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At least 343 records · Page 19

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling human comprehension of data visualizations

This project was inspired by two needs. The first is a need for tools to help scientists and engineers to design effective data visualizations for communicating information, whether to the user of a system, an analyst who must make decisions based on complex data, or in the context of a technical report or publication. Most scientists and engineers are not trained in visualization design, and they could benefit from simple metrics to assess how well their visualization's design conveys the intended message. In other words, will the most important information draw the viewer's attention? The second is the need for cognition-based metrics for evaluating new types of visualizations created by researchers in the information visualization and visual analytics communities. Evaluating visualizations is difficult even for experts. However, all visualization methods and techniques are intended to exploit the properties of the human visual system to convey information efficiently to a viewer. Thus, developing evaluation methods that are rooted in the scientific knowledge of the human visual system could be a useful approach. In this project, we conducted fundamental research on how humans make sense of abstract data visualizations, and how this process is influenced by their goals and prior experience. We then used that research to develop a new model, the Data Visualization Saliency Model, that can make accurate predictions about which features in an abstract visualization will draw a viewer's attention. The model is an evaluation tool that can address both of the needs described above, supporting both visualization research and Sandia mission needs.

97 MATHEMATICS AND COMPUTING↗

Electronic Medical Record Integration for Streamlined DXA Reporting

Dual-energy X-ray absorptiometry (DXA) is the most frequently performed examination to assess bone mineral density in clinical practice. Aside from images and graphical displays, many numerical values are part of DXA reports. These values are typically manually entered into the formal report through the electronic medical record or PACS workstation. The process takes time and is prone to errors. Exporting the DXA numerical data via HL7 engine to the electronic medical record was proposed to improve reporting efficiency and accuracy. The output from the DXA unit computer was reconfigured to export the report content via the HL7 interface engine into the electronic medical record. Radiology interpretive reporting was subsequently done directly in the electronic medical record. In the evaluation of errors, 100 preliminary DXA reports before the change and 100 after the change were examined. These reports were analyzed for errors that included decimal change, number transposition, negative number issue, other incorrect number error, and failure to include prior exam for comparison. In addition, report turnaround times were evaluated before and after the changes were made. Reporting time evaluations included 1-year volume prior to change (3915 reports) and 1 month post-change (206 reports). Of 100 DEXA exams before the change, 15 final reports contained 25 numerical errors. After the change, no numerical errors in the reports were identified. Exam end to final report time decreased from 2159 to 625 min on average. Automating data transmittal from the DXA modality for report generation improves accuracy and turnaround time. This approach did not require any third party software, and healthcare information security concerns were negated since we are using our standard workstations. Secondary to the affordability and applicability to the large percentage of the population using electronic medical record systems, this type of automated workflow is recommended.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Penetrating power in radiography of high-Z materials as a function of bremsstrahlung spectrum endpoint energy

A modified radiographer’s equation is derived and fitted to simulation data so as to describe the increase in radiographic signal that comes with increasing bremsstrahlung spectrum endpoint energy. The dose contained in the incident spectrum follows an E28 power law, as often cited. However, the direct flux penetrating through a heavy, high-Z material, obeys a weaker scaling due to hardening of the radiation. The resultant expression depends on the thickness of the scene being radiographed, the composition of high-Z materials in the scene, and any filtering by other low-Z materials, such as Al or Be. The expression exhibits two asymptotic limits: a ‘thick’ limit at which radiation is extremely hardened and only a weak benefit to increasing endpoint energy is observed (also the most attenuating limit and therefore of dubious physical significance), and a ‘thin’ limit at which a minimum of high-Z material is present and the penetrating dose exhibits the 2.8 power scaling inherent in the incident spectrum. Behavior for intermediate thicknesses of W and Al are obtained by modeling incident and attenuated dose using the DOSECALC code and the Bayes’ Inference Engine (BIE). These data guide the optimization of MeV radiography over a wide range of energies where pair production plays a significant role in photon scattering.

36 MATERIALS SCIENCE↗

Innovative Hot Lab Concept for Advanced D and D Application - 19175

Hot Labs are used in the nuclear industry for various purposes: maintenance of nuclear reactor, sampling and testing of fuel, inspection activities and decommissioning. Despite their vast use, their current designs and operations do not meet entirely today's needs and requirements of the operations nor tomorrow's. This paper will give an overview of the research and investigations performed around Hot Cells design and concept in order to integrate new operability modes and functions. The overall idea is to bring modularity, flexibility and adaptability to the Hot Lab nuclear industry. Taking the key principles of Model Based System Engineering, an interoperable data model, the most advanced digital technologies (Building Information Modelling - BIM, Virtual Reality / Augmented Reality, Artificial Intelligence), and looking at all the life-cycle of such a facility, a concept design of a new type of Hot Lab has been developed. Four mains aspects are implemented during this study: Implement the principles of the Industry 4.0; use modular and flexible solutions; explore the concept of in service maintenance and predictive maintenance; optimise the decommissioning and dismantling process by taking into account the entire life-cycle of the facility. The design was developed as a case study taking several assumptions to adapt to any project. The design developed demonstrates that modularity and flexibility can be brought in without compromising the core safety functions of such a facility. This Hot Lab concept brings the current Hot Lab to the next level as the design has been adapted to meet the current operational needs, implement novel ideas and consider its entire life-cycle. This paper will demonstrate how decommissioning and dismantling operations can become more efficient and safer with such a concept. In addition, the Model Based System Engineering approach used from the beginning of the design phase allows to have an optimum architecture during its entire lifetime. It also allowed to flag new topics to be further developed for the benefit of the nuclear industry as a whole. A first example would be the development of the Control System using digital tools and artificial intelligence to run remotely controlled equipment inside the Hot Lab. Assystem is an international engineering group. As a key participant in the nuclear industry for over 50 years, the Group supports its clients in managing their capital expenditure throughout their asset life-cycles. Assystem can offer support in project management, design, digital engineering, industrial control systems, security and safety and industrial digitalisation. Assystem's Imagine program is an internal program intending to serve as an incubator for the development of innovations. The Innovative Hot Lab project integrates one of the four innovation projects Assystem choose to develop and invest in. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The Novel Charfuel® Coal Refining Process 18 TPD Pilot Plant Project for Co- Producing an Upgraded Coal Product, and Commercially Valuable Co- Products: Area of Interest #3 – Coal Beneficiation Pilot Plant Testing (Final Report)

Operation of Carbon Fuels, LLC’s (“CF”) existing, permitted 18 TPD pilot plant located in Golden, Colorado using two individually ranked (ASTM D 388) coal types (two campaigns), employing the novel Charfuel® coal refining process to produce an upgraded coal product and a number of high-valued organic and inorganic coproducts (for which there presently exists large commercial markets) in order to produce engineering and product data which will then be utilized toward the design of a commercial scale integrated facility (pre-feed document). Carbon Fuels, LLC has developed the Charfuel® Coal Refining Process which refines domestically abundant, raw coal (in the same manner as crude oil is refined) to produce the identical, high value co-products that are refined from crude oil. Thus, gasoline, jet fuel, “green diesel”, fuel oil, and marine fuels, as well as petrochemicals such as benzene, toluene, xylene, and methanol are refined from raw coal using this process. The Charfuel® Coal Refining Process is not a coal conversion process, like pyrolysis, or indirect liquefaction. Nor is it an alternative energy system. Rather it is a coal refining process that has the ability to economically produce products traditionally associated with the refining of crude oil but using only abundant, raw coal as the refinery feed stock. The Charfuel® Coal Refining Process is more economical than crude oil refining and is environmentally benign. Therefore, this value added process yields a return on investment well above 50% for a commercial facility. Furthermore, the Charfuel® process, unlike alternatives such as ethanol and hydrogen, can utilize the existing transportation, delivery, and other petroleum based systems. Hence, there is no need for new engines, pipelines, tankers, or product acceptance. As a result, the profitability of the process is increased. Objectives: (1) Operation of the integrated 18 tpd pilot plant, using two coal types (ranks); (2) Demonstration of process flexibility in being able to produce different products (gas, liquid, and char), as well as determination of operating parameters for identifying scale up criteria for two coal types (ranks); (3) Generation of engineering and design information (process specifications) for use in designing a commercial scale plant (scale-up); (4) Determination of important environmental issues surrounding the process and the products such as fate of trace elements (mercury and other heavy metals) and distributions of SO2, NOx, and CO 2 by analysis of effluent streams; (5) Production of sufficient product to allow reliable commercial economic evaluation of both the refined coal product and the coproducts; and, (6) Assessment of longer-term reliability of unit operations. Period 1: reconfiguration of the 18 TPD plant to meet specific FOA requirements and to qualify the facility for operation; and, Period 2: operation of the 18 TPD plant for two campaigns using two coals types (ranks) which are widely commercially used and abundant - the first being a subbituminous (Powder River Basin (“PRB”)) coal, and the second a bituminous (Illinois #6) coal.

01 COAL, LIGNITE, AND PEAT↗

Reliable extrapolation of deep neural operators informed by physics or sparse observations

Deep neural operators can learn nonlinear mappings between infinite-dimensional function spaces via deep neural networks. As promising surrogate solvers of partial differential equations (PDEs) for real-time prediction, deep neural operators such as deep operator networks (DeepONets) provide a new simulation paradigm in science and engineering. Pure data-driven neural operators and deep learning models, in general, are usually limited to interpolation scenarios, where new predictions utilize inputs within the support of the training set. However, in the inference stage of real-world applications, the input may lie outside the support, i.e., extrapolation is required, which may result to large errors and unavoidable failure of deep learning models. Here, we address this challenge of extrapolation for deep neural operators. First, we systematically investigate the extrapolation behavior of DeepONets by quantifying the extrapolation complexity, via the 2-Wasserstein distance between two function spaces and propose a new strategy of bias–variance trade-off for extrapolation with respect to model capacity. Subsequently, we develop a complete workflow, including extrapolation determination, and we propose five reliable learning methods that guarantee a safe prediction under extrapolation by requiring additional information—the governing PDEs of the system or sparse new observations. The proposed methods are based on either fine-tuning a pre-trained DeepONet or multifidelity learning. We demonstrate the effectiveness of the proposed framework for various types of parametric PDEs. Furthermore, our systematic comparisons provide practical guidelines for selecting a proper extrapolation method depending on the available information, desired accuracy, and required inference speed.

42 ENGINEERING↗

Evaluating the Applicability of Data on Total Solar-Radiation Intensity Derived from Various Sources of Actinometric Information

In designing generating solar-engineering devices, the first priority is the predesign study of the potential of local resources of solar energy at the places where they may be located. Currently, actinometric information is obtained in several ways. They include direct measurement of solar-radiation characteristics at meteorological stations or from satellites and analytical methods for calculating intensity of solar radiation. Despite the significant number of sources of actinometric information, it seems impossible to evaluate the potential of incoming solar energy in the region, to substantiate the composition and parameters of solar-power-plant equipment, and to predict its operation at the initial stage. Using the example of the town of Kamyshin in Volgograd oblast, the sufficiency of required actinometric information is analyzed for further solar-engineering calculations and the data accuracy and limits of their applicability are estimated.

14 SOLAR ENERGY↗

Data management and processing workflow for the Materials Physics and Engineering group beamlines at the Advanced Photon Source

The ability to store, organize, process and distribute experimental data effectively, efficiently and securely is particularly important for large user facilities like the Advanced Photon Source. In this article, the deployment of the APS Data Management System (DM) at the 1-ID and 6-BM beamlines of the APS is described. These two beamlines support a wide range of experimental techniques and generate data at relatively high rates, making them ideal candidates to illustrate the deployment and customization of the DM system and its tools. Using several usage examples at these beamlines, various capabilities of the DM system are described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Development and evaluation of a skeletal mechanism for EHN additized gasoline mixtures in large Eddy simulations of HCCI combustion

Advanced Low Temperature Combustion modes, such as the Sandia proposed Additive-Mixing Fuel Injection (AMFI), can unlock significant potential to boost fuel conversion efficiency and ultimately improve the energy conversion of internal combustion engines. This is a novel improved combustion process that is enabled by supplying small (<5%) variable amounts of autoignition improver to the fuel to enhance the engine operation and control. Common, diesel-fuel ignition-quality enhancing additive, 2-ethylexyl nitrate (EHN), is doped into gasoline to enable Sandia LTGC + AMFI combustion. This manuscript focuses on the development of a reduced sub-mechanism for EHN chemical kinetics at engine relevant conditions that is implemented into a skeletal mechanism for chemical kinetic studies of gasoline surrogate fuels. The mechanism validation utilized zero-dimensional numerical simulations and comparison to shock tube ignition-delay data of pure and EHN-doped n-heptane. Additional validation is presented with Homogeneous Charge Compression-Ignition (HCCI) engine data of pure and EHN-doped research-grade E10 gasoline. Then, the mechanism was deployed in a 3-D computational fluid dynamics (CFD) using Large Eddy Simulations (LES) to model the HCCI engine experiments of 0.4% vol EHN additized E10 gasoline at several equivalence ratios. Simulations showed a very good performance of the mechanism, and the model accurately reproduced (a) the ignition point, (b) combustion phasing, (c) combustion duration, and (d) the peak of the heat release rates of the engine experiments. The results show that EHN promotes Low-Temperature Heat Release, ultimately driving the gasoline to autoignite at thermodynamic conditions where the fuel would not otherwise ignite. Overall, this work demonstrates a viable reduced chemical-kinetic mechanism for EHN and shows that it can be combined with a skeletal gasoline mechanism for CFD-LES analysis of well-mixed LTGC that matches well with experimental results. The CFD-LES analysis also shows the spatial distribution of EHN-fuel interactions that control the autoignition throughout the combustion chamber.

Guleria, Gaurav↗

Machine-learning error models for approximate solutions to parameterized systems of nonlinear equations

Here, this work proposes a machine-learning framework for constructing statistical models of errors incurred by approximate solutions to parameterized systems of nonlinear equations. These approximate solutions may arise from early termination of an iterative method, a lower-fidelity model, or a projection-based reduced-order model, for example. The proposed statistical model comprises the sum of a deterministic regression-function model and a stochastic noise model. The method constructs the regression-function model by applying regression techniques from machine learning (e.g., support vector regression, artificial neural networks) to map features (i.e., error indicators such as sampled elements of the residual) to a prediction of the approximate-solution error. The method constructs the noise model as a mean-zero Gaussian random variable whose variance is computed as the sample variance of the approximate-solution error on a test set; this variance can be interpreted as the epistemic uncertainty introduced by the approximate solution. This work considers a wide range of feature-engineering methods, data-set-construction techniques, and regression techniques that aim to ensure that (1) the features are cheaply computable, (2) the noise model exhibits low variance (i.e., low epistemic uncertainty introduced), and (3) the regression model generalizes to independent test data. Finally, numerical experiments performed on several computational-mechanics problems and types of approximate solutions demonstrate the ability of the method to generate statistical models of the error that satisfy these criteria and significantly outperform more commonly adopted approaches for error modeling.

97 MATHEMATICS AND COMPUTING↗

Multi-scale modeling of microstructure dependent intergranular brittle fracture using a quantitative phase-field based method

In this study, the fracture behavior of brittle materials is strongly influenced by their underlying microstructure that needs explicit consideration for accurate prediction of fracture properties and the associated scatter. In this work, a hierarchical multi-scale approach is pursued to model microstructure sensitive brittle fracture. A quantitative phase-field based fracture model is utilized to capture the complex crack growth behavior in the microstructure and the related parameters are calibrated from lower length scale atomistic simulations instead of engineering scale experimental data. The workability of this approach is demonstrated by performing porosity dependent intergranular fracture simulations in UO 2 and comparing the predictions with experiments.

36 MATERIALS SCIENCE↗

A foundation model for non-destructive defect identification from vibrational spectra

Defects are ubiquitous in solids and strongly influence materials’ functional properties. However, non-destructive characterization and quantification of defects, especially when multiple types coexist, remain a long-standing challenge. Here, we introduce DefectNet, a foundation machine learning model that predicts the chemical identity and concentration of substitutional point defects with multiple coexisting elements directly from vibrational spectra, specifically phonon density-of-states (PDoS). Trained on over 16,000 simulated spectra from 2,000 semiconductors, DefectNet employs a tailored attention mechanism to identify up to six distinct defect elements at concentrations ranging from 0.2% to 25%. The model generalizes well to unseen crystals across 56 elements and can be fine-tuned on experimental data. Validation using inelastic scattering measurements of SiGe alloys and MgB 2 superconductor demonstrates its accuracy and transferability. Furthermore, our work establishes vibrational spectroscopy as a viable, non-destructive probe for bulk point defect quantification, and highlights the promise of foundation models in data-driven defect engineering.

artificial intelligence↗

The human dimensions of energy use in buildings: A review

The “human dimensions” of energy use in buildings refer to the energy-related behaviors of key stakeholders that affect energy use over the building life cycle. Stakeholders include building designers, operators, managers, engineers, occupants, industry, vendors, and policymakers, who directly or indirectly influence the acts of designing, constructing, living, operating, managing, and regulating the built environments, from individual building up to the urban scale. Among factors driving high-performance buildings, human dimensions play a role that is as significant as that of technological advances. However, this factor is not well understood, and, as a result, human dimensions are often ignored or simplified by stakeholders. This work presents a review of the literature on human dimensions of building energy use to assess the state-of-the-art in this topic area. The paper highlights research needs for fully integrating human dimensions into the building design and operation processes with the goal of reducing energy use in buildings while enhancing occupant comfort and productivity. This research focuses on identifying key needs for each stakeholder involved in a building's life cycle and takes an interdisciplinary focus that spans the fields of architecture and engineering design, sociology, data science, energy policy, codes, and standards to provide targeted insights. Greater understanding of the human dimensions of energy use has several potential benefits including reductions in operating cost for building owners; enhanced comfort conditions and productivity for building occupants; more effective building energy management and automation systems for building operators and energy managers; and the integration of more accurate control logic into the next generation of human-in-the-loop technologies. The review concludes by summarizing recommendations for policy makers and industry stakeholders for developing codes, standards, and technologies that can leverage the human dimensions of energy use to reliably predict and achieve energy use reductions in the residential and commercial buildings sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress

Fis1-mediated mitochondrial localization of Drp1 and excessive mitochondrial fission occur in human pathologies associated with oxidative stress. However, it is not known how Fis1 detects oxidative stress and what structural changes in Fis1 enable mitochondrial recruitment of Drp1. We find that conformational change involving α1 helix in Fis1 exposes its only cysteine, Cys41. In the presence of oxidative stress, the exposed Cys41 in activated Fis1 forms a disulfide bridge and the Fis1 covalent homodimers cause increased mitochondrial fission through increased Drp1 recruitment to mitochondria. Our discovery of a small molecule, SP11, that binds only to activated Fis1 by engaging Cys41, and data from genetically engineered cell lines lacking Cys41 strongly suggest a role of Fis1 homodimerization in Drp1 recruitment to mitochondria and excessive mitochondrial fission. The structure of activated Fis1-SP11 complex further confirms these insights related to Cys41 being the sensor for oxidative stress. Importantly, SP11 preserves mitochondrial integrity and function in cells during oxidative stress and thus may serve as a candidate molecule for the development of treatment for diseases with underlying Fis1-mediated mitochondrial fragmentation and dysfunction.

59 BASIC BIOLOGICAL SCIENCES↗

OASIS: Offsetting Active Reconstruction Attacks in Federated Learning

Federated Learning (FL) has garnered significant attention for its potential to protect user privacy while enhancing model training efficiency. For that reason, FL has found its use in various domains, from health care to industrial engineering, especially where data cannot be easily exchanged due to sensitive information or privacy laws. However, recent research has demonstrated that FL protocols can be easily compromised by active reconstruction attacks executed by dishonest servers. These attacks involve the malicious modification of global model parameters, allowing the server to obtain a verbatim copy of users' private data by inverting their gradient updates. Tackling this class of attack remains a crucial challenge due to the strong threat model. In this paper, we propose a defense mechanism, namely OASIS, based on image augmentation that effectively counteracts active reconstruction attacks while preserving model performance. We first uncover the core principle of gradient inversion that enables these attacks and theoretically identify the main conditions by which the defense can be robust regardless of the attack strategies. We then construct our defense with image augmentation showing that it can undermine the attack principle. Comprehensive evaluations demonstrate the efficacy of the defense mechanism highlighting its feasibility as a solution.

deep neural networks↗

Flow Mechanisms and Diffusion Combustion of Turbulent Jets

The problem of flow and combustion of turbulent jets of fuel gas in the external medium of an oxidant (air) is solved with regard to the existence of the actual boundary of the turbulent flow region of a jet. Based on the ideas of the friction force of the external flow acting on the boundary of a jet, the entrainment equation for the external medium is derived that closes the system of equations of motion of turbulent jets. The physical meaning of the dissipation rate of the turbulent energy of a jet is interpreted as the work of the friction force. To describe the combustion kinetics, the limit of instantaneous reactions corresponding to the diffusion combustion mode is used. Calculations of the effective reaction rates for reactants and the volumes occupied by them are based on the representation of a turbulent medium as an aggregation of independent turbulent particles—vortices—whose random contacts lead to the mixing and combustion of reacting substances [31]. The concomitant phenomena of flow and combustion are analyzed, including radiation effects. In particular, it is shown that the apparent increase in the combustion temperature with increasing Reynolds number is in fact attributed to the relative decrease of thermal radiation losses. Qualitative agreement is obtained between the results of the theoretical calculations of the length of a combustion torch and experimental data.

42 ENGINEERING↗