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At least 469 records · Page 26

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. We applied DAP-seq to >90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA- and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike towards a desired phenotype.

09 BIOMASS FUELS↗

Evaporation Sub-model Development for Volume of Fluid (eVOF) Method Applicable to Spray-Wall Interaction Including Film Characteristics with Validation at High Pressure and Temperature Conditions (Final Report)

Internal combustion engines have seen a great evolution over the last several decades through application of high pressure direct injection, multiple injections, and other technologies to reduced fuel consumption, NOx, and PM. Although combustion systems with advanced injection strategies have been studied extensively, there exists a significant fundamental knowledge gap on the fuel-spray interactions with the piston surface and chamber walls. Advanced computational codes validated with experimental techniques have to be developed for accurate representation of the drop impingement, fuel film formation, and vaporization. Current engine CFD spray models utilize a Lagrangian framework for modeling which lacks critical considerations of the physics pertaining to these interactions and thus requiring extensive parameterization, tuning and validation. The team from Michigan Technological University, University of Massachusetts Dartmouth, and Argonne National Laboratory is composed of experts in sprays, combustion, engines and CFD with a wide spectrum of knowledge including specific expertise in the area under consideration. In the proposed work, a VOF modeling approach has been adopted for the spray-wall interaction, film formation and spreading, and vaporization. With the inclusion of a vaporization submodel, a more predictive and accurate simulation of the spray-film was performed without extensive need of parameterization and tuning. Extensive experimentation of the spray-wall interaction under the range of conditions matching the thermodynamic and surface temperatures that occur in diesel and gasoline engines were conducted to validate the SWI submodels and for development of the evaporation sub-model, which has been implemented in the Converge software.

42 ENGINEERING↗

Moving from residual lignocellulosic biomass into high–value products: Outcomes from a long–term international cooperation

Major progress in the bioprocessing of lignocellulose to fuels and value-added chemicals has created the possibility of a low carbon-footprint economy. However, the current complexity and associated costs of lignocellulose conversion result in a higher price for ethanol than for fossil fuels. The cost of cellulosic ethanol production will be lowered by further progress in development of biorefinery technology that produces both ethanol and high-value chemicals with bio-based products that are beginning to penetrate consumer markets in the USA, Brazil, and worldwide. The cost-effectiveness of low carbon-footprint bioproducts will benefit from advances in supplying large amounts of biomass solids to the biorefinery. We describe here outcomes from a successful long-term international cooperation between the Laboratory of Renewable Resources Engineering (LORRE) at Purdue University in the United States and Brazil's Agricultural Research Corporation (EMBRAPA) and Federal University of Sâo Carlos (UFSCar), which has contributed practical pathways to enhance the biorefinery concept. Furthermore, this paper gives an overview of developments that address fundamental knowledge of lignocellulosic biomass pretreatment hydrolysis under optimized operational conditions and bioreactor configurations, and the science and engineering that contributes to the effective production of fuel and ethanol and value-added products from biomass.

09 BIOMASS FUELS↗

Heavy-Duty Low-Temperature and Diesel Combustion & Heavy-Duty Combustion Modeling (FY 2018 Annual Progress Report)

Regulatory drivers and market demands for lower pollutant emissions, lower carbon dioxide emissions, and lower fuel consumption motivate the development of clean and fuel-efficient engine operating strategies. Most current production engines use a combination of both in-cylinder and exhaust emission control strategies to achieve these goals. The emissions and efficiency performance of in-cylinder strategies depend strongly on flow and mixing processes associated with fuel injection. Both heavy- and light-duty engine/vehicle manufacturers use multiple-injection strategies to reduce noise, emissions, and fuel consumption. For both conventional and low-temperature diesel combustion, the state of knowledge and modeling tools for multiple injections are far less advanced than for single-injection strategies. Engine efficiency is limited to some degree by tradeoffs that must be accepted to meet particulate matter (including soot) emissions limits. Recent work on this project has filled some knowledge gaps on soot oxidation with multiple injections, and the current work for Fiscal Year (FY) 2018 addresses knowledge gaps on soot formation for multiple injections. While total in-cylinder soot is readily measured, discerning formation from oxidation is difficult. The FY 2018 experiments are designed to create in-cylinder conditions at the threshold of soot formation, where processes that affect soot formation can be more readily discerned. Soot formation pathways under such conditions are fraught with uncertainties, and soot models significantly overpredict polyaromatic hydrocarbon (PAH) and soot, so experimental data at these conditions will provide much needed data for improvements to PAH and soot models.

