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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structure of human TRPV4 in complex with GTPase RhoA

Transient receptor potential (TRP) channel TRPV4 is a polymodal cellular sensor that responds to moderate heat, cell swelling, shear stress, and small-molecule ligands. It is involved in thermogenesis, regulation of vascular tone, bone homeostasis, renal and pulmonary functions. TRPV4 is implicated in neuromuscular and skeletal disorders, pulmonary edema, and cancers, and represents an important drug target. The cytoskeletal remodeling GTPase RhoA has been shown to suppress TRPV4 activity. Here, we present a structure of the human TRPV4-RhoA complex that shows RhoA interaction with the membrane-facing surface of the TRPV4 ankyrin repeat domains. The contact interface reveals residues that are mutated in neuropathies, providing an insight into the disease pathogenesis. We also identify the binding sites of the TRPV4 agonist 4α-PDD and the inhibitor HC-067047 at the base of the S1-S4 bundle, and show that agonist binding leads to pore opening, while channel inhibition involves a π-to-α transition in the pore-forming helix S6. Our structures elucidate the interaction interface between hTRPV4 and RhoA, as well as residues at this interface that are involved in TRPV4 disease-causing mutations. They shed light on TRPV4 activation and inhibition and provide a template for the design of future therapeutics for treatment of TRPV4-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2025

Exploring strain rate effects upon 3D materials using high speed in situ X-ray tomoscopy

Cellular materials are ubiquitous in our modern society. They may be stochastic gas-blown foams (e.g., polyurethane), foamed starches (e.g., cereals), or, in this case, 3D printed microlattices. Failure in these materials is often driven by surface or sub-surface defects, which may be nucleated at a surface roughness, an interior void, or inclusion interfaces that may not be typically observable. Obfuscating our understanding further, bulk materials are known to exhibit strain-rate-dependent mechanical response, making a subsurface understanding of damage even more critical. For the first time, an in situ uniaxial mechanical loading stage that simultaneously rotates specimens up to 18 Hz was fielded at a synchrotron for 3D tomographic imaging. This capability opens a plethora of materials science opportunities to explore strain rate effects in materials and examining deformation, fracture, and delamination’s (in composites) for a complete 3D picture (movie) of material response. We demonstrate the deformation of 3D printed polymer lattice structures, of three different material types, at 0.25, 1.1, and 2.2 s −1 strain rates. We successfully imaged the 3D deformation of these materials and can directly compare the same printed structure to the three material types at three strain rates, all in 3D. Material point method simulations were applied to one of the materials to better understand the role of voids on the 3D printed structure’s performance.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Novel Zinc Binding Group for HDAC6 Inhibition

Histone deacetylases (HDAC’s) are key regulatory enzymes in gene transcription and cellular motility through the deacetylation of lysine residues. These enzymes bear a distinct clinical significance, as the upregulation of HDACs has been associated with oncogenesis for many hematological malignancies and proliferation of other neurodegenerative or immune disorders. There are four different classes of HDACs, three of which require zinc for catalysis. Among the zinc dependent isozymes, HDAC6 is thought to be a particularly desirable therapeutic target, as its selective inhibition in malignant cells is accompanied by fewer associated toxicities in comparison to pan‐HDAC inhibition. Therefore, optimizing HDAC6 inhibitor selectivity has the potential to yield great clinical significance. This selectivity is often conferred by designing inhibitors with bulky capping groups and a hydrophobic linker region, which make favorable interactions in the hydrophobic region of the HDAC6 active site. Many inhibitors contain a hydroxamate zinc‐binding group, which can coordinate with bidentate or monodentate geometry. In efforts to optimize HDAC6 selectivity by exploring alternative zinc‐binding groups, a unique inhibitor containing an oxadiazole ring was discovered. Surprisingly, the crystal structure of its complex with HDAC6 reveals that the oxadiazole undergoes a ring opening reaction to yield an acylhydrazide that binds with an extended conformation in the active site.

Cragin, Abigail↗
NASA NTRS2004

To Boldly Go: America's Next Era in Space. The Universe Now and Beyond

Dr. France Cordova, NASA's Chief Scientist opened this, the third session in the NASA Administrator's Seminar Series, by asking the following question: 'What would be a bold and aspiring agenda for America's next era in space?' It aimed at answering the following questions: What do we know about the universe? How do we know it? (Dr. Cordova also mentioned that the first seminar was about the definition of cellular life and how to recognize it, and featured as speakers, Dr. Lynn Margoles and Dr. Leslie Orgle.) Administrator Daniel S. Goldin was introduced; he welcomed the attendees, and remarked that NASA personnel have a critical need to explain to Congress and the public why a space program is important. Congress and the public pay for the space programs. Therefore the programs' importance cannot remain in the sole domain of scientists. The first speaker, Dr. Vera Ruben of the Department of Terrestrial Magnetism at the Carnegie Institute of Washington, was introduced as an art historian expert in cosmology and an observational astronomer. Dr. Ruben brought up a number of questions regarding the substance, location, and origin of dark matter, radiation, galaxies, and the lumpy structure of galaxies in space, as well as the age and density of our universe. The next speaker was Dr. Bohdan Paczynski, a theoretical astrophysicist from Princeton University's Department of Astrophysical Sciences. The final speaker, Dr. Linda Schale is a cosmologist from the University of Texas at Austin. She was said to be a 'paleontologist of the human mind' who tries 'to understand mechanisms people use to understand the world'. The concluding discussion centered on why NASA scientists don t communicate better with people who are not highly educated. This is a big concern because to continue its work, NASA needs to communicate the importance of its goals to the average person. Additional information is included in the original extended abstract.

Source record↗
NASA NTRS2003

Neural Development Under Conditions of Spaceflight

One of the key tasks the developing brain must learn is how to navigate within the environment. This skill depends on the brain's ability to establish memories of places and things in the environment so that it can form cognitive maps. Earth's gravity defines the plane of orientation of the spatial environment in which animals navigate, and cognitive maps are based on this plane of orientation. Given that experience during early development plays a key role in the development of other aspects of brain function, experience in a gravitational environment is likely to be essential for the proper organization of brain regions mediating learning and memory of spatial information. Since the hippocampus is the brain region responsible for cognitive mapping abilities, this study evaluated the development of hippocampal structure and function in rats that spent part of their early development in microgravity. Litters of male and female Sprague-Dawley rats were launched into space aboard the Space Shuttle Columbia on either postnatal day eight (P8) or 14 (P14) and remained in space for 16 days. Upon return to Earth, the rats were tested for their ability to remember spatial information and navigate using a variety of tests (the Morris water maze, a modified radial arm maze, and an open field apparatus). These rats were then tested physiologically to determine whether they exhibited normal synaptic plasticity in the hippocampus. In a separate group of rats (flight and controls), the hippocampus was analyzed using anatomical, molecular biological, and biochemical techniques immediately postlanding. There were remarkably few differences between the flight groups and their Earth-bound controls in either the navigation and spatial memory tasks or activity-induced synaptic plasticity. Microscopic and immunocytochemical analyses of the brain also did not reveal differences between flight animals and ground-based controls. These data suggest that, within the developmental window studied, microgravity has minimal long-term impact on cognitive mapping function and cellular substrates important for this function. Any differences due to development in microgravity were transient and returned to normal soon after return to Earth.

Kosik, Kenneth S.↗
DOE OSTI2025

ExaCA v2.0: A versatile, scalable, and performance portable cellular automata application for additive manufacturing solidification

The previously established ExaCA software for performance portable alloy grain structure simulation has been updated to better represent the solidification behavior during complex alloy processing conditions, such as those encountered during metal additive manufacturing (AM), and for improved performance and scalability. Here, an extension to the time–temperature history input data format and the core ExaCA algorithm to include an arbitrary number of melting and solidification events yielded improved prediction of texture for various melt pool geometries, expanding the range of AM-relevant conditions that can be accurately simulated. Improved heat transport process simulation coupling, including the creation of large raster datasets from single track time–temperature history data and in-memory coupling with the new, performance portable finite difference code Finch, were also demonstrated in example studies on the effect of multilayer AM microstructure predictions on hatch spacing and cell size, respectively. Additional new features are detailed and demonstrated, including the ability to perform simulations using various interfacial response function forms, execute simulations on state-of-the-art hardware, improved usability through post-processing versatility, and improved strong and weak scaling performance. The performance, physics, and versatility improvements demonstrated here will further enable large-scale studies on AM process–microstructure relationships that were not previously possible. Furthermore, the usability improvements and ability to run coupled AM process–microstructure simulations using the Finch-ExaCA workflow will facilitate broader use of this open-source software by the computational materials community.

36 MATERIALS SCIENCE↗
NASA NTRS2024

Improved Mechanical Performance in FDM Cellular Frame Structures through Partial Incorporation of Faces

The utilization of lattice-type cellular architectures has seen a significant increase, owing to their predictable shape and the ability to fabricate templated porous materials through low-cost 3D-printing methods. Frames based on atomic lattice structures such as face-centered cubic (FCC), body-centered cubic (BCC), or simple cubic (SC) have been utilized. In FDM, the mechanical performance has been impeded by stress concentration at the nodes and melt-solidification interfaces arising from layer-by-layer deposition. Adding plates to the frames has resulted in improvements with a concurrent increase in weight and hot-pocket-induced dimensional impact in the closed cells formed. In this paper, we explore compressive performance from the partial addition of plates to the frames of a SC-BCC lattice. Compression testing of both single unit cells and 4 × 4 × 4 lattices in all three axial directions is conducted to examine stress transfer to the nearest neighbor and assess scale-up stress transfer. Our findings reveal that hybrid lattice structure unit cells exhibit significantly improved modulus in the range of 125% to 393%, specific modulus in the range of 13% to 120%, and energy absorption in the range of 17% to 395% over the open lattice. The scaled-up lattice modulus increased by 8% to 400%, specific modulus by 2% to 107%, and energy absorption by 37% to 553% over the lattice frame. Parameters that emerged as key to improved lightweighting.

FDM↗
DOE OSTI2023

Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata

Abstract The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 ’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata , the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel Z-DNA binding domains in giant viruses

Z-nucleic acid structures play vital roles in cellular processes and have implications in innate immunity due to their recognition by Zα domains containing proteins (Z-DNA/Z-RNA binding proteins, ZBPs). Although Zα domains have been identified in six proteins, including viral E3L, ORF112, and I73R, as well as, cellular ADAR1, ZBP1, and PKZ, their prevalence across living organisms remains largely unexplored. In this study, we introduce a computational approach to predict Zα domains, leading to the revelation of previously unidentified Zα domain-containing proteins in eukaryotic organisms, including non-metazoan species. Our findings encompass the discovery of new ZBPs in previously unexplored giant viruses, members of the Nucleocytoviricota phylum. Through experimental validation, we confirm the Zα functionality of select proteins, establishing their capability to induce the B-to-Z conversion. Additionally, we identify Zα-like domains within bacterial proteins. While these domains share certain features with Zα domains, they lack the ability to bind to Z-nucleic acids or facilitate the B-to-Z DNA conversion. Our findings significantly expand the ZBP family across a wide spectrum of organisms and raise intriguing questions about the evolutionary origins of Zα-containing proteins. Moreover, our study offers fresh perspectives on the functional significance of Zα domains in virus sensing and innate immunity and opens avenues for exploring hitherto undiscovered functions of ZBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Development of high throughput and in vitro assays for analyzing RNA modifications

Modifications on RNAs play major roles in their stability, translation, and enzymatic activity. Despite its importance, the current techniques are insufficient to study the structure and function of RNA modifications. Indeed, the National Academies of Science, Engineering and Medicine indicate that developing new tools and further study the function of RNA modifications is strategically a high priority for advancing science in the coming years (https://www.nationalacademies.org/our-work/toward-sequencing-and-mapping-of-rna-modifications). RNA modifications occur in all domains of life controlling processes such as RNA turnover, translation regulation, cellular defenses and bioproduction. Our preliminary data indicated that the insulin mRNA might get ADP-ribosylated by the ADP-ribosyltransferase PARP12. RNA ADP-ribosylation has been described in Escherichia coli. Combined to the fact that ADP-ribosyltransferase (PARP) genes are conserved throughout evolution we hypothesize that this modification might play essential roles in cells. Therefore, we proposed to develop sequencing techniques and in vitro enzymatic assays to identify and validate ADP-ribosylation motifs and sites. Here we report the development of RNA-seq and qPCR assays to identify ADP-ribosylated RNAs, in addition to a nicotinamide adenosine dinucleotide (NