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DOE OSTI2020

A substantial role of soil erosion in the land carbon sink and its future changes

Realistic representation of land carbon sink in climate models is vital for predicting carbon climate feedbacks in a changing world. Although soil erosion that removes land organic carbon has increased substantially since the onset of agriculture, it is rarely included in the current generation of climate models. Using an Earth system model with soil erosion represented, we estimated that on average soil erosion displaces 5% of newly fixed land organic carbon downslope annually in the continental US. In the lower Mississippi river basin and the Cascades, the fraction can be as large as 40%. About 12% of the eroded organic carbon is eventually exported to inland waters, which is equal to 14% of the simulated net carbon gain by terrestrial ecosystems. By comparing the eroded organic carbon export to rivers with the particulate organic carbon export to oceans, we demonstrated that a large fraction of the carbon export to rivers could have been mineralized in inland waters. Importantly, with a direct comparison of eroded and exported soil organic carbon and land net carbon uptake, we found that Earth system models that ignore soil erosion likely offset the erosional carbon loss by increasing heterotrophic respiration implicitly. But as soil erosion and heterotrophic respiration respond differently to a warming climate, this unrealistic compensation would lead to biased predictions of future land carbon sink.

Tan, Zeli↗

DOE OSTI2020

Terrestrial radiative cooling: Using the cold universe as a renewable and sustainable energy source

Photonic materials designed at wavelength scales have enabled a range of emerging energy technologies, from solid-state lighting to efficient photovoltaics that have transformed global energy landscapes. Daytime passive radiative cooling materials shed heat from the ground to the cold universe by taking advantage of the terrestrial thermal radiation that is as large as the renewable solar energy. Newly developed photonic materials permit subambient cooling under direct sunshine, and their applications are expanding rapidly enabled by scalable manufacturing. We review here the recent advancement of daytime subambient radiative cooling materials, which allow energy-efficient cooling and are paving the way toward technologies that harvest the coldness from the universe as a new renewable energy source.

Science & Technology - Other Topics↗

DOE OSTI2021

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2

Targeting the main protease of SARS-CoV-2 Inside host cells, the RNA genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is translated into two polyproteins that are cleaved to give the individual viral proteins. The main viral protease, known as Mpro or 3CLpro, plays a key role in these cleavages, making it an important drug target. Drayman et al . identified eight drugs that target 3CLpro from a library of 1900 clinically safe drugs. Because of the challenge of working with SARS-CoV-2, they started by screening for drugs that inhibit the replication of a human coronavirus that causes the common cold. They then evaluated the top hits for inhibiting SARS-CoV-2 replication and for inhibiting 3CLpro. Masitinib, a broad antiviral, inhibited the main proteases of coronaviruses and picornaviruses and was effective in reducing SARS-CoV-2 replication in mice.

Drayman, Nir↗

DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

DOE OSTI2021

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗

DOE OSTI2021

Double band inversion in the topological phase transition of Ge 1-x Sn x alloys

Abstract We use first-principles simulation and alchemical mixing approximation to reveal the unique double band inversion and topological phase transition in Ge Sn alloys. Wave function parity, spatial charge distribution and surface state spectrum analyses suggest that the band inversion in Ge Sn is relayed by its first valence band. As the system evolves from Ge to -Sn, its conduction band moves down, and inverts with the first and the second valence bands consecutively. The first band inversion makes the system nontrivial, while the second one does not change the topological invariant of the system. Both of the band inversions yield surface modes spanning the individual inverted gaps, but only the surface mode in the upper gap associates with the nontrivial nature of tensile-strained -Sn.

Physics↗

DOE OSTI2026

Data for An End-to-End Pipeline for Succinic Acid Production at an Industrially Relevant Scale Using Issatchenkia orientalis

Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

Metabolomics↗

DOE OSTI2026

Data for Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5-Aminolevulinic Acid Production

Biological production of 5‐aminolevulinic acid (5‐ALA) has received growing attentionover theyears.However, thereis the tradeoff between 5‐ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5‐ALA. To address this limitation, we engineered an acid‐tolerant yeast, Issatchenkia orientalis SD108, for 5‐ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5‐ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5‐ALA was improved from 28mg/L to 120‐, 150‐, and 300mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5‐ALA to 510mg/L, a 13‐fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid‐tolerant I. orientalis SD108ΔPDC has a high potential for 5‐ALA production at a large scale in the future.

Bioproducts↗

DOE OSTI2026

Data for High Yield Production of 3-Hydroxypropionic Acid Using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Bioproducts↗

DOE OSTI2020

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

TESS Hunt for Young and Maturing Exoplanets (THYME). IV. Three Small Planets Orbiting a 120 Myr Old Star in the Pisces–Eridanus Stream

Young exoplanets can offer insight into the evolution of planetary atmospheres, compositions, and architectures. We present the discovery of the young planetary system TOI 451 (TIC 257605131, Gaia DR2 4844691297067063424). TOI 451 is a member of the 120 Myr old Pisces–Eridanus stream (Psc–Eri). We confirm membership in the stream with its kinematics, its lithium abundance, and the rotation and UV excesses of both TOI 451 and its wide-binary companion, TOI 451 B (itself likely an M-dwarf binary). We identified three candidate planets transiting in the Transiting Exoplanet Survey Satellite data and followed up the signals with photometry from Spitzer and ground-based telescopes. The system comprises three validated planets at periods of 1.9, 9.2, and 16 days, with radii of 1.9, 3.1, and 4.1 R {sub ⨂}, respectively. The host star is near-solar mass with V = 11.0 and H = 9.3 and displays an infrared excess indicative of a debris disk. The planets offer excellent prospects for transmission spectroscopy with the Hubble Space Telescope and the James Webb Space Telescope, providing the opportunity to study planetary atmospheres that may still be in the process of evolving.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Physical Yukawa couplings in heterotic string compactifications

One of the challenges of heterotic compactification on a CalabiYau threefold is to determine the physical (27) 3 Yukawa couplings of the resulting four-dimensional $\mathcal{N}$ = 1 theory. In general, the calculation necessitates knowledge of the Ricci-flat metric. However, in the standard embedding, which references the tangent bundle, we can compute normalized Yukawa couplings from the Weil-Petersson metric on the moduli space of complex structure deformations of the Calabi-Yau manifold. In various examples (the Fermat quintic, the intersection of two cubics in $\mathbb{P}$ 5 , and the TianYau manifold), we calculate the normalized Yukawa couplings for (2,1)-forms using the Weil-Petersson metric obtained from the Kodaira-Spencer map. In cases where $h^{1,1}$ = 1 , this is compared to a complementary calculation based on performing period integrals. A third expression for the normalized Yukawa couplings is obtained from a machine learned approximate Ricci-flat metric making use of explicit harmonic representatives. Finally, the excellent agreement between the different approaches opens the door to precision string phenomenology.

Butbaia, Giorgi↗

DOE OSTI2022

The first crystal structure of a xylobiose-bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase family 30, subfamily 10

Xylobiose is a prebiotic sugar that has applications in functional foods. This report describes the first X-ray crystallographic structure models of apo and xylobiose-bound forms of a xylobiohydrolase (XBH) from Acetivibrio clariflavus. This xylan-active enzyme, a member of the recently described glycoside hydrolase family 30 (GH30), subfamily 10, phylogenetic clade has been shown to strictly release xylobiose as its primary hydrolysis product. Inspection of the apo structure reveals a glycone region X-2-binding slot. When X-2 binds, the non-reducing xylose in the -2 subsite is highly coordinated with numerous hydrogen bond contacts while contacts in the -1 subsite mostly reflect interactions typical for GH30 and enzymes in clan A of the carbohydrate-active enzymes database (CAZy). This structure provides an explanation for the high functional specificity of this new bacterial GH30 XBH subfamily.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Chapter 14: Sustainable Biomass Conversion Process Assessment

Process intensification and integration for sustainable design play an essential role in addressing and alleviating severe sustainable development challenges. It is prudent to evaluate a process design in its early stage development to ensure the process can achieve sustainability goals. The primary goal of a sustainability evaluation is to assess the impact of systems on areas sought to be protected and maintained over time, such as human well-being and ecosystems (Schaubroeck, T. and Rugani, B. (2017). A revision of what life cycle sustainability assessment should entail: towards modeling the net impact on human well-being. Journal of Industrial Ecology 21 (6): 1464-1477). Parenthetically, sustainable process design to convert biomass to fuels and chemicals plays an integral part in the bioeconomy sustainability. It is recognized that the integration of sustainability in process design is core to the mission in developing renewable fuels and should be considered a necessary practice in biorefinery design. This study demonstrates the use of Gauging Reaction Effectiveness for ENvironmental Sustainability of Chemistries with a multi-Objective Process Evaluator (GREENSCOPE) as a tool to help track progress on process sustainability performance attributed to conversion improvement. With the incorporation of a wide range of indicators, GREENSCOPE captures the multi-dimensional aspect of the process design and operation. As opposed to conventional techno-economic analysis and life cycle assessment (in which the focuses are limited to economic and environmental aspects), GREENSCOPE enables the consideration of process intensification and integration for sustainable design. A high-octane gasoline production from woody biomass feedstock is used as a case study to demonstrate the approach.

biomass↗

DOE OSTI2022

Radio-Frequency Rapid Thermal Processing Enabling Spatial Phase Transformation and Nanocrystallization of Soft Magnetic Amorphous Alloys

Thermal processing of soft magnetic amorphous and nanocrystalline alloys is explored under the influence of radio-frequency induction-heating techniques. Direct induction-heating concepts based on longitudinal and transverse flux heating are examined and the details of electromagnetic fields interaction with metallic strips are discussed by analytical calculations as well as finite element analysis. Initial experimental results confirming spatial control of phase transformations and nanocrystallization within a single strip of Finemet Fe-based amorphous ribbons are reported. Here, the degree to which primary and secondary crystallization temperature are achieved depends on the spacing between the ribbon relative to the induction coil as well as the coil design and configuration. For transverse coil configurations, the local temperature and therefore microstructural evolution is different across the lateral dimension of processed ribbons, with reduced gap sizes producing enhanced peak temperatures and larger temperature distributions with greater spatial variation in microstructure. In addition, indirect susceptor-based induction heating under tension is performed and the impact of microstructure is demonstrated. Herein, potential for exploiting spatially optimized phase transformations is illustrated through electromagnetic field–assisted processing in a scalable manufacturing process with amorphous and nanocrystalline soft magnetic alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Half‐Fused Diketopyrrolopyrrole‐Based Conjugated Donor–Acceptor Polymer for Ambipolar Field‐Effect Transistors

Abstract A novel building block, denoted as half‐fused diketopyrrolopyrrole (DPP) (9‐(3‐octadecylhenicosyl)‐8‐(thiophen‐2‐yl)‐7 H ‐pyrrolo[3,4‐ a ]thieno[3,2‐ g ]indolizine‐7,10(9 H )‐dione), in which one of the flanking thiophene units is fused to one of the DPP rings via a carbon‐carbon double bond at the N‐position is reported. The half‐fused DPP is successfully utilized as an electron acceptor to prepare the conjugated donor–acceptor polymer PTFDFT , which exhibits ambipolar semiconducting behavior in ambient air. Theoretical calculations and absorption spectral studies show that the backbone of PTFDFT is more planar compared to the reference polymer with conventional DPP units. As a result, PTFDFT shows a narrow bandgap and low lowest unoccupied molecular orbital level. The more planar backbone with fewer side chains favors the dense packing of the polymer chains of PTFDFT with a short π–π stacking distance (3.49 Å). Grazing‐incidence wide‐angle X‐ray scattering data further confirm the predominant edge‐on packing mode of the PTFDFT polymer chains on the substrate. As expected, the PTFDFT thin film shows excellent ambipolar semiconducting properties under ambient conditions, reaching 2.23 and 1.08 cm 2 V −1 s −1 for the n‐ and p‐channels, respectively. In addition, complementary‐like inverter with gain value as high as 141 is successfully constructed using the PTFDFT thin film.

Shi, Dandan↗

DOE OSTI2020

Observation of Unconventional Dynamics of Domain Walls in Uniaxial Ferroelectric Lead Germanate

Application of scanning probe microscopy techniques such as piezoresponse force microscopy (PFM) opens the possibility to re-visit the ferroelectrics previously studied by the macroscopic electrical testing methods and establish a link between their local nanoscale characteristics and integral response. It is reported that the nanoscale PFM studies and phase-field modeling of the static and dynamic behavior of the domain structure in the well-known ferroelectric material lead germanate Pb 5 Ge 3 O 11 . Here, several unusual phenomena are revealed: 1) domain formation during the paraelectric-to-ferroelectric phase transition, which exhibits an atypical cooling rate dependence; 2) unexpected electrically induced formation of the oblate domains due to the preferential domain walls motion in the directions perpendicular to the polar axis, contrary to the typical domain growth behavior observed so far; 3) absence of the bound charges at the 180 degrees head-to-head (H-H) and tail-totail (T-T) domain walls, which typically exhibit a significant charge density in other ferroelectrics due to the polarization discontinuity. This strikingly different behavior is rationalized by the phase field modeling of the dynamics of uncharged H-H and T-T domain walls. The results provide a new insight into the emergent physics of the ferroelectric domain boundaries, revealing unusual properties not exhibited by conventional Ising-type walls.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Fibril Network Strategy Enables High‐Performance Semitransparent Organic Solar Cells

Abstract The development of semitransparent organic solar cells (ST‐OSCs) represents a significant step toward the commercialization of OSCs. However, the trade‐off between power conversion efficiency (PCE) and average visible transmittance (AVT) restricts further improvements of ST‐OSCs. Herein, it is demonstrated that a fibril network strategy can enable ST‐OSCs with a high PCE and AVT simultaneously. A wide‐bandgap polymer PBT1‐C‐2Cl that can self‐assemble into a fibril nanostructure is used as the donor and a near‐infrared small molecule Y6 is adopted as the acceptor. It is found that a tiny amount of PBT1‐C‐2Cl in the blend can form a high speed pathway for hole transport due to the well distributed fibril nanostructure, which increases the transmittance in the visible region. Meanwhile, the acceptor Y6 guarantees sufficient light absorption. Using this strategy, the optimized ST‐OSCs yield a high PCE of 9.1% with an AVT of over 40% and significant light utilization efficiency of 3.65% at donor/acceptor ratio of 0.25:1. This work demonstrates a simple and effective approach to realizing high PCE and AVT of ST‐OSCs simultaneously.

Xie, Yuanpeng↗