02 PETROLEUM↗

Evaporation Submodel Development for Volume of Fluid (eVOF) Method Applicable to Spray-Wall Interaction Including Film Characteristics with Validation at High Pressure and Temperature Conditions

Internal combustion engines have seen a great evolution over the last several decades through application of high pressure direct injection, multiple injections, and other technologies to reduced fuel consumption, NOx, and PM. Although combustion systems with advanced injection strategies have been studied extensively, there exists a significant fundamental knowledge gap on the fuel-spray interactions with the piston surface and chamber walls. Advanced computational codes validated with experimental techniques have to be developed for accurate representation of the drop impingement, fuel film formation, and vaporization. Current engine CFD (Computational Fluid Dynamics) spray models utilize a Lagrangian framework for modeling which lacks critical considerations of the physics pertaining to these interactions and thus requiring extensive parameterization, tuning and validation. The team from Michigan Technological University, University of Massachusetts Dartmouth, and Argonne National Laboratory is composed of experts in sprays, combustion, engines and CFD with a wide spectrum of knowledge including specific expertise in the area under consideration. In the proposed work, a VOF (Volume of Fluid) modeling approach has been adopted for the spray-wall interaction, film formation and spreading, and vaporization. With the inclusion of a vaporization submodel, a more predictive and accurate simulation of the spray-film was performed without extensive need of parameterization and tuning. Extensive experimentation of the spray-wall interaction under the range of conditions matching the thermodynamic and surface temperatures that occur in diesel and gasoline engines were conducted to validate the SWI submodels and for development of the evaporation submodel, which has been implemented in the flow solver.

42 ENGINEERING↗

Modeling Nanosecond-Pulsed Spark Discharge and Flame Kernel Evolution

Dilute combustion, either using exhaust gas recirculation or with excess air, is considered a promising strategy to improve the thermal efficiency of internal combustion engines. However, the dilute air-fuel mixture, especially under intensified turbulence and high-pressure conditions, poses significant challenges for ignitability and combustion stability, which may limit the attainable efficiency benefits. In-depth knowledge of the flame kernel evolution to stabilize ignition and combustion in a challenging environment is crucial for effective engine development and optimization. To date, a comprehensive understanding of ignition processes that result in the development of fully predictive ignition models usable by the automotive industry does not yet exist. Spark-ignition consists of a wide range of physics that includes electrical discharge, plasma evolution, joule-heating of gas, and flame kernel initiation and growth into a self-sustainable flame. In this study, an advanced approach is proposed to model spark-ignition energy deposition and flame kernel growth. To decouple the flame kernel growth from the electrical discharge, a nanosecond-pulsed high-voltage discharge is used to trigger spark-ignition in an optically accessible small ignition test vessel with a quiescent mixture of air and methane. Initial conditions for the flame kernel, including its thermodynamic state and species composition, are derived from a plasma-chemical equilibrium calculation. The geometric shape and dimension of the kernel are characterized using a multi-dimensional thermal plasma solver. Here, the proposed modeling approach is evaluated using a high-fidelity computational fluid dynamics procedure to compare the simulated flame kernel evolution against flame boundaries from companion Schlieren images.

