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At least 199 records · Page 11

Chemoinformatic-Guided Engineering of Polyketide Synthases

Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A significant challenge is re-engineering a partially reductive PKS module to produce a saturated β-carbon through a reductive loop (RL) exchange. In this work, we sought to establish that chemoinformatics, a field traditionally used in drug discovery, offers a viable strategy for RL exchanges. We first introduced a set of donor RLs of diverse genetic origin and chemical substrates into the first extension module of the lipomycin PKS (LipPKS1). Product titers of these engineered unimodular PKSs correlated with chemical structure similarity between the substrate of the donor RLs and recipient LipPKS1, reaching a titer of 165 mg/L of short-chain fatty acids produced by the host Streptomyces albus J1074. Finally, expanding this method to larger intermediates that require bimodular communication, we introduced RLs of divergent chemosimilarity into LipPKS2 and determined triketide lactone production. Collectively, we observed a statistically significant correlation between atom pair chemosimilarity and production, establishing a new chemoinformatic method that may aid in the engineering of PKSs to produce desired, unnatural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of physics-informed neural networks (PINNs) solution to coupled thermal and hydraulic processes in silty sands

Abstract The accurate modeling of water and heat transport in soils is crucial for both geo-environmental and geothermal engineering. Traditional modeling methods are problematic because they require well-defined boundaries and initial conditions. Recently, physics-informed neural networks (PINNs), which incorporate partial differential equations (PDEs) to solve forward and inverse problems, have attracted increasing attention in machine learning research. In this study, we applied PINNs to tackle hydraulic and thermal transport coupling forward problems in silty sands. A fully connected deep neural network was utilized for training. This neural network model leverages automatic differentiation to apply the governing equations as constraints, based on the mathematical approximations established by the neural network itself. We conducted forward problems and compared the solutions derived from PINNs with those from Finite Element Method (FEM) simulations. The forward problem results demonstrate the PINNs model’s capability in predicting hydraulic transport, heat transport, and thermal–hydraulic coupling in silty sands under various boundary conditions. The PINNs exhibited great performance in simulating the thermal–hydraulic coupling problem. The accuracy of the PINNs solutions shows its potential for simulation in geotechnical engineering.

Feng, Yuan↗

Development of simplified model for injection rate prediction of diesel injectors during transient and steady operation

Determining the injection rate of the diesel injector during the transient short injection operations is a critical matter to enhance the combustion process by improving air/fuel mixture formation. In this regard, numerous injection models have been suggested in the literature to predict the injection rate accurately. However, such algorithms have not precisely predicted the rate of injection (ROI) in transient short injection events. In addition, most of those models require many input parameters to characterize hydraulic and mechanical subsystems in the injector, which can make them inconvenient to tune for different injector specifications, in other words not suitable for universal usage. Therefore, our study aims to develop a simple injection model that can predict injection rate precisely in the short and long injection durations considering relatively fewer input parameters. The model traces the pressure variation inside the sac based on the bulk modulus theory to predict nozzle exit velocity, thus the injection rate of the injector. In the algorithm, the bulk modulus of fuel (E) and discharge coefficients of the nozzle hole and needle seat (C d,H and C d,N ) have been considered to vary rather than set constant during the injection process since such flow parameters would have a critical impact on the flow development at the transient stage, thus affecting the injection rate of diesel injectors. Here with this modelling strategy, the accuracy of the new model on ROI prediction was confirmed with acceptable model error for both short and long injection durations by validating against experimental results. To understand the effect of the new model scheme on ROI prediction, ROI results with the new model have been discussed by comparing it with the ROI results predicted with constant flow parameters.

42 ENGINEERING↗

Evaluating the Performance of Random Forest and Iterative Random Forest Based Methods when Applied to Gene Expression Data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3. We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

iRF-Loop, expression network, Populus Trichocarpa↗

Toward high efficiency at high temperatures: Recent progress and prospects on InGaN-Based solar cells

III-nitride InGaN material is an ideal candidate for the fabrication of high performance photovoltaic (PV) solar cells, especially for high-temperature applications. Over the past decade, significant efforts have been made to improve the PV performance of InGaN-based solar cells. In this paper, we perform a comprehensive review of the recent developments in InGaN-based solar cells. The topics of discussion include theoretical modeling, material epitaxy, device engineering, and high-temperature measurement. Particularly, we highlight subjects such as substrate technology, and properties that are unique to InGaN materials such as polarization control and their positive thermal coefficient. To date, outstanding high-temperature InGaN-based solar cells with quantum efficiency approaching 80% at 450 °C have been demonstrated. In conclusion, future innovations in epitaxy science, device engineering, and integration methods are required to further advance the efficiency and expand the applications of InGaN-based solar cells.

