Gene Discovery and Evaluating Phenotypic Impacts of DNA Designs in Sorghum
Sorghum transcriptome variation to study gene discovery and evaluating phenotypic impacts of DNA design.
Genetics↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4 . The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas , land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
59 BASIC BIOLOGICAL SCIENCES↗
Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens
The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS.
59 BASIC BIOLOGICAL SCIENCES↗
Solid-state ionics: The key to the discovery and domination of lithium batteries: some learnings from β-alumina and titanium disulfide
We report solid state ionics, the study of fast ion transport in solids, expanded explosively after the discovery of sodium ion transport in b-alumina 50 years ago and has revolutionized energy storage. Lithium ion batteries have come from a dream with titanium disulfide to enabling the communications revolution and are enabling renewable energy. Much can be learnt from these early studies, that will allow the attainment of a fossil-free society and a sustainable environment.
36 MATERIALS SCIENCE↗
Phase-field-guided design of record-high piezoelectricity and discovery of simultaneous high light transparency and high piezoelectricity in relaxor ferroelectrics
Here, the phase-field method has been extensively applied to predicting the domain structures and their responses to external fields and understanding experimentally observed domain states under different electromechanical conditions in ferroelectric heterostructures. This article highlights the successful examples of phase-field applications in guiding the design of relaxor ferroelectric ceramics and crystals with record-high piezoelectricity and the discovery of simultaneous high light transparency and piezoelectricity of relaxor ferroelectric crystals for a wide range of biomedical, robotics, and optoelectronics applications.
36 MATERIALS SCIENCE↗
Additive manufacturing of high-strength multiphase nanostructures in the binary Ni–Nb system for the discovery of new types of superalloys
Abstract Ni-based superalloys have been studied extensively due to their impressive mechanical properties, including strength and creep resistance at high temperatures. Growing interest surrounding additive manufacturing (AM) methods has led to recent investigations of alloys that are traditionally difficult to process, including Ni-based superalloys. Recent work has shown that AM methods enable high-throughput materials discovery and optimization of difficult- or impractical-to-process alloys, including those with high or even majority refractory element compositions. This work focuses on AM-enabled investigations of composition-dependent mechanical and microstructural properties for Ni–Nb binary alloys. Specifically, we report on the mechanical behavior of compositionally-graded Ni x Nb 1− x and uniform composition Ni 59.5 Nb 40.5 specimens made with AM. The AM fabrication process resulted in extraordinarily high strength, attributed to the formation of a dual-phase microstructure consisting of δ-Ni 3 Nb and µ-Ni 6 Nb 7 intermetallic compounds with nanostructured and multimodal grain size and eutectic lamellar spacing. Graphic Abstract
Jones, M. R.↗
CALPHAD-based Bayesian optimization to accelerate alloy discovery for high-temperature applications
Two crucial properties influencing the performance of high-temperature alloys are coefficient of thermal expansion (CTE) and phase constitution. It is desirable to have alloys with low CTE, which reduces CTE mismatch with the surface oxide and the likelihood of oxide spallation. Reducing the amount of brittle intermetallic phases such as Sigma (σ) enhances alloy ductility and processability. Here, we propose a multi-objective Bayesian Optimization (BO) model to simultaneously minimize CTE (at an operational temperature of 1150 °C) and T σ (temperature when the Sigma phase completely dissolves in the metal matrix), properties which are obtained from high-throughput CALculation of PHAse Diagrams (CALPHAD). The model successfully identifies several alloys with CTE ≤ 2 × 10 –5 /K and T σ ≤ 500 °C by exploring just 7% of the nickel–chromium–cobalt–aluminum–iron (Ni–Cr–Co–Al–Fe) composition space. Such multi-objective alloy design frameworks can be used to inform additive manufacturing experiments and accelerate alloy discovery for high-temperature energy applications.
36 MATERIALS SCIENCE↗
Symmetry relation database and its application to ferroelectric materials discovery
To investigate the displacive phase transition at the atomic scale, we have implemented a numerical algorithm to automate the detection of the symmetry relations between any two candidate crystal structures. Using this algorithm, here we systematically screen all possible polar–nonpolar structure pairs from the Materials Project database and establish a library of ~4500 pairs that can be connected through a continuous phase transition with small atomic displacements. From this database, we identify several new ferroelectric materials. In addition, the database may also be used in other areas, such as material structure prediction and new materials discovery.
36 MATERIALS SCIENCE↗
Discovery of Innovative Polymers for Next-Generation Gas-Separation Membranes using Interpretable Machine Learning
Polymer membranes perform innumerable separations with far-reaching environmental implications. Despite decades of research on membrane technologies, design of new membrane materials remains a largely Edisonian process. To address this shortcoming, we demonstrate a generalizable, accurate machine-learning (ML) implementation for the discovery of innovative polymers with ideal separation performance. Specifically, multitask ML models are trained on available experimental data to link polymer chemistry to gas permeabilities of He, H2, O2, N2, CO2, and CH4. Here, we interpret the ML models and extract chemical heuristics for membrane design, through Shapley Additive exPlanations (SHAP) analysis. We then screen over nine million hypothetical polymers through our models and identify thousands of candidates that lie well above current performance upper bounds. Notably, we discover hundreds of never-before-seen ultrapermeable polymer membranes with O2 and CO2 permeability greater than 104 and 105 Barrer, respectively. These hypothetical polymers are capable of overcoming undesirable trade-off relationship between permeability and selectivity, thus significantly expanding the currently limited library of polymer membranes for highly efficient gas separations. High-fidelity molecular dynamics simulations confirm the ML-predicted gas permeabilities of the promising candidates, which suggests that many can be translated to reality.
Yang, Jason↗
Preshot Report for the NIF Discovery Science DDCyl Campaign: D_Hyd_DDCyl_DRT_DDD/EEE/FFF
The first Discovery Science shot day with the NIF DDCyl campaign demonstrated that Rayleigh-Taylor instability growth during the deceleration phase is scale-invariant for targets that varied in radial dimension and implosion time-scale by a factor of three. Smaller cylindrical implosions at the OMEGA laser facility were compared to the larger cylinders fielded in our first NIF outing. Both sets of targets had an initial m = 20 sinusoidal perturbation machined on the inner surface of an embedded aluminum marker layer, with the amplitude larger by the same factor of three for the NIF-scale targets. We observed growth factors of 14 at late time (t=λ = 7:7 ns, where λ = 1 for OMEGA and λ = 3 for NIF). These used a high density (300 mg/cm³) CH foam core, providing a very long period of deceleration before the rebounding shock hit the incoming spike tips, but the final convergence was only CR≈ 2:25. For our second shot day with this campaign, we are attempting to increase the convergence ratio to CR≥ 5 before reshock, while still measuring instability growth during the convergence/deceleration phase. As discussed in previous reports, the best way to increase convergence before reshock is to lower the density of the central foam. The preshot designs called for the use of a 30 mg/cm³ CH foam, though the as-built foams are closer to 40-42 mg/cm³, which is predicted to result in a final CR≈ 5:1 before reshock. Other than the lower foam density, the target design is identical to those used previously.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
AI Automated Discovery of New Climate Water System Knowledge from Models and Observations
This paper addresses focus area 3, “Insight gleaned from complex data.” Science Challenge: The climate-water system is highly complex, containing a multitude of positive and negative feedbacks, time scales stretching many orders-of-magnitudes, and non-linear, connected processes. Powerful artificial intelligence (AI) methods can revolutionize and automate the discovery of new knowledge and relationships in the climate-water system, which will improve understanding and predictability of extreme hydrological events.
54 ENVIRONMENTAL SCIENCES↗
sCO 2 Brayton Energy Conversion Customer Discovery
All energy production systems need efficient energy conversion systems. Current Rankine cycles use water to generate steam at temperatures where efficiency is limited to around 40%. As existing fossil and nuclear power plants are decommissioned due to end of effective life and/or societies’ desire for cleaner generation options, more efficient energy conversion is needed to keep up with increasing electricity demands. Modern energy generation technologies, such as advanced nuclear reactors and concentrated solar, coupled to high efficiency sCO 2 conversion systems provide a solution to efficient, clean energy systems. Leading R&D communities worldwide agree that the successful development of sCO 2 Brayton power cycle technology will eventually bring about large-scale changes to existing multi-billion-dollar global markets and enable power applications not currently possible or economically justifiable. However, all new technologies face challenges in the path to commercialization and the electricity sector is distinctively risk averse. The Sandia sCO 2 Brayton team needs to better understand what the electricity sector needs in terms of new technology risk mitigation, generation efficiency, reliability improvements above current technology, and cost requirements which would make new technology adoption worthwhile. Relying on the R&D community consensus that a sCO 2 power cycle will increase the revenue of the electrical industry, without addressing the electrical industry’s concerns, significantly decreases the potential for adoption at commercial scale. With a clear understanding of the market perspectives on technology adoption, including military, private sector, and utilities customers, the Sandia Brayton Team can resolve industry concerns for smoother development and faster transition to commercialization. An extensive customer discovery process, similar to that executed through the NSF’s I-Corp program, is necessary in order to understand the pain points of the market and articulate the value proposition of Brayton systems in terms that engage decision makers and facilitate commercialization of the technology.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
White paper on NIF Discovery Science and frontier regimes of HEDP
Over the past two decades, experimental capabilities at high energy density (HED) facilities such as the National Ignition Facility (NIF), Omega, and Omega EP lasers, and the Z pulsed power facility are able to make precision measurements of fundamental quantities such as equations of state (EOS), material phase, opacities, and ionization levels Z. Flow based quantities are also being studied, such as hydrodynamic instabilities, evolution into turbulence, turbulent dynamo magnetic field amplification, magnetic reconnection; plasma instabilities, plasma wakefield particle acceleration; and relativistic plasma phenomena, such as (e + ,e - ) pair creation. Experimental regimes can be created that reproduce conditions relevant to planetary and exoplanet interiors, stellar interiors, the interiors of brown dwarfs, and the envelope conditions of white dwarf stars. Diagnostic techniques have been developed hand in hand with these new experimental regimes that can be accessed. In this white paper, a brief summary of key experimental achievements from the NIF Discovery Science (basic science) program will be presented; followed by a discussion of current challenges, needs, and potential paths forward.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Visualization for Scientific Discovery, Decision-Making, and Communication
Visualization–the use of visual elements to explore data, form hypotheses, or convey conclusions–is an integral part of the scientific process. Starting from an initial exploration of new data to illustrating outcomes to the general public, visualization is one of the most intuitive and powerful modes of communication. With the explosion of new data sources and types, unprecedented volumes of data, and new technologies, such as virtual reality and AI, visualization has become increasingly essential but also ever more challenging. Department of Energy’s (DOE) Office of Advanced Scientific Computing Research (ASCR) sponsored a Basic Research Needs workshop in January 2022 to understand the major opportunities and grand challenges in visualization tools and technologies for scientific computing, with a special focus on DOE-relevant applications and goals. The workshop identified five priority research directions (PRDs) for visualization to support scientific discovery, decision-making, and communication.
97 MATHEMATICS AND COMPUTING↗
A Muon Collider Facility for Physics Discovery
Muon colliders provide a unique route to deliver high energy collisions that enable discovery searches and precision measurements to extend our understanding of the fundamental laws of physics. The muon collider design aims to deliver physics reach at the highest energies with costs, power consumption and on a time scale that may prove favorable relative to other proposed facilities. In this context, a new international collaboration has formed to further extend the design concepts and performance studies of such a machine. This effort is focused on delivering the elements of a $\sim$10 TeV center of mass (CM) energy design to explore the physics energy frontier. The path to such a machine may pass through lower energy options. Currently a 3 TeV CM stage is considered. Other energy stages could also be explored, e.g. an s-channel Higgs Factory operating at 125 GeV CM. We describe the status of the R&D and design effort towards such a machine and lay out a plan to bring these concepts to maturity as a tool for the high energy physics community.
43 PARTICLE ACCELERATORS↗
Synthesis of motif and symmetry for accelerated learning, discovery, and design of electronic structures for energy conversion applications (Final Technical Report)
The overall goal of the projects is to develop a framework to incorporate structure motifs and crystal/orbital symmetries into the data-driven materials discovery infrastructure. The PI proposed to develop structure-motif- and symmetry-based graph convolutional networks for effective learning and efficient predictions of electronic structures and related properties. Fundamental understanding of the roles of structure motif and symmetry will establish new hypothesis and design rules, which will be combined with high-throughput computations based on density functional theory to discover novel light absorbers, transparent conductors, as well as 2D light emitting materials and heterojunctions for optoelectronics.
36 MATERIALS SCIENCE↗
IX Cell Wall Research Conference 2022 (IXCWRC): Cell wall research for new fundamental discoveries and applications in plant biology
This application is for securing funds to offset the registration fees and lodging costs for US-based early career investigators (ERCs) to participate to the IX Cell Wall Research Conference 2022 (IXCWRC 2022): Cell wall research for new fundamental discoveries and applications in plant biology. The conference will be held in East Lansing, Michigan on June 13-17, 2022. The conference will focus on the plant cell wall. Plant cells are encapsulated by the cell wall, a dynamic structure that protects them, enables them to interface with the external environment and supports the growth of the entire organism. There is a growing interest in understanding the complex processes necessary to build and deconstruct the plant cell wall. A better understanding of how the cell wall is synthesized during plant growth and in response to the environment, and how it is deconstructed for a broad variety of applications can inform and improve biotechnological processes for increasing biomass yield and improving industrial processes for the recovery of valuable, sustainable polymers. Acquiring such knowledge requires the exchange of new ideas and results as well as the development and application of new technologies. The IXCWRC 2022 aims to reach this goal by providing an opportunity for an open forum to discuss new ideas and theories and develop collaborations for scientists across the globe in a diverse and supportive environment. A distinction of the IXCWRC 2022 from all the preceding plant cell wall conferences will be its focus on the training and inclusion of the next generation of scientists, the ERCs. The overall goal of this application is to broaden the participation of ERCs with a focus on underrepresented communities. The specific goal of this application is to secure support for registration and lodging for US-based ERCs to attend the conference. Priority will be given to ERCs from underrepresented communities in science. We expect that support from DOE will allow the development of an exciting and innovative program to discuss the latest scientific advances in cell wall biology research, advance the next generation of plant cell wall researchers and foster the foundations of an inclusive community in science.
59 BASIC BIOLOGICAL SCIENCES↗
Accelerated Discovery of Solar Thermochemical Hydrogen Production Materials via High-Throughput Computational and Experimental Methods
In this project, combinatorial synthesis and testing methods were combined with high-throughput materials theory calculations to greatly accelerate the discovery of thermodynamically suitable candidates for green hydrogen production via a two-stage solar thermochemical water splitting (STCH) process. Over the course of the project, more than 8000 quinary and higher oxide compositions were computationally screened for STCH viability, and detailed stability calculations were performed for more than 30 of the most promising identified compositional archetypes. As a result, three new STCH capable compositional families were discovered and experimentally verified. The first, Ce x Sr 2-x MnO 4 (CSM), represents the first known Ruddlesden-Popper compound to show STCH activity, and thus demonstrates that perovskite-related structures may hold promise for this application. The second family, Sr 1-x Ce x MnO 3 (SCM), is the simple perovskite sister-analog to CSM. Sr 0.7 Ce 0.3 MnO 3 (SCM30), a member of this compositional family, was found to produce the highest hydrogen yields of any compound tested in this project, exceeding the end of project milestone target of > 150 μmol H 2 /gram oxide at a reduction temperature of 1350 °C, although only at steam-to-hydrogen ratios greater than 1000:1. Finally, we proved that a third novel Sr-and Mn-containing family, Sr 1-x Ca x Ti 1-y Mn y O 3 (SCTM), which was identified by Materials Project tools, also splits water. The behavior of the SCTM system was found to be similar to the previously discovered Sr 1-x La x Al 1-y Mn y O 3 (SLMA) family, albeit with lower H 2 yields. Across the three thrusts of the project (computational, combinatorial, and bulk testing), five journal articles were published. As part of Program End Analysis and Data Dissemination, relevant data used for the publications was uploaded to the HydroGEN Data Hub for public access, and in certain cases, results were added to public materials databases.
08 HYDROGEN↗