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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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At least 37 records · Page 2

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

Computationally-driven discovery of second harmonic generation in EuBa 3 (B 3 O 6 ) 3 through inversion symmetry breaking

Nonlinear optical (NLO) crystals with superior properties are significant for advancing laser technologies and applications. Introducing rare earth metals to borates is a promising and effective way to modify the electronic structure of a crystal to improve its optical properties in the visible and ultraviolet range. In this work, we computationally discover inversion symmetry breaking in EuBa 3 (B 3 O 6 ) 3 , which was previously identified as centric, and demonstrate noncentrosymmetry via synthesizing single crystals for the first time by the floating zone method. We determine the correct space group to be P 6¯. The material has a large direct bandgap of 5.56 eV and is transparent down to 250 nm. The complete anisotropic linear and nonlinear optical properties were also investigated with a d 11 of ∼0.52 pm/V for optical second harmonic generation. Further, it is Type I and Type II phase matchable. This work suggests that rare earth metal borates are an excellent crystal family for exploring future deep ultraviolet (DUV) NLO crystals. It also highlights how first principles computations combined with experiments can be used to identify noncentrosymmetric materials that have been wrongly assigned to be centrosymmetric.

He, Jingyang (ORCID:0000000238863659)↗

Discovery of Extended Tidal Tails around the Globular Cluster Palomar 13

We use photometry from the DECam Legacy Survey to detect candidate tidal tails extending ~5° on either side of the Palomar 13 globular cluster. The tails are aligned with the proper motion of Palomar 13 and are consistent with its old, metal-poor stellar population. We identify three RR Lyrae stars (RRLs) that are plausibly associated with the tails, in addition to four previously known in the cluster. From these RRLs, we find that the mean distance to the cluster and tails is 23.6 ± 0.2 kpc and estimate the total (initial) luminosity of the cluster to be , consistent with previous claims that its initial luminosity was higher than its current luminosity. Combined with previously determined proper motion and radial velocity measurements of the cluster, we find that Palomar 13 is on a highly eccentric orbit (e ~ 0.8) with a pericenter of ~9 kpc and an apocenter of ~69 kpc, and a recent pericentric passage of the cluster ~75 Myr ago. We note a prominent linear structure in the interstellar dust map that runs parallel to the candidate tidal features, but conclude that reddening due to dust is unlikely to account for the structure that we observe. If confirmed, the Palomar 13 stellar stream would be one of very few streams with a known progenitor system, making it uniquely powerful for studying the disruption of globular clusters, the formation of the stellar halo, and the distribution of matter within our Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗

Space‐Time Causal Discovery in Earth System Science: A Local Stencil Learning Approach

Causal discovery tools enable scientists to infer meaningful relationships from observational data, spurring advances in fields as diverse as biology, economics, and climate science. Despite these successes, the application of causal discovery to space-time systems remains immensely challenging due to the high-dimensional nature of the data. For example, in climate sciences, modern observational temperature records over the past few decades regularly measure thousands of locations around the globe. To address these challenges, we introduce Causal Space-Time Stencil Learning (CaStLe), a novel meta-algorithm for discovering causal structures in complex space-time systems. CaStLe leverages regularities in local space-time dependencies to learn governing global dynamics. This local perspective eliminates spurious confounding and drastically reduces sample complexity, making space-time causal discovery practical and effective. For causal discovery, CaStLe flexibly accepts any appropriately adapted time series causal discovery algorithm to recover local causal structures. These advances enable causal discovery of geophysical phenomena that were previously unapproachable, including non-periodic, transient phenomena such as volcanic eruption plumes. Regularities in local space-time dependencies are transformed into informative spatial replicates, which actually improve CaStLe's performance when applied to ever-larger spatial grids. We successfully apply CaStLe to discover the atmospheric dynamics governing the climate response to the 1991 Mount Pinatubo volcanic eruption. We provide validation experiments to demonstrate the effectiveness of CaStLe over existing causal-discovery frameworks on a range of geophysics-inspired benchmarks while identifying the method's limitations and domains where its assumptions may not hold.