14 SOLAR ENERGY↗

Novel Chalcopyrites for Advanced Photoelectrochemical Water Splitting

With the support of DoE’s EERE office, our team has established a unique tool-chest of capabilities, including theoretical modeling (Lawrence Livermore National Laboratory: LLNL), state-of-the-art synthesis (Hawaii Natural Energy Institute: HNEI, Stanford, and the National Renewable Energy Laboratory: NREL) and advanced materials and interfaces characterization (University of Nevada, Las Vegas: UNLV, and Lawrence Berkeley National Laboratory: LBNL), to accelerate the development of high efficiency and durable chalcopyrite materials for advanced photoelectrochemical (PEC) water splitting. Using this synergistic approach, we have successfully created new wide bandgap chalcopyrite photocathodes generating over 10 mA/cm 2 , developed innovative strategies to protect them from corrosion, and engineered novel integration methods to circumvent thin film materials mechanical, chemical and thermal incompatibility. In Task 1 “Modeling and synthesis of chalcopyrite photocathodes”, we expanded our library of wide bandgap chalcopyrites for PEC water splitting. With support from LLNL’s “Computational Materials Diagnostics and Optimization of PEC Devices”, LBNL’s “photophysical” and NREL’s “I-III-VI Compound Semiconductors for Water-Splitting” nodes, we investigated two new chalcopyrite candidates for PEC water splitting: Cu(In,Al)Se 2 and Cu(In,B)Se 2 . We also further developed ordered vacancy compounds, such as CuGa 3 Se 5 , with unprecedented durability during PEC waters splitting in acidic solutions. In Task 2 “Interfaces engineering for enhanced efficiency and durability”, we addressed both the non-ideal band-edge positions of chalcopyrites with respect to water redox potentials, as well as their chemical instability under PEC water splitting, with a buried-junctions approach. With help from NREL’s “High-Throughput Experimental Thin Film Combinatorial Capabilities” and “Corrosion Analysis of Materials” nodes, we engineered environmentally friendly n-type buffers, including Mn x Zn 1-x O, to adjust the chalcopyrite band-edge positions and achieved photovoltages as high as 925 mV. Also, we integrated non-precious catalytic-protecting layers, such as WO 3 , to enhance the water splitting long-term stability of chalcopyrite absorbers. Finally, in Task 3 “Hybrid photoelectrode device integration”, we proposed an innovative method to bond wide bandgap photocathodes onto narrow bandgap PV drivers at room temperature using conductive polymers. Our semi-monolithic approach addressed fundamental processing incompatibility issues, as both the photocathode and the PV driver are processed separately. Proof-of-concept whole-chalcopyrite tandems were obtained by consecutive exfoliation and transfer of fully integrated 1.85 eV CuGa 3 Se 5 and 1.13 eV CuInGaSe 2 stacks from their Mo/SLG substrates onto a new single FTO host substrate.

08 HYDROGEN↗

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

59 BASIC BIOLOGICAL SCIENCES↗

A safe reinforcement learning algorithm for supervisory control of power plants

Traditional control theory-based methods require tailored engineering for each system and constant fine-tuning. In power plant control, one often needs to obtain a precise representation of the system dynamics and carefully design the control scheme accordingly. Model-free Reinforcement learning (RL) has emerged as a promising solution for control tasks due to its ability to learn from trial-and-error interactions with the environment. It eliminates the need for explicitly modeling the environment’s dynamics, which is potentially inaccurate. However, the direct imposition of state constraints in power plant control raises challenges for standard RL methods. To address this, we propose a chance-constrained RL algorithm based on Proximal Policy Optimization for supervisory control. Our method employs Lagrangian relaxation to convert the constrained optimization problem into an unconstrained objective, where trainable Lagrange multipliers enforce the state constraints. In conclusion, our approach achieves the smallest distance of violation and violation rate in a load-follow maneuver for an advanced Nuclear Power Plant design.

constrained optimization↗

A Systematic Approach to Light Load Calculation for DG Un-Intentional Islanding

With the influx of distributed generation (DG) penetration, power utilities have adopted active anti-islanding protection methods to prevent an unintentional islanding condition. One commonly used protection scheme is implemented through the use of a transfer trip from the upline connected substation to the DG facility and is required when the capacity of connected DGs exceed a certain threshold of local minimum load. The threshold established by standard IEEE 1547.2-2009 states that a 3:1 minimum load to generation ratio is acceptable to ensure the DG will not sustain an unintentional island. However, the term “minimum load” is not precisely defined in any standard, and in practice, a light load value is chosen by engineers through manual methods that can be inconsistent, not representative and change drastically based on various cases. To solve this problem, this paper proposes a new light load calculation method creating consistency and better accuracy; the method has been implemented in. NET C# application and is used within Dominion Energy.

