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DOE OSTI2024

High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology (Final Technical Report)

Fatty acids can be produced biosynthetically in microbes and these compounds can serve as precursors to biodiesels and other high value oleochemicals. However, progress on engineering fatty acid biosynthesis, and biofuel synthesis more generally, has been hindered by current quantification methods that are either indirect or not amenable to high-throughput or single-cell resolution screening. In this project, we assembled an interdisciplinary team with complimentary expertise in synthetic biology and microscopy, metabolic engineering, and chemical imaging to address these challenges. We used chemical imaging to directly measure lipid biosynthesis in Escherichia coli engineered to produce fatty acids, obtaining detailed single-cell resolution measurements. We deployed stimulated Raman scattering (SRS) microscopy in concert with multiplexed genome engineering and gene circuit design strategies from synthetic biology to optimize production of fatty acids. These results provided novel insight into cell-to-cell heterogeneity present in biofuel production strains. In addition, we introduced new chemical imaging methods which are label-free and do not require fluorescent reporters. These efforts were complemented by other studied developing foundational tools for regulation and control, which offer excellent potential for advancing researchers’ ability to rapidly design, build, and test strains for enhanced biofuel synthesis.

09 BIOMASS FUELS↗

DOE OSTI2021

Fermi acceleration in relativistic collisionless plasma shocks correlates with anisotropic energy gains

Collisionless shocks generated by two colliding relativistic electron-positron plasma shells are studied using particle-in-cell simulations. Shocks are mediated by the Weibel instability (WI), and the kinetic energy of the fastest accelerated particles is found to be anisotropically modified by WI-induced electric fields. Specifically, we show that all particles interacting with the shock bifurcate into two groups based on their final relativistic Lorentz factor γ: slow (γ < γ bf ) and fast (γ < γ bf ), where γ bf is the bifurcation Lorentz factor that was found to be approximately twice the initial (upstream) Lorentz factor γ0. We have found that the kinetic energies of the slow particles are equally affected by the longitudinal and transverse components of the shock electric field, whereas the fast particles are primarily accelerated by the transverse field component.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Strong reconnection electric fields in shock-driven turbulence

Turbulent magnetic reconnection in a quasi-parallel shock under parameters relevant to the Earth's bow shock is investigated by means of a two-dimensional particle-in-cell simulation. The addressed aspects include the reconnection electric field, the reconnection rate, and the electron and the ion outflow speeds. In the shock transition region, many current sheets are generated in shock-driven turbulence, and electron-only reconnection and reconnection where both ions and electrons are involved can occur in those current sheets. The electron outflow speed in electron-only reconnection shows a positive correlation with the theoretical speed, which is close to the local electron Alfvén speed, and a strong convection electric field is generated by the large electron outflow. As a result, the reconnection electric field becomes much larger than those in the standard magnetopause or magnetotail reconnection. In shock-driven reconnection that involves ion dynamics, both electron outflows and ion outflows can reach of the order of 10 times the Alfvén speed in the X-line rest frame, leading to a reconnection electric field the same order as that in electron-only reconnection. An electron-only reconnection event observed by the magnetospheric multiscale mission downstream of a quasi-parallel shock is qualitatively similar to those in the simulation and shows that the outflow speed reaches approximately half the local electron Alfvén speed, supporting the simulation prediction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Toward the core-edge coupling of delta-f and total-f gyrokinetic models

The coupling of core reduced delta-f and edge total-f gyrokinetic models could enable a significant speed-up of the whole device modeling simulations. It is thus interesting to compare these models in the core where they will be coupled. The main difference between these models is the presence of the zeroth order term on the right-hand side of the total-f gyrokinetic equation. This term is responsible for driving a radial electric field that is also associated with Geodesic acoustic mode-like oscillations. To investigate the coupling between these models, the subsequent large-scale gyrokinetic 3D turbulence simulations have been performed starting from an already saturated gyrokinetic axisymmetric equilibria (collisions are not included). This work has also been extended to couple different axisymmetric and turbulent models available in XGC. It is shown that the radial electric field and its drive have to be taken care of consistently while coupling different models together.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Wide Band Gap Chalcogenide Semiconductors

Wide band gap semiconductors are essential for today’s electronic devices and energy applications because of their high optical transparency, controllable carrier concentration, and tunable electrical conductivity. The most intensively investigated wide band gap semiconductors are transparent conductive oxides (TCOs), such as tin-doped indium oxide (ITO) and amorphous In–Ga–Zn–O (IGZO), used in displays and solar cells, carbides (e.g., SiC) and nitrides (e.g., GaN) used in power electronics, and emerging halides (e.g., γ-CuI) and 2D electronic materials (e.g., graphene) used in various optoelectronic devices. Compared to these prominent materials families, chalcogen-based (Ch = S, Se, Te) wide band gap semiconductors are less heavily investigated but stand out because of their propensity for p-type doping, high mobilities, high valence band positions (i.e., low ionization potentials), and broad applications in electronic devices such as CdTe solar cells. This manuscript provides a review of wide band gap chalcogenide semiconductors. First, we outline general materials design parameters of high performing transparent semiconductors, as well as the theoretical and experimental underpinnings of the corresponding research methods. We proceed to summarize progress in wide band gap (EG > 2 eV) chalcogenide materials—namely, II–VI MCh binaries, CuMCh 2 chalcopyrites, Cu 3 MCh 4 sulvanites, mixed-anion layered CuMCh(O,F), and 2D materials—and discuss computational predictions of potential new candidates in this family, highlighting their optical and electrical properties. Then, we finally review applications—for example, photovoltaic and photoelectrochemical solar cells, transistors, and light emitting diodes—that employ wide band gap chalcogenides as either an active or passive layer. Overall, by examining, categorizing, and discussing prospective directions in wide band gap chalcogenides, this Review aims to inspire continued research on this emerging class of transparent semiconductors and thereby enable future innovations for optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Recent advancements in high performance polymer electrolyte fuel cell electrode fabrication – Novel materials and manufacturing processes

The global effort to introduce polymer electrolyte fuel cells for clean and renewable energy to the market is increasing the demand for high performance, robust and affordable membrane electrode assemblies (MEAs). There is not yet a standard method for large scale production of MEAs, or the methods employed are generally unsatisfactory in terms of quality and performance. A large number of published data of newly developed catalyst and electrolyte materials, claim to improve the state of the art, but are often not fully comparable due to different experimental studies and experimental designs. This article summarizes the trends in material developments and emerging MEA-manufacturing techniques. The materials and techniques are systematically compared in terms of cell performance and scalability. Current and future scientific challenges are identified and analysed based on published findings over the past five years. Finally, the results of the cited papers have been quantitatively compared to each other and to the internal benchmarks used in each cited work to provide a complete picture of the state of the art in PEFC MEA manufacturing.

25 ENERGY STORAGE↗

DOE OSTI2020

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

The co-expression extrapolation (COXEN) method has been successfully used in multiple studies to select genes for predicting the response of tumor cells to a specific drug treatment. Here, we enhance the COXEN method to select genes that are predictive of the efficacies of multiple drugs for building general drug response prediction models that are not specific to a particular drug. The enhanced COXEN method first ranks the genes according to their prediction power for each individual drug and then takes a union of top predictive genes of all the drugs, among which the algorithm further selects genes whose co-expression patterns are well preserved between cancer cases for building prediction models. We apply the proposed method on benchmark in vitro drug screening datasets and compare the performance of prediction models built based on the genes selected by the enhanced COXEN method to that of models built on genes selected by the original COXEN method and randomly picked genes. Models built with the enhanced COXEN method always present a statistically significantly improved prediction performance (adjusted p-value ≤ 0.05). Our results demonstrate the enhanced COXEN method can dramatically increase the power of gene expression data for predicting drug response.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Asymmetric battery having a semi-solid cathode and high energy density anode

Embodiments described herein relate generally to devices, systems and methods of producing high energy density batteries having a semi-solid cathode that is thicker than the anode. An electrochemical cell can include a positive electrode current collector, a negative electrode current collector and an ion-permeable membrane disposed between the positive electrode current collector and the negative electrode current collector. The ion-permeable membrane is spaced a first distance from the positive electrode current collector and at least partially defines a positive electroactive zone. The ion-permeable membrane is spaced a second distance from the negative electrode current collector and at least partially defines a negative electroactive zone. The second distance is less than the first distance. A semi-solid cathode that includes a suspension of an active material and a conductive material in a non-aqueous liquid electrolyte is disposed in the positive electroactive zone, and an anode is disposed in the negative electroactive zone.

Tan, Takahiro↗

DOE OSTI2022

Asymmetric battery having a semi-solid cathode and high energy density anode

Tan, Taison↗

DOE OSTI2021

Transition characteristics and electron kinetics in microhollow cathode discharges

We demonstrate the transition characteristics and electron kinetics of microdischarges in a microgap with a cathode having microstructures using two-dimensional particle-in-cell/Monte Carlo collision (2d3v) simulations. It is found that the microdischarge is inside the hollow cavity at lower pressures, forming microhollow cathode discharges (MHCDs), while the dominant discharge moves outside the cavity at higher pressures, locating above the cathode rectangular protrusion tip. The spatial distributions of the microdischarge parameters (e.g., electric potential and electron density) are presented by capturing the transition characteristics. The electron kinetics of the microdischarges are examined based on the moment analysis of the electron Boltzmann equation. The collisional and non-collisional components of the electron power absorption are decomposed, which were seldomly investigated for microdischarges previously. The results provide fundamental insights into MHCD formation with a structured electrode at varying pressure conditions, which could be beneficial for the design and fabrication of microplasma devices in practical applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Faraday rotation study of plasma bubbles in GeV wakefield accelerators

We visualize plasma bubbles driven by 0.67 PW laser pulses in a plasma of density ne≈5×1017cm−3 by imaging Faraday rotation patterns imprinted on linearly polarized probe pulses of wavelength λpr=1.05 μm and duration τpr=2 or 1 ps that cross the bubble's path at right angles. When the bubble captures and accelerates tens to hundreds of pC of electron charges, we observe two parallel streaks of length cτpr straddling the drive pulse propagation axis, separated by ∼45 μm, in which probe polarization rotates by 0.3° to more than 5° in opposite directions. Accompanying simulations show that they result from Faraday rotation within portions of dense bubble side walls that are pervaded by the azimuthal magnetic field of accelerating electrons during the probe transit across the bubble. Analysis of the width of the streaks shows that quasi-monoenergetic high-energy electrons and trailing lower energy electrons inside the bubble contribute distinguishable portions of the observed signals, and relativistic flow of sheath electrons suppresses Faraday rotation from the rear of the bubble. The results demonstrate favorable scaling of Faraday rotation diagnostics to 40× lower plasma density than previously demonstrated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Investigation of boosted proton energies through proton radiography of target normal sheath acceleration fields in the multi-ps regime

Multi-kilojoule, multi-picosecond short-pulse lasers, such as the National Ignition Facility-Advanced Radiographic Capability laser and the OMEGA-Extended Performance laser, which have been constructed over the last two decades, enable exciting opportunities to produce high-brightness, high-energy laser-driven proton sources for applications in high-energy-density science like proton fast ignition for inertial fusion energy, particle radiography, and materials science studies. Results on these platforms have demonstrated enhanced accelerated proton energies and electron temperatures when compared to established scaling laws. Recent work has developed a new scaling for proton TNSA in the multi-ps regime. However, this new physics in the multi-ps regime motivates the need to understand the origin of the enhancement in proton energies. Toward this goal, here this work presents the first measurements of the TNSA accelerating sheath field in the multi-ps regime for pulse durations of 0.6, 5, and 10 ps. This measurement was achieved by using a separate TNSA proton source to radiograph the spatiotemporal profile of the accelerating sheath that is responsible for proton acceleration. The use of stacked radiochromic film detectors allows for a discrete time profile of the radiographs, thus enabling the measurement of the temporal and spatial evolution of the accelerating field. In performing this measurement, we extract quantities such as the sheath strength as a function of time and pulse duration, which shows that longer pulse durations sustain a stronger electric field for a longer duration when compared to sub-ps laser pulses, which may enable the observed boosted proton energies and proton conversion efficiencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

The distribution-based remapping of the nodal mass and momentum between arbitrary meshes for staggered arbitrary Lagrangian-Eulerian hydrodynamics

We present a new distribution-based remapping of the nodal mass and momentum between arbitrary source (Lagrangian) and arbitrary target (rezoned) meshes for indirect staggered arbitrary Lagrangian-Eulerian hydrodynamics. Here, the method is based on the following ideas: define cell-centered momentum and mass on the source mesh; conservatively remap those cell-centered quantities from source to target meshes; and use local constrained optimization for each cell of the target mesh to conservatively distribute cell mass and momentum to the nodes of the cell. This new method is efficient, conservative, accurate and bounds preserving.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis

Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A Novel and Secure Pseudovirus Reporter System Based Assay for Neutralizing and Enhancing Antibody Assay Against Marburg Virus

Marburg virus (MARV) is one of the principal members of the filovirus family, which can cause fatal hemorrhagic fever in humans. There are currently no prophylactic and therapeutic drugs on the market, and the high pathogenicity and infectivity of MARV make its research highly dependent on biosafety level 4 conditions, severely hindering the development of vaccines and therapies. Therefore, the development of medicines, such as MARV serological diagnosis, vaccines, and therapeutic antibody drugs, urgently needs a safe, convenient, and biosafety level 2 detection method to measure the neutralizing activity of MARV antibodies. To this end, we report a neutralization assay relying on a Rabies virus (RABV) reverse genetic operating system. We constructed infectious clones carrying the eGFP reporter gene and the full length of the original unmodified MARV GP gene. Based on the critical parameters of phylogenetic analysis, recombinant viruses targeting representative strains in the two major MARV lineages were successfully rescued. These pseudoviruses are safe in mice, and their inability to infect cells after being neutralized by antibodies can be visualized under a fluorescence microscope. We tested the system using the neutralizing antibody MR191. MR191 can significantly block the infection of BSR cells with pseudovirus. We compared it with the traditional lentivirus-type pseudovirus system to verify the system’s credibility and obtained the same results as reported in the literature. In general, we have established a safe and visualized method for evaluating the neutralizing activity of MARV antibodies. Compared with traditional methods, it has the advantages of convenient operation, short cycle, and low cost. It is a candidate method that can replace actual viruses for a neutralization assay.

Bi, Jinhao↗

DOE OSTI2021

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

CrossLink: General Overview [Slides]

Problem: Traditional mesh generation approaches are labor intensive and have limited robustness when applied to parametric design exploration and optimization of complex geometries. While automatic mesh generation approaches exist, they tend to generate tetrahedral or mixed-hybrid meshes which are generally unsuitable for physics applications with strong shock waves, thin boundary layers, and strong gradients. In addition, simulations sizes in the billions of cells are becoming more common with traditional mesh generation methods quickly reaching scalability limits. Solution: CrossLink offers a topology-based mesh generation approach with unstructured block-filling methods and a scalable mesh generation engine. In addition, CrossLink incorporates a python-based API for seamless workflow integration and robust repeatability of the geometry handling and mesh generation process. This makes it ideal for parametric design study and optimization of complex geometries. Finally, future versions of CrossLink will offer a parametric mesh capability that optimizes a high-order mesh and enables reconstruction of the final mesh in memory by the physics solver.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

CrossLink: Advancements in Scalable Unstructured Mesh Generation [Slides]

Traditional mesh generation approaches are labor intensive and have limited robustness when applied to parametric design exploration and optimization of complex geometries. While automatic mesh generation approaches exist, they tend to generate tetrahedral or mixed-hybrid meshes which are generally unsuitable for physics applications with strong shock waves, thin boundary layers, and strong gradients. In addition, simulations sizes in the billions of cells are becoming more common with traditional mesh generation methods quickly reaching scalability limits. CrossLink offers a topology-based mesh generation approach with unstructured block-filling methods and a scalable mesh generation engine. In addition, CrossLink incorporates a python based API for seamless workflow integration and robust repeatability of the geometry handling and mesh generation process. This makes it ideal for parametric design study and optimization of complex geometries. Finally, future versions of CrossLink will offer a parametric mesh capability that optimizes a high-order mesh and enables reconstruction of the final mesh in memory by the physics solver.

97 MATHEMATICS AND COMPUTING↗