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Constrained Bayesian Optimization of Criticality Experiments at LLNL [Slides]
The design of criticality experiments is typically an iterative process that employs a Monte Carlo transport code. The goal is to find a design that optimizes some variable, like the sensitivity of a response to a cross section, while simultaneously ensuring criticality. The high fidelity of the Monte Carlo code is a great asset, but it makes exploring the design space computationally expensive. Herein, we present how a constrained Bayesian optimization algorithm can be used to efficiently design a criticality experiment. It uses Gaussian processes as a surrogate model to probe the design space and to reduce the number of code executions that are needed to find the optimum. We demonstrate constrained Bayesian optimization with a Pu-239/polyethylene solution system and a TEX experiment that is designed for critical ity safety validation of a nuclear waste model at the Hanford Site. For both systems, a global optimum was found within 75 Monte Carlo simulations.
NSLS-II longitudinal impedance budget
From the beginning of the NSLS-II project, the vacuum chamber of the NSLS-II storage ring has been optimized to reduce its impedance. The optimization, performed in close collaboration with the Diagnostic, Vacuum, RF, and Mechanical Engineering groups, has been achieved via calculating the impedance of the vacuum chamber components with the use of both analytical and numerical tools, with the numerical computations carried out with the GdfidL code. Fore reliable NSLS-II operation with the total beam current of 500 mA, each component of the vacuum chamber has been individually optimized to minimize the beam-induced heating and to prevent single-bunch and coupled-bunch instabilities. In this study, the impedance calculation and optimization know-how are summarized for all the chamber components, and the total longitudinal impedance budget is analyzed. As a result of this extensive research and engineering effort, the design beam current of 500 mA has been recently accumulated in NSLS-II without any major problem caused by collective effects.
Unusual Role of Point Defects in Perovskite Nickelate Electrocatalysts
Low-cost transition-metal oxide is regarded as a promising electrocatalyst family for an oxygen evolution reaction (OER). The classic design principle for an oxide electrocatalyst believes that point defect engineering, such as oxygen vacancies (VO .. ) or heteroatom doping, offers the opportunities to manipulate the electronic structure of material toward optimal OER activity. Oppositely, in this work, we discover a counterintuitive phenomenon that both VO .. and an aliovalent dopant (i.e., proton (H + )) in perovskite nickelate (i.e., NdNiO 3 (NNO)) have a considerably detrimental effect on intrinsic OER performance. Detailed characterizations unveil that the introduction of these point defects leads to a decrease in the oxidative state of Ni and weakens Ni-O orbital hybridization, which triggers the local electron-electron correlation and a more insulating state. Evidenced by first-principles calculation using the density functional theory (DFT) method, the OER on nickelate electrocatalysts follows the lattice oxygen mechanism (LOM). The incorporation of point defect increases the energy barrier of transformation from OO*(V O ) to OH*(V O ) intermediates, which is regarded as the rate-determining step (RDS). Furthermore, this work offers a new and significant perspective of the role that lattice defects play in the OER process.
Bioconversion of Agave Bagasse Lignin to Medium-Chain-Length Polyhydroxyalkanoates by Pseudomonas putida
Inadequate disposal of Agave tequilana bagasse (ATB) brings environmental and economic issues to tequila producing regions. Recent works have proposed technologies for valorization of the polysaccharide’s fractions of ATB. However, lignin bioconversion has not been investigated due to its recalcitrant nature. In this work, a systematic pretreatment is proposed to release the lignocellulosic fractions and produce medium-chain-length polyhydroxyalkanoates (PHA) from the lignin fraction of ATB. Nuclear magnetic resonance (NMR) analyses revealed that ATB lignin contained 63% of β-O-4 interunit linkages, making this lignin more suitable for pretreatment and biodegradation compared to other lignins. Exploratory experiments revealed that two-stage fermentation is suitable for PHA production from ATB lignin using wild type and engineered Pseudomonas putida strains. PHA increased from 0.09 to 0.39 g/L compared to single batch fermentation. Further improvement to 0.76 g/L was possible by using a central composite design to optimize the inoculum, substrate, and nitrogen concentrations. Finally, PHA depolymerase gene phaZ was knocked out from P. putida and tested at optimal conditions, enabling a PHA titer of 0.97 g/L. Analyses by NMR and GC-MS confirmed lignin derivatives consumption and decrease of β-O-4 linkages. This study lays the foundations to enable agave lignin bioprocessing and opens new avenues for ATB biorefineries.
Dual Enhancement of Thermostability and Activity of Xylanase through Computer-Aided Rational Design
In the realm of enzyme engineering, the dual enhancement of thermostability and activity remains a challenge. Herein, we employed a computer-aided approach integrating folding free energy calculations and evolutionary analysis to engineer Paecilomyces thermophila xylanase into a hyperthermophilic enzyme for application in the paper and pulp industry. Through the computational rational design, XynM9 with superior thermostability and enhanced activity was designed. Its optimal reaction temperature increases by 10 °C to 85 °C, its T m increases by 10 °C to 93 °C, and its half-life increases 11-fold to 5.8 h. Additionally, its catalytic efficiency improves by 57% to 3926 s –1 mM –1 . Molecular dynamics simulations revealed that XynM9 is stabilized by more hydrogen bonds and salt bridges than wild-type xylanase. The mutant’s narrower catalytic cleft enhances the substrate-binding affinity, thus improving the catalytic efficiency. In harsh conditions at 80 °C and pH 10, using XynM9 significantly reduced both hemicellulose and lignin, which makes it a good candidate for use in the paper and pulp process. Finally, our study presents an accurate and efficient strategy for the dual enhancement of enzyme properties, guiding further improvement of computational tools for protein stabilization.
Offline Arterial Signal Timing Optimization based on Virtual Phase Link Model - A Real-world Case Study
Conventional signal timing for arterial usually takes bottom-up approaches. Engineers optimize each individual intersection first and then coordinate them by adjusting the offsets. This work is based on the Virtual Phase-Link (VPL) model, a street traffic model designed for online traffic model predictive control, to obtain a top-down offline arterial signal timing. We Studied the Shallowford Rd. in Chattanooga, TN and found that the inconsistency in intersection capacities along the arterial could lead to some intersections becoming bottlenecks. Signal timing is a significant factor that affect the intersection capacities. We realized that the VPL-based model can guarantee the consistency in intersections along an arterial. We therefore adopted the VPL-based model and developed an offline signal timing optimization approach. The proposed timing derived from the VPL-based offline signal timing optimization showed very good results in simulation. The Chattanooga Department of Transportation adopted the optimized timing obtained from the proposed approach and gave positive feedbacks to the research team. We also collected field experiment data, which demonstrated overall energy reductions and speed improvements on some sections of the Shallowford Rd. arterial. We will continue the experiment when the COVID-19 pandemic impact subsides to have a more robust quantitative evaluation.
IEA Wind Task 32 and Task 37: Optimizing Wind Turbines with Lidar-Assisted Control Using Systems Engineering
Lidar-assisted control is a promising technology for reducing the levelized cost of energy from wind turbines, but quantifying its impact at the overall system level requires sophisticated systems engineering analysis and optimization frameworks. The joint workshop on Optimizing Wind Turbines with Lidar-Assisted Control Using Systems Engineering was held by the International Energy Agency Wind Task 32 (Lidar) and Task 37 (Systems Engineering) in October 2019 to address this challenge. This paper summarizes the outcome of the workshop and presents a road map for further research. The most promising applications of lidar-assisted control identified at the workshop and discussed here include 1) increasing annual energy production, 2) decreasing capital expenditure costs by reducing design loads, 3) extending turbine lifetime by reducing operating loads, and 4) enabling wind turbine class upgrades. For each application, we review the state of the art and highlight remaining research needs. Finally, we discuss strategies for addressing these research needs by conducting high-fidelity systems engineering optimizations.
Extremum seeking for optimal control problems with unknown time-varying systems and unknown objective functions
We consider the problem of optimal feedback control of an unknown, noisy, time-varying, dynamic system that is initialized repeatedly. Examples include a robotic manipulator which must perform the same motion, such as assisting a human, repeatedly and accelerating cavities in particle accelerators which are turned on for a fraction of a second with given initial conditions and vary slowly due to temperature fluctuations. In this paper, we present an approach that applies to systems of practical interest. The method presented here is model independent; does not require knowledge of the objective function; is robust to measurement noise; is applicable for any set of initial conditions; is applicable to simultaneously controlling an arbitrary number of parameters; and may be implemented with a broad range of continuous or discontinuous functions such as sine or square waves. For systems with convex cost functions we prove that our algorithm will produce controllers that approach the minimal cost. For linear systems we reproduce the cost minimizing linear quadratic regulator optimal controller that could have been designed analytically had the system and cost function been known. We demonstrate the effectiveness of the algorithm with simulation studies of noisy and time-varying systems.
An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening
High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.
Computational fluid dynamics modeling and analysis of silica nanoparticle synthesis in a flame spray pyrolysis reactor
Flame Spray Pyrolysis (FSP) is a method for large-scale production of nanoparticles and nanoscale powders employed in a wide range of industrial applications. Particle size and morphology are complex functions of the physicochemical phenomena occurring in the FSP reactor. An extensive study of FSP-related phenomena can be utilized to develop effective strategies for achieving desired particle size/morphology and scaling up the overall yield of an FSP system. In this work, a computational fluid dynamics (CFD) model of an FSP reactor is developed to simulate the coupling of key phenomena involved in the particle synthesis process: liquid spray breakup and evaporation, mixing, combustion, and particle formation/growth of silica nanoparticles. Herein, the particle sizes and their distributions from the CFD simulations are validated against experimental data. Subsequently, the simulations are utilized to investigate the impact of process parameters on the resultant flame dynamics and particle growth. Firstly, the CFD results show that the particle sizes are strongly correlated with the precursor concentration in the solvent. At lower precursor concentrations, the spread of the distribution is relatively insensitive to the value of the concentration. At higher concentrations, the spread is higher as the collision probability between particles is higher. Secondly, increasing the pilot flow rate increases the length of the pilot flames impacting the local ignition location of the spray flame. Lastly, it is shown that the dispersion gas flow rate strongly influences the spray flame shape. This shape can be used for control of particle growth as it helps determine the regions of high temperature and the residence time of the particles in the high temperature region enabling the design and process optimization of the FSP reactor.
Stress-sensitivity of fracture conductivity of Tuscaloosa Marine Shale cores
Production decline from wells producing from shale rocks is typically quite rapid. One possible factor responsible for such decline is loss in fracture conductivity. This is true in the case of the Tuscaloosa Marine shale reservoir. In this work, the stress-dependent fracture conductivity of TMS core samples is investigated using five propped cores under varying stress conditions. In addition, the effects of static rock mechanical properties and rock mineralogy on conductivity decline are investigated. The mineralogy of each core sample was determined by X-ray Diffraction analysis. Fracture conductivity was measured using a Hassler-type pressure core holder with a pressure rating of 15,000 psi (103.42 MPa). Estimated rock mechanical properties showed that shale anisotropy could affect fracture conductivity. The time decline in conductivity revealed two possible decline trends, a) decline from the reduction in induced fracture width, and b) decline from the healing of developed micro-cracks. An exponential decline in fracture conductivity with increasing confinement pressure was observed with an average decline rate constant of 3.15 x 10 -10 mPa -1 . While rock mineralogy did not have any clear relationship with conductivity decline, the effects of rock mechanical properties were only important at 10.34 MPa confinement pressure and above. The observation showed that a high Young's modulus correlate to high conductivity, whereas a high Poisson's ratio correlate to low conductivity. This study provides useful observations for optimizing fracture design to enhance well productivity in the TMS.
Microwave Heating-Induced Temperature Gradients in Liquid–Liquid Biphasic Systems
Microwaves (MWs) can enable the electrification and intensification of chemical manufacturing. They have been applied to various unit separations, such as drying, distillation, and extraction, entailing gas–liquid and solid–liquid systems. However, a limited quantitative understanding of MW-heated liquid–liquid biphasic systems related to extraction exists. This work measures the temporal and spatial temperature difference between an aqueous and an organic phase in batch and continuous microfluidic modes. We demonstrate permanent temperature differences between phases over 35 °C and spatiotemporal periodic and quasiperiodic oscillations modulated by the flow patterns. The temperature differences are primarily driven by the faster absorption rate of MW irradiation by the aqueous phase versus the slower heat transfer from the aqueous phase to the organic phase. These are amplified by low specific interfacial area and modifications of the electromagnetic field. We employ a multiphysics model to predict the temperature difference in a batch system. The model is in good agreement with the experiments. We demonstrate a strong effect of input power, dielectric properties of organic solvents, the volume of solvents, and the volume ratio between phases on the temperature difference. A simple analytical model describes the temperature difference and provides design principles. Furthermore, the combined approach offers new insights into the design and optimization of the MW-heated biphasic systems.
Materials and methods used in the ice making process
A detailed survey of ice mold and evaporator metal surfaces, physical structures, operational conditions, materials of construction, design of different equipment was reviewed and analyzed. The key objective was to identify different ice related processes’ materials, structures, and operating conditions for designing, optimizing, and applying advance materials to lower ice adhesion strength.
A New Approach to Predict Hydrogeological Parameters Using Shear Waves from the Multichannel Analysis of Surface Waves Method
For near-surface contaminant characterization, the accurate prediction of hydrogeological parameters in anisotropic and heterogeneous environments has been a challenge since the last decades. However, recent advances in near-surface geophysics have facilitated the use of geophysical data for hydrogeological characterization in the last few years. A pseudo 3-D high resolution P-wave shallow seismic reflection survey was performed at the P Reactor Area, Savannah River Site, South Carolina in order to delineate and predict migration pathways of a large contaminant plume including trichloroethylene. This contaminant plume originates from the northwest section of the reactor facility that is located within the Upper Atlantic Coastal Plain. The data were collected with 40 Hz geophones, an accelerated weight-drop as seismic source and 1 m receiver spacing with near- and far-offsets of 0.5 and 119.5 m, respectively. In such areas with near-surface contaminants, a detailed subsurface characterization of the vadose zone hydraulic parameters is very important. Indeed, an inexpensive method of deriving such parameters by the use of seismic reflection surveys is beneficial, and our approach uses the relationship between seismic velocity and hydrogeological parameters together with empirical observations relating porosity to permeability and hydraulic conductivity. Shear wave velocity ( V s ) profiles were estimated from surface wave dispersion analysis of the seismic reflection data and were subsequently used to derive hydraulic parameters such as porosity, permeability, and hydraulic conductivity. Additional geophysical data including core samples, vertical seismic profiling, surface electrical resistivity tomography, natural gamma and electrical resistivity logs allowed for a robust assessment of the validity and geological significance of the estimated V s and hydrogeological models. The results demonstrate the usefulness of this approach for the upper 15 m of shallow unconsolidated sediments even though the survey design parameters were not optimal for surface wave analysis due to the higher than desired frequency geophones.
Enhancement of disposal efficiency for deep geological repositories based on three design factors - Decay heat optimization, increased thermal limit of the buffer and double-layer concept
This study investigates the enhancement of disposal efficiency for deep geological repositories (DGRs) based on three design factors: decay heat optimization, increased thermal limit of the buffer, and double-layer concept using coupled thermo-hydro-mechanical (THM) numerical simulations. Decay heat optimization is achieved by iteratively emplacing spent nuclear fuels having the maximum and minimum decay heat in a canister. Disposal areas can be reduced by 20 % to 40 % compared to the current reference disposal system in Korea (KRS+) in accordance with the combinations of the three design factors, alleviating challenges in site selection for the DGR. This study additionally identifies an optimal layer spacing of 500 m for the double-layer concept in the viewpoint of the buffer temperature, where thermal interaction between the upper and lower layers nearly disappears. However, determining the ultimate disposal and layer spacing requires engineering judgement, considering not only the thermal performance of the DGR but also various factors such as cost and difficulties of the construction and rock mass stability. DGRs designed with an increased thermal limit of the buffer poses a greater probability of rock mass failure around disposal tunnels and deposition holes due to elevated thermal stresses. Densely arranged heat sources for the DGRs with enhanced disposal efficiency lead to larger temperature increase even at the far-field scale, raising a possibility of thermally driven fracture shear activation with associated hydraulic, mechanical, and seismic changes.
Rapid Flux Phenotyping to Accelerate Metabolic Engineering of Cyanobacteria
This project established a rapid flux phenotyping platform to accelerate metabolic engineering of cyanobacterial hosts. As proof of principle, we applied this platform to optimize cyanobacterial production of isobutyraldehyde and ethylene in Synechococcus PCC 7942, as well as lysine and fatty acids in the fast-growing strain S ynechococcus PCC 7002. By matching the throughput of strain characterization to the rate of strain generation, this research provided the foundation for a rational “design-build-test-learn” cycle for metabolic engineering of cyanobacteria and other bioenergy-relevant microbes.
Active and machine learning-based approaches to rapidly enhance microbial chemical production
In order to make renewable fuels and chemicals from microbes, new methods are required to engineer microbes more intelligently. Computational approaches, to engineer strains for enhanced chemical production typically rely on detailed mechanistic models (e.g., kinetic/stoichiometric models of metabolism)—requiring many experimental datasets for their parameterization—while experimental methods may require screening large mutant libraries to explore the design space for the few mutants with desired behaviors. To address these limitations, we developed an active and machine learning approach (ActiveOpt) to intelligently guide experiments to arrive at an optimal phenotype with minimal measured datasets. In this study, ActiveOpt was applied to two separate case studies to evaluate its potential to increase valine yields and neurosporene productivity in Escherichia coli. In both the cases, ActiveOpt identified the best performing strain in fewer experiments than the case studies used. This work demonstrates that machine and active learning approaches have the potential to greatly facilitate metabolic engineering efforts to rapidly achieve its objectives.