Chen, Le↗

Noble Gas Management: SBMOF 1 vs. NUCON Carbon

Pacific Northwest National Laboratory (PNNL), in collaboration with Flibe Energy, Inc., demonstrated the fabrication of metal organic frameworks (MOFs) into engineered beads to manage off-gases released from molten salt reactors. Among the many MOF options, SBMOF 1 was selected as an ideal sorbent to manage off-gases released from a molten salt reactor because its pore size is optimal. The SBMOF 1 was synthesized and fabricated into engineered particles using three different methods, with and without polymers. All the engineered particles were exposed to Co-60 radiation (1,000 kGy) to demonstrate their radiation stability. Single column breakthrough experiments were performed at different temperatures, activation conditions, flow rates, and off-gas compositions to optimize the Xe capacity at the breakthrough point and at saturation. The Xe loading in SBMOF 1 was compared with that of standard solid sorbent (Nucon carbon) under identical conditions. Based on the single column experiments, SBMOF 1 outperforms the Nucon carbon at all the temperatures and reduces the mass (to as little as 55%) of sorbent needed to achieve the same performance as carbon. The bed volume is also reduced, down to 48% of that of Nucon carbon, when the MOF is used. These results clearly demonstrate improvement in the amount of adsorbent needed and show a reduction in bed volume compared to traditional sorbent material.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Multifunctional Conjugated Ligand Engineering for Stable and Efficient Perovskite Solar Cells

Surface passivation is an effective way to boost the efficiency and stability of perovskite solar cells (PSCs). However, a key challenge faced by most of the passivation strategies is reducing the interface charge recombination without imposing energy barriers to charge extraction. Here, a novel multifunctional semiconducting organic ammonium cationic interface modifier inserted between the light-harvesting perovskite film and the hole-transporting layer is reported. It is shown that the conjugated cations can directly extract holes from perovskite efficiently, and simultaneously reduce interface non-radiative recombination. Together with improved energy level alignment and the stabilized interface in the device, a triple-cation mixed-halide medium-bandgap PSC with an excellent power conversion efficiency of 22.06% (improved from 19.94%) and suppressed ion migration and halide phase segregation, which lead to a long-term operational stability, is demonstrated. Finally, this strategy provides a new practical method of interface engineering in PSCs toward improved efficiency and stability.

36 MATERIALS SCIENCE↗

Low Energy Implantation into Transition-Metal Dichalcogenide Monolayers to Form Janus Structures

Atomically-thin two-dimensional (2D) materials face significant energy barriers for synthesis and processing into functional metastable phases such as Janus structures. Here, in this study, the controllable implantation of hyperthermal species from pulsed laser deposition (PLD) plasmas is introduced as a top-down method to compositionally engineer 2D monolayers. The kinetic energies of Se clusters impinging on suspended monolayer WS 2 crystals were controlled in the <10 eV/atom range with in situ plasma diagnostics to determine the thresholds for selective top layer replacement of sulfur by selenium for the formation of high quality WSSe Janus monolayers at low (300 °C) temperatures, and bottom layer replacement for complete conversion to WSe 2 . Atomic-resolution electron microscopy and spectroscopy in tilted geometry confirm the WSSe Janus monolayer. Molecular dynamics simulations reveal that Se clusters implant to form disordered metastable alloy regions, which then recrystallize to form highly ordered structures, opening the door for low-energy implantation by PLD as a novel method to explore the synthesis of 2D Janus layers and alloys of variable composition.

2D materials↗

Propagation of Noise Uncertainty Through Virtual Strain Gauge Formulations for 2D Digital Image Correlation

The effect of displacement uncertainty is examined on 2-dimensional strain, calculated using linear surfaces fitted to the displacement field. A classical engineering error propagation method is used to calculate uncertainty in Green-Lagrangian strain calculations. The derived uncertainty is compared to a Monte Carlo simulation and discrepancies under 2% are seen between these two methods. The effect of virtual strain gauge size, displacement uncertainty, and boundaries on the region of interest on the strain uncertainty are considered. Here, an exponential decay relationship is observed between strain uncertainty and virtual strain gauge size, while a linear relationship is seen between strain and displacement uncertainty. For boundaries in the region of interest, strain uncertainty is affected by the reduced number of points available to perform the regression.

42 ENGINEERING↗

Development and evaluation of an agar capture system (ACS) for high-throughput screening of insoluble particulate substrates with bacterial growth and enzyme activity assays

In this work, we describe a method for containing insoluble particulates for use as substrates in either bacterial growth or enzyme assays. This method was designed for high-throughput screening of environmental or engineered bacteria. Benchmarking this method with several model bacteria uncovered phenotypes not observable with the particulate substrates alone.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Computational Practices (Rev. 1)

This manual will attempt to motivate the use of an automated build system for the purposes of computational science and engineering. As part of this motivation, the surrounding computational practices of version control, documen tation, compute environment management, and regression testing will also be addressed as applied to the practice of computational engineering. Specifically, this manual intends to motivate the adoption of these traditional software engineering practices for use in research and production engineering simulation projects. This manual is not the first such effort in the greater scientific computing community. In fact, the authors relied heavily on the lesson plans of the Software Carpentry, established to teach computing skills to researchers in 1998. As the intention for this manual is to lay out fundamental practices of engineering computing, it will not attempt to fully teach the underlying concepts and will instead reference the well designed lesson plans of the Software Carpentry. Where possible, this manual will explain to general computing practices and concepts and limit discussion of specific software implementations to examples or vehicles for practice in concrete application. The specific software taught by the Software Carpentry curriculum is an excellent starting point to learn the core concepts of computational engi neering. However, the authors have found that applications to engineering simulation and analysis require translation of these software development concepts into the language and workflows of computational engineers. Adopting these computational tools may require engineers to re-imagine their workflows in some combination of traditional engineer ing and software concepts. It has also been necessary to extend existing software build systems for engineering practices beyond the simple wrap ping of engineering software execution. Where necessary, examples of specific software and their method of extension to engineering simulations will be given, with reference to the User Manual for recommended practical use. Where this manual relies on specific implementation examples, it should be understood that the practicing engineer may find that different software is more amenable to their specific work. It is always the overall collection of computational practices is more important than any specific software implementation. The ability to recognize which concepts are implemented by a software package will make a practicing engineer agile to changing project needs, computing resources, numeric solvers, programming languages, and even available funding.

42 ENGINEERING↗

Near-field radiative heat transfer between irregularly shaped dielectric particles modeled with the discrete system Green's function method

Near-field radiative heat transfer (NFRHT) between irregularly shaped dielectric particles made of SiO 2 and morphology characterized by Gaussian random spheres is studied. Particles are modeled using the discrete system Green's function (DSGF) approach, which is a volume integral numerical method based on fluctuational electrodynamics. This method is applicable to finite, three-dimensional objects, and all system interactions are defined independent of thermal excitation by a generalized system Green's function. The DSGF method is deemed suitable to model NFRHT between irregularly shaped particles after verification against the analytical solution for chains of two and three SiO 2 spheres. The NFRHT results reveal that geometric irregularity in particles leads to a reduction of the total conductance from that of comparable perfect spheres at vacuum separation distances smaller than the particle size, a regime in which NFRHT is a surface phenomenon. At vacuum separation distances larger than the particle size, NFRHT becomes a volumetric process, and the total conductance between irregularly shaped particles converges to that of comparable perfect spheres. Spectral analysis reveals, however, that particle irregularity leads to damping and broadening of resonances at all separation distances, thereby highlighting the importance of the DSGF method for spectral engineering in the near field. The reduced spectral coherence when particle size is larger than the vacuum separation distance is attributed to coupling of surface phonon-polaritons within the randomly generated, distorted particle features. For particle size smaller than the vacuum separation distance, resonance broadening and damping are linked with the multiple localized surface phonon modes supported by the composite spherical harmonic morphologies of the Gaussian random spheres. In conclusion, this paper has direct implications for thermal management of packed particle systems, with applications in radiative property control, electronics, energy conversion, and nanomanufacturing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Methods of producing lipid-derived compounds and host cells thereof

The present disclosure relates to genetically engineered host cells and methods of producing a lipid-derived compound by employing such host cells. In particular embodiments, the host cell includes a first mutant gene encoding a cytoplasmic tRNA thiolation protein. Optionally, the host cell can include other mutant genes for decreasing fatty alcohol catabolism, decreasing re-importation of secreted fatty alcohol, or displaying other useful characteristics, as described herein.

Coradetti, Samuel↗