42 ENGINEERING↗

Accelerating Learning with Set-Based Concurrent Engineering

The traditional design approach for product development is to develop a design based on customer requirements and technical knowledge, build the product according to the detail requirements provided, and then test the product to validate that it works as intended. The team typically starts by identifying a single design approach and spends their time validating a single design during testing. Design teams often encounter issues in the course of development with performance, manufacturability, interfaces and more. To compensate for test failures, teams often build in time into the schedule for additional design loopbacks. Further, when the loopbacks lead to change, the late changes are costly and risky, causing the team to focuses on "fixing the bare minimum" to meet cost and schedule expectations.

42 ENGINEERING↗

A causal perspective on reliability assessment

Causality in an engineered system pertains to how a system output changes due to a controlled change or intervention on the system or system environment. Engineered systems designs reflect a causal theory regarding how a system will work, and predicting the reliability of such systems typically requires knowledge of this underlying causal structure. The aim of this work is to introduce causal modeling tools that inform reliability predictions based on biased data sources. We present a novel application of the popular structural causal modeling (SCM) framework to reliability estimation in an engineering application, illustrating how this framework can inform whether reliability is estimable and how to estimate reliability given a set of data and assumptions about the subject matter and data generating mechanism. When data are insufficient for estimation, sensitivity studies based on problem-specific knowledge can inform how much reliability estimates can change due to biases in the data and what information should be collected next to provide the most additional information. We apply the approach to a pedagogical example related to a real, but proprietary, engineering application, considering how two types of biases in data can influence a reliability calculation.

42 ENGINEERING↗

IL-Net: Using Expert Knowledge to Guide the Design of Furcated Neural Networks

Deep neural networks (DNN) excel at extracting patterns. Through representation learning and automated feature engineering on large datasets, such models have been highly successful in computer vision and natural language applications. Designing optimal network architectures from a principled or rational approach however has been less than successful, with the best successful approaches utilizing an additional machine learning algorithm to tune the network hyperparameters. However, in many technical fields, there exist established domain knowledge and understanding about the subject matter. In this work, we develop a novel furcated neural network architecture that utilizes domain knowledge as high-level design principles of the network. We demonstrate proof-of-concept by developing IL-Net, a furcated network for predicting the properties of ionic liquids, which is a class of complex multi-chemicals entities. Compared to existing state-of-the-art approaches, we show that furcated networks can improve model accuracy by approximately 20-35%, without using additional labeled data. Lastly, we distill two key design principles for furcated networks that can be adapted to other domains.

Sakloth, Khushmeen↗

Additive Manufacturing of Fuel Injectors

Additive manufacturing (AM), also known as 3D-printing, has been shifting from a novelty prototyping paradigm to a legitimate manufacturing tool capable of creating components for highly complex engineered products. An emerging AM technology for producing metal parts is the laser powder bed fusion (L-PBF) process; however, industry manufacturing specifications and component design practices for L-PBF have not yet been established. Solar Turbines Incorporated (Solar), an industrial gas turbine manufacturer, has been evaluating AM technology for development and production applications with the desire to enable accelerated product development cycle times, overall turbine efficiency improvements, and supply chain flexibility relative to conventional manufacturing processes (casting, brazing, welding). Accordingly, Solar teamed with EWI on a joint two-and-a-half-year project with the goal of developing a production L-PBF AM process capable of consistently producing high-nickel alloy material suitable for high temperature gas turbine engine fuel injector components. The project plan tasks were designed to understand the interaction of the process variables and their combined impact on the resultant AM material quality. The composition of the high-nickel alloy powders selected for this program met the conventional cast Hastelloy X compositional limits and were commercially available in different particle size distributions (PSD) from two suppliers. Solar produced all the test articles and both EWI and Solar shared responsibility for analyzing them. The effects of powder metal input stock, laser parameters, heat treatments, and post-finishing methods were evaluated. This process knowledge was then used to generate tensile, fatigue, and creep material properties data curves suitable for component design activities. The key process controls for ensuring consistent material properties were documented in AM powder and process specifications. The basic components of the project were: • Powder metal input stock: Powder characterization, dimensional accuracy, metallurgical characterization, and mechanical properties evaluation. • Process parameters: Laser parameter effects, post-printing heat-treatment development, mechanical properties evaluation, and post-finishing technique. • Material design curves: Room and elevated temperature tensiles, low cycle fatigue, and creep rupture properties curves generated. • AM specifications: Key metal powder characteristics, laser parameters, and heat-treatment controls identified.

