SRD) values at capture rates exceeding 90%. At the Technology Centre Mongstad (TCM) pilot plant, the technology achieved an SRD of 2.55 GJ/t-CO2 at 95% capture, utilizing an intercooler and a 5°C temperature approach in the lean/rich solvent cross exchanger. To meet varying carbon capture targets for Front End Engineering and Design (FEED) studies and to enable real-time optimization and advanced process control, an efficient optimization model is required. This model needs to minimize energy demand for a given capture rate and determine optimal operating parameters in response to fluctuating flue gas conditions. While an existing Aspen Plus simulation model, developed by RTI and SLB, accurately matches TCM plant data, its sequential modular (SM) strategy is too slow for real-time applications due to recycle streams and tight heat integration inherent in solvent-based carbon capture processes. Although an equation-oriented (EO) modeling strategy is more suitable for optimizing these processes, its adoption has been limited by several factors: feature limitations in Aspen Plus EO mode (e.g., lack of balance block support), a less user-friendly interface for variable identification and loop solving, complex troubleshooting of convergence issues, and the necessity for accurate initial values.

carbon capture↗

Soft Matter Thermal and Mechnical Devices

The participant company, Treau, makes homes and buildings more comfortable with quiet, energy efficient, and easy to install heating and cooling systems. They entered the Cyclotron Road program with an idea for a heat exchanger and compressor and a general idea that the building heating and cooling sector was the best first target market. While at Cyclotron Road, they used the Cyclotron Road program staff and Berkeley Lab expertise to better understand the needs of the heating and cooling equipment market. This was critical to understand who the end customer was, and what features were needed in this market. They were then able to conduct product development with this target market/customer in mind. The Cyclotron Road program was also critical in building a manufacturing and scale-up plan that allowed the participant to build a credible growth and fundraising strategy. By the end of the program, the participant had a working prototype testing at Berkeley Lab’s HVAC testing facilities.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Mechanistic Modeling of Creep and Aging for Time Extrapolation in LPBF 316 SS - LANL

A polycrystal constitutive model was extended to quantify the effects heterogeneity in the microstructure, porosity, and internal stresses on the mechanical response (creep, tensile) of 316H steel processed by additive manufacturing. The starting point is a recently developed and fully calibrated advanced microstructuresensitive mechanistic constitutive model fit to literature data pertaining to conventionally processed steels. The model is embedded within the full field fast Fourier transform framework (LApx) and several hundred simulations were performed. Synthetic microstructures with different grain aspect ratios were generated using the Neper package to study the role of grain morphology on the mechanical responses. The effect of initial cell interior dislocation density, cell-wall density, precipitate content, porosity, and internal stresses on creep rates are quantified for different polycrystalline microstructures. The study allowed to prospectively quantify the role of distinct features of the microstructure on the mechanical response under tension and creep loading scenarios. Critically it is found that minor anisotropies in the tensile response of samples, emanating from the aspect ratio of grains correlated into significant differences in creep rate as a function of loading directions. The study also allows to identify initial microstructure porosities below which the materials response only moderately degraded by the initial microstructure.

36 MATERIALS SCIENCE↗

Inverters: A Pivotal Role in PV Generated Electricity

This presentation discusses the pivotal role inverters play in PV generated electricity. Topics include: the inverter as the center of the system--increasingly becoming the brain, with more features and capabilities (hybrid systems, safety, islanding, monitoring, etc.); increasing inverter-based generated electricity associated with many renewable energy sources; increased dependence for grid support and forming capability; communication within the grid and security increasingly required; increasing complexity leads to more chances to fail; as in most PV segments, there is cost reduction pressure, which makes it more challenging to keep the reliability high.

ENGINEERING,SOLAR ENERGY↗

Predicting the proximity to macroscopic failure using local strain populations from dynamic in situ X-ray tomography triaxial compression experiments on rocks

Predicting the proximity of large-scale dynamic failure is a critical concern in the engineering and geophysical sciences. Here we use evolving contractive, dilatational, and shear strain deformation preceding failure in dynamic X-ray tomography experiments to examine which strain components best predict the proximity to failure. We develop machine learning models to predict the proximity to failure using time series of three-dimensional local incremental strain tensor fields acquired in rock deformation experiments under stress conditions of the upper crust. Three-dimensional scans acquired in situ throughout triaxial compression experiments provide a distribution of density contrasts from which we estimate the three-dimensional incremental strain that accumulates between each scan acquisition. Training machine learning models on multiple experiments of six rock types provides suites of feature importance that indicate the predictive power of each feature. Comparing the average importance of groups of features that include information about each strain component quantifies the ability of the contractive, dilatational and shear strain to predict the proximity of macroscopic failure. A total of 24 models of four machine learning algorithms with six rock types indicate that 1) the dilatational strain provides the best predictive power of the strain components, and 2) the intermediate values (25th-75th percentile) of the strain population provide the best predictive power of the statistics of the strain populations. In addition, the success of the predictions of models trained on one rock type and tested on other rock types quantifies the similarities and differences of the precursory strain accumulation process in the six rock types. These similarities suggest the potential existence of a unified theory of brittle rock deformation for a range of rock types.

58 GEOSCIENCES↗

Monitoring and prediction of porosity in laser powder bed fusion using physics-informed meltpool signatures and machine learning

In this work we accomplished the monitoring and prediction of porosity in laser powder bed fusion (LPBF) additive manufacturing process. This objective was realized by extracting physics-informed meltpool signatures from an in-situ dual-wavelength imaging pyrometer, and subsequently, analyzing these signatures via computationally tractable machine learning approaches. Porosity in LPBF occurs despite extensive optimization of processing conditions due to stochastic causes. Hence, it is essential to continually monitor the process with in-situ sensors for detecting and mitigating incipient pore formation. In this work a tall cuboid-shaped part (10 mm × 10 mm × 137 mm, material ATI 718Plus) was built with controlled porosity by varying laser power and scanning speed. This test caused various types of porosity, such as lack-of-fusion and keyhole formation, with varying degrees of severity in the part. The meltpool was continuously monitored using a dual-wavelength imaging pyrometer installed in the machine. Physically intuitive process signatures, such as meltpool length, temperature distribution, and ejecta (spatter) characteristics, were extracted from the meltpool images. Subsequently, relatively simple machine learning models, e.g., K-Nearest Neighbors, were trained to predict both the severity and type of porosity as a function of these physics-informed meltpool signatures. These models resulted in a prediction accuracy exceeding 95% (statistical F1-score). The same analysis was carried out with a complex, black-box deep learning convolutional neural network which directly used the meltpool images instead of physics-informed features. The convolutional neural network produced a comparable F1-score in the range of 89–97%. Finally, these results demonstrate that using pragmatic, physics-informed meltpool signatures within a simple machine learning model is as effective for flaw prediction in LPBF as using a complex and computationally demanding black-box deep learning model.

36 MATERIALS SCIENCE↗

effect of ambient pressure on the behavior of single-component fuels in a gasoline multi-hole injector

The injection characteristics of neat ethanol and pure isooctane are studied under different ambient pressure and temperature conditions. Injection underflash-boiling conditions can enhance liquid atomization and evaporation, providing the possibility of improvement in the fuel/air mixing. These superheated conditions often introduce phenomena that are not taken into account in the standard modeling of sprays for engine applications. The present work proposes a numerical investigation of the behavior of Engine Combustion Network's 8-hole spray-G injector, starting at the subcooled nominal condition and reducing the ambient pressure at constant low temperature to reach the flare flash-boiling condition. To initialize the properties of the injected fuel, the flow in the nozzle is simulated with a Eulerian approach, handling the two phases with a mixture model and the phase change, due to cavitation and flash boiling, with the Homogenous Relaxation Model. A map of the mixture's kinematic and thermal behavior is obtained at the interface between the injector and the chamber to initialize the Lagrangian simulations. A literature-based vaporization model is implemented to obtain the proper description of the characteristic features of a multi-hole spray under super-heated conditions, like plume-plume interaction. The numerical representation of the spray is validated in terms of penetration and radial spreading on DBI images, reproducing the light attenuation profiles caused by the presence of the liquid spray. Simulations show that coupled nozzle flow and spray calculations capture the spray morphology and shape better compared to calculations performed without considering the nozzle flow simulation details, especially under flare flash conditions.

Nocivelli, Lorenzo↗