Nichol, J. Jake [Univ. of New Mexico, Albuquerque,↗

A perspective on Bayesian methods applied to materials discovery and design

For more than two decades, there has been increasing interest in developing frameworks for the accelerated discovery and design of novel materials that could enable promising and transformative technologies. The Integrated Computational Materials Engineering (ICME) program called for integrating computational tools to establish linkages along process-structure-property-performance (PSPP) chains. The Materials Genome Initiative called for integrating experiments and computations within data science frameworks as a strategy to accelerate the materials development cycle. While these frameworks and paradigms have been quite influential, traditional ICME or data science-based approaches tend to have some limitations, mainly when querying the materials space is costly and very little information is available. Bayesian methods are more suitable in this context due to their efficiency gains. To this end, the materials discovery problem is framed as a Bayesian Optimization (BO). Different examples in which BO has been applied to solve materials discovery problems are presented. The methods/examples discussed include BO under model uncertainty, multi-information source BO, multi-objective and multi-constraint BO, and batch BO. Bayesian Materials Discovery is a promising area of research that is likely to become more influential as more attention is put on autonomous materials discovery platforms. Therefore, a discussion is provided on the potential development of such methods to increase the ability of existing platforms in materials discovery. Here, the ultimate goal is to pave the way to autonomous materials discovery.

36 MATERIALS SCIENCE↗

Accelerating Computational Materials Discovery with Machine Learning and Cloud High-Performance Computing: from Large-Scale Screening to Experimental Validation

High-throughput computational materials discovery has promised significant acceleration of the design and discovery of new materials for many years. Despite a surge in interest and activity, the constraints imposed by large-scale computational resources present a significant bottleneck. Furthermore, examples of large-scale computational discovery carried through experimental validation remain scarce, especially for materials with product applicability. In this paper, we demonstrate how this vision became reality by first combining state-of-the-art artificial intelligence (AI) models and traditional physics-based models on cloud high performance computing (HPC) resources to quickly navigate through more than 32 million candidates and predict around half a million potentially stable materials. Focusing on solid-state electrolytes for battery applications, our discovery pipeline further identified 18 promising candidates with new compositions and rediscovered a decade’s worth of collective knowledge in the field as a byproduct. By employing around one thousand virtual machines in the cloud, this process took less than 80 hours. We then synthesized and experimentally characterized the structures and conductivities of our top candidates, the Na x Li 3-x YCl 6 (0.5 ≤ x ≤ 2.5) series, demonstrating the potential of these compounds to serve as solid electrolytes. Additional candidate materials are currently under experimental investigation that could offer more examples of the computational discovery of new phases of Li- and Na-conducting solid electrolytes. We believe this unprecedented approach of synergistically integrating AI models and cloud HPC not only accelerates materials discovery but also showcases the potency of AI-guided experimentation in unlocking transformative scientific breakthroughs with real-world applications.

36 MATERIALS SCIENCE↗

Explaining and predicting human behavior and social dynamics in simulated virtual worlds: reproducibility, generalizability, and robustness of causal discovery methods

Ground Truth program was designed to evaluate social science modeling approaches using simulation test beds with ground truth intentionally and systematically embedded to understand and model complex Human Domain systems and their dynamics Lazer et al. (Science 369:1060–1062, 2020). Our multidisciplinary team of data scientists, statisticians, experts in Artificial Intelligence (AI) and visual analytics had a unique role on the program to investigate accuracy, reproducibility, generalizability, and robustness of the state-of-the-art (SOTA) causal structure learning approaches applied to fully observed and sampled simulated data across virtual worlds. In addition, we analyzed the feasibility of using machine learning models to predict future social behavior with and without causal knowledge explicitly embedded. In this paper, we first present our causal modeling approach to discover the causal structure of four virtual worlds produced by the simulation teams—Urban Life, Financial Governance, Disaster and Geopolitical Conflict. Our approach adapts the state-of-the-art causal discovery (including ensemble models), machine learning, data analytics, and visualization techniques to allow a human-machine team to reverse-engineer the true causal relations from sampled and fully observed data. We next present our reproducibility analysis of two research methods team’s performance using a range of causal discovery models applied to both sampled and fully observed data, and analyze their effectiveness and limitations. We further investigate the generalizability and robustness to sampling of the SOTA causal discovery approaches on additional simulated datasets with known ground truth. Our results reveal the limitations of existing causal modeling approaches when applied to large-scale, noisy, high-dimensional data with unobserved variables and unknown relationships between them. We show that the SOTA causal models explored in our experiments are not designed to take advantage from vasts amounts of data and have difficulty recovering ground truth when latent confounders are present; they do not generalize well across simulation scenarios and are not robust to sampling; they are vulnerable to data and modeling assumptions, and therefore, the results are hard to reproduce. Finally, when we outline lessons learned and provide recommendations to improve models for causal discovery and prediction of human social behavior from observational data, we highlight the importance of learning data to knowledge representations or transformations to improve causal discovery and describe the benefit of causal feature selection for predictive and prescriptive modeling.

97 MATHEMATICS AND COMPUTING↗

Accelerating scientific discoveries through data-driven innovations

Developing artificial intelligence (AI) and machine learning (ML) methods that can accelerate scientific discoveries and advance science has become one of the important research directions for the AI/ML research community. It has been gaining increasing attention from researchers in diverse scientific areas, including biomedical science, materials science, climate science, physics, chemistry, and many others. Data-driven AI/ML innovations to enable reliable predictions and optimal decision making for scientific discoveries face several critical challenges, among which are high system complexity, large search space, incomplete knowledge, and small data, all of which demand novel strategies to effectively address them. Meeting these challenges and thereby accelerating scientific discoveries and industrial innovations, calls for research that can take full advantage of the latest advances in AI/ML to integrate data-driven techniques with scientific knowledge and is able to execute them in modern high-performance computing (HPC) environments at scale. This Patterns special collection "Accelerating scientific discoveries through data-driven innovations" features articles that showcase the promising roles of AI/ML and data-driven modeling in accelerating scientific discoveries and may inspire the next wave of data-driven innovations in various scientific domains.

97 MATHEMATICS AND COMPUTING↗

Drug discovery efforts at George Mason University

With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Computational catalyst discovery: Active classification through myopic multiscale sampling

We report the recent boom in computational chemistry has enabled several projects aimed at discovering useful materials or catalysts. We acknowledge and address two recurring issues in the field of computational catalyst discovery. First, calculating macro-scale catalyst properties is not straightforward when using ensembles of atomic-scale calculations [e.g., density functional theory (DFT)]. We attempt to address this issue by creating a multi-scale model that estimates bulk catalyst activity using adsorption energy predictions from both DFT and machine learning models. The second issue is that many catalyst discovery efforts seek to optimize catalyst properties, but optimization is an inherently exploitative objective that is in tension with the explorative nature of early-stage discovery projects. In other words, why invest so much time finding a “best” catalyst when it is likely to fail for some other, unforeseen problem? We address this issue by relaxing the catalyst discovery goal into a classification problem: “What is the set of catalysts that is worth testing experimentally?” Here, we present a catalyst discovery method called myopic multiscale sampling, which combines multiscale modeling with automated selection of DFT calculations. It is an active classification strategy that seeks to classify catalysts as “worth investigating” or “not worth investigating” experimentally. Our results show an ~7–16 times speedup in catalyst classification relative to random sampling. These results were based on offline simulations of our algorithm on two different datasets: a larger, synthesized dataset and a smaller, real dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1

The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM (“SAR by X-ray Poses Quickly”) platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or “undruggable” targets, allows for (i) hit generation; (ii) the mapping of protein–ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.

59 BASIC BIOLOGICAL SCIENCES↗

Hierarchical Gaussian process-based Bayesian optimization for materials discovery in high entropy alloy spaces

Bayesian optimization (BO) is a powerful and data-efficient method for iterative materials discovery and design, particularly valuable when prior knowledge is limited, underlying functional relationships are complex or unknown, and the cost of querying the materials space is significant. Traditional BO methodologies typically utilize conventional Gaussian Processes (cGPs) to model the relationships between material inputs and properties, as well as correlations within the input space. However, cGP-BO approaches often fall short in multi-objective optimization scenarios, where they are unable to fully exploit correlations between distinct material properties. Leveraging these correlations can significantly enhance the discovery process, as information about one property can inform and improve predictions about others. Here, this study addresses this limitation by employing advanced kernel structures to capture and model multi-dimensional property correlations through multi-task (MTGPs) or deep Gaussian Processes (DGPs), thus accelerating the discovery process. We demonstrate the effectiveness of MTGP-BO and DGP-BO in rapidly and robustly solving complex materials design challenges that occur within the context of complex multi-objective optimization over FCC FeCrNiCoCu high entropy alloy (HEA) spaces, where traditional cGP-BO approaches fail. Furthermore, we highlight how the differential costs associated with querying various material properties can be strategically leveraged to make the materials discovery process more cost-efficient.

36 MATERIALS SCIENCE↗

Mass Spectrometry-Based Approaches for Clinical Biomarker Discovery in Traumatic Brain Injury

Purpose of Review: Precision treatments to address the multifaceted pathophysiology of traumatic brain injury (TBI) are desperately needed, which has led to the intense study of fluid-based protein biomarkers in TBI. Mass Spectrometry (MS) is increasingly being applied to biomarker discovery and quantification in neurological disease to explore the proteome, allowing for more flexibility in biomarker discovery than commonly encountered antibody-based assays. In this narrative review, we will provide specific examples of how MS technology has advanced translational research in traumatic brain injury (TBI) focusing on clinical studies, and looking ahead to promising emerging applications of MS to the field of Neurocritical Care. Recent Findings: Proteomic biomarker discovery using MS technology in human subjects has included the full range of injury severity in TBI, though critically ill patients can offer more options to biofluids given the need for invasive monitoring. Blood, urine, cerebrospinal fluid, brain specimens, and cerebral extracellular fluid have all been sources for analysis. Emerging evidence suggests there are distinct proteomic profiles in radiographic TBI subtypes, and that biomarkers may be used to distinguish patients sustaining TBI from healthy controls. Metabolomics may offer a window into the perturbations of ongoing cerebral insults in critically ill patients after severe TBI. Summary: Emerging MS technologies may offer biomarker discovery and validation opportunities not afforded by conventional means due to its ability to handle the complexities associated with the proteome. In conclusion, while MS techniques are relatively early in development in the neurosciences space, the potential applications to TBI and neurocritical care are likely to accelerate in the coming decade.

59 BASIC BIOLOGICAL SCIENCES↗

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On-the-fly closed-loop materials discovery via Bayesian active learning

Active learning—the field of machine learning (ML) dedicated to optimal experiment design—has played a part in science as far back as the 18th century when Laplace used it to guide his discovery of celestial mechanics. In this work, we focus a closed-loop, active learning-driven autonomous system on another major challenge, the discovery of advanced materials against the exceedingly complex synthesis-processes-structure-property landscape. We demonstrate an autonomous materials discovery methodology for functional inorganic compounds which allow scientists to fail smarter, learn faster, and spend less resources in their studies, while simultaneously improving trust in scientific results and machine learning tools. This robot science enables science-over-the-network, reducing the economic impact of scientists being physically separated from their labs. The real-time closed-loop, autonomous system for materials exploration and optimization (CAMEO) is implemented at the synchrotron beamline to accelerate the interconnected tasks of phase mapping and property optimization, with each cycle taking seconds to minutes. We also demonstrate an embodiment of human-machine interaction, where human-in-the-loop is called to play a contributing role within each cycle. This work has resulted in the discovery of a novel epitaxial nanocomposite phase-change memory material.

36 MATERIALS SCIENCE↗

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.

Biosensors↗

Discovery of chalcogenides structures and compositions using mixed fluxes

Advancements in many modern technologies rely on the continuous need for materials discovery. However, the design of synthesis routes leading to new and targeted solid-state materials requires understanding of reactivity patterns. Advances in synthesis science are necessary to increase efficiency and accelerate materials discovery. We present a highly effective methodology for the rational discovery of materials using high-temperature solutions or fluxes having tunable solubility. This methodology facilitates product selection by projecting the free-energy landscape into real synthetic variables: temperature and flux ratio. We demonstrate the effectiveness of this technique by synthesizing compounds in the chalcogenide system of A(Ba)-Cu-Q(O) (Q = S or Se; A = Na, K or Rb) using mixed AOH/AX (A = Li, Na, K or Rb; X = Cl or I) fluxes. We present 30 unreported compounds or compositions, including more than ten unique structural types, by systematically varying the temperature and flux ratios without requiring changing the proportions of starting materials. Additionally, we found that the structural dimensionality of the compounds decreases with increasing reactant solubility and temperature. This methodology serves as an effective general strategy for the rational discovery of inorganic solids.

36 MATERIALS SCIENCE↗