36 MATERIALS SCIENCE↗

Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields. IMPORTANCE To engineer novel metabolic pathways into P. putida , a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.

59 BASIC BIOLOGICAL SCIENCES↗

Towards elastic in situ analysis for high-performance computing simulations

In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. We demonstrate the use of Colza with the Deep Water Impact and the AMR-Wind simulations, coupling them with the ParaView Catalyst and Ascent in situ libraries, and show that Colza enables dynamic rescaling of these widely-used frameworks with no interruption to the simulation or staging service. Here, we highlight the challenges of enabling such elasticity, which requires overcoming these frameworks' reliance on MPI, using distinct engineering approaches, namely dependency injection and dependency overload. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.

97 MATHEMATICS AND COMPUTING↗

The selective role of ECM components on cell adhesion, morphology, proliferation and communication in vitro

Cell binding to the extracellular matrix (ECM) is essential for cell and tissue functions. In this context, each tissue consists of a unique ECM composition, which may be responsible for tissue-specific cell responses. Due to the complexity of ECM-cell interactions—which depend on the interplay of inside-out and outside-in signaling cascades, cell and tissue specificity of ECM-guidance is poorly understood. In this paper, we investigate the role of different ECM components like laminin, fibronectin, and collagen type I with respect to the essential cell behaviour patterns: attachment dynamics such as adhesion kinetic and force, formation of focal adhesion complexes, morphology, proliferation, and intercellular communication. A detailed in vitro comparison of fibroblasts, endothelial cells, osteoblasts, smooth muscle cells, and chondrocytes reveals significant differences in their cell responses to the ECM: cell behaviour follows a cell specific ligand priority ranking, which was independent of the cell type origin. Fibroblasts responded best to fibronectin, chondrocytes best to collagen I, the other cell types best to laminin. This knowledge is essential for optimization of tissue-biomaterial interfaces in all tissue engineering applications and gives insight into tissue-specific cell guidance. -- Highlights: • We analyse the impact of ECM components on cell behaviour in vitro. • We compare five different cell types, using the same culture conditions. • The ECM significantly guides all cell responses. • Cell behaviour follows a cell specific ligand-priority ranking. • This gives insight in tissue formation and is essential for biomedical applications.

60 APPLIED LIFE SCIENCES↗

Roadmap Document for Pacific Northwest National Laboratory Contribution to the Open Modeling Framework

The Cooperative Research Network (CRN) of the National Rural Electric Cooperative Association (NRECA) has identified GridLAB-D as a tool that would provide significant benefit to its member utilities. However, they have also noted that the complexity of the tool would be a significant barrier for adoption. As can often happen in complex simulation environments, as the available capabilities and flexibility increases, the usability of the software decreases except for a few “power” users; this is not unique to GridLAB-D. While GridLAB-D has expanded to a considerable user base, with a few notable exceptions (e.g., American Electric Power) most users are focused on research and development. As a result, NRECA/CRN has proposed an Open Modeling Framework (OMF) designed to make the capabilities of GridLAB-D, and other advanced grid tools, available via a web interface. This will allow utility users to access many of the capabilities of GridLAB-D, with little to no knowledge of the tool itself. Other components will be layered over the simulation engines to provide the user with business support functions, allowing full business case scenarios to be created from the technical data generated within the simulations. Because of the open availability and potential national benefit of the OMF, PNNL has been tasked with supporting NRECA/CRN’s development of the tool, with a focus on incorporating GridLAB-D within the OMF structure and expanding GridLAB-D capabilities to support OMF functions. The GridLAB-D enhancements will be provided first to the OMF developers, but will also be delivered to the wider GridLAB-D community after validation via the community repository. This report is intended to provide a roadmap for the intended enhancements to be delivered by PNNL. Seven tasks were identified in cooperation with NRECA/CRN – each is briefly discussed, including potential outcomes and deadlines.

distribution↗

SRNL CRP progress report [Development of Melt Processed Ceramics for Nuclear Waste Immobilization]

A multi-phase ceramic waste form is being developed at the Savannah River National Laboratory (SRNL) for treatment of secondary waste streams generated by reprocessing commercial spent nuclear. The envisioned waste stream contains a mixture of transition, alkali, alkaline earth, and lanthanide metals. Ceramic waste forms are tailored (engineered) to incorporate waste components as part of their crystal structure based on knowledge from naturally found minerals containing radioactive and non-radioactive species similar to the radionuclides of concern in wastes from fuel reprocessing. The ability to tailor ceramics to mimic naturally occurring crystals substantiates the long term stability of such crystals (ceramics) over geologic timescales of interest for nuclear waste immobilization [1]. A durable multiphase ceramic waste form tailored to incorporate all the waste components has the potential to broaden the available disposal options and thus minimize the storage and disposal costs associated with aqueous reprocessing.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Melt Processed Crystalline Ceramic Waste Forms for Advanced Nuclear Fuel Cycles: CRP T21027 1813: Processing technologies for high level waste, formulation of matrices and characterization of waste forms, Task 17208 (Final Report)

A multi-phase ceramic waste form is being developed at the Savannah River National Laboratory (SRNL) for treatment of secondary waste streams generated by reprocessing commercial spent nuclear. The envisioned waste stream contains a mixture of transition, alkali, alkaline earth, and lanthanide metals. Ceramic waste forms are tailored (engineered) to incorporate waste components as part of their crystal structure based on knowledge from naturally found minerals containing radioactive and non-radioactive species similar to the radionuclides of concern in wastes from fuel reprocessing. The ability to tailor ceramics to mimic naturally occurring crystals substantiates the long term stability of such crystals (ceramics) over geologic timescales of interest for nuclear waste immobilization [1]. A durable multi-phase ceramic waste form tailored to incorporate all the waste components has the potential to broaden the available disposal options and thus minimize the storage and disposal costs associated with aqueous reprocessing. This report summarizes results from three years of work on the IAEA Coordinated Research Project on “Processing technologies for high level waste, formulation of matrices and characterization of waste forms” (T21027), and specific task “Melt Processed Crystalline Ceramic Waste Forms for Advanced Nuclear Fuel Cycles” (17208).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Melt Processed Crystalline Ceramic Waste Forms for Advanced Nuclear Fuel Cycles CRP T21027 1813: Processing technologies for high level waste, formulation of matrices and characterization of waste forms, Task 17208 (Final Report)

A multi-phase ceramic waste form is being developed at the Savannah River National Laboratory (SRNL) for treatment of secondary waste streams generated by reprocessing commercial spent nuclear. The envisioned waste stream contains a mixture of transition, alkali, alkaline earth, and lanthanide metals. Ceramic waste forms are tailored (engineered) to incorporate waste components as part of their crystal structure based on knowledge from naturally found minerals containing radioactive and non-radioactive species similar to the radionuclides of concern in wastes from fuel reprocessing. The ability to tailor ceramics to mimic naturally occurring crystals substantiates the long term stability of such crystals (ceramics) over geologic timescales of interest for nuclear waste immobilization. A durable multi-phase ceramic waste form tailored to incorporate all the waste components has the potential to broaden the available disposal options and thus minimize the storage and disposal costs associated with aqueous reprocessing. This report summarizes results from three years of work on the IAEA Coordinated Research Project on “Processing technologies for high level waste, formulation of matrices and characterization of waste forms” (T21027), and specific task “Melt Processed Crystalline Ceramic Waste Forms for Advanced Nuclear Fuel Cycles” (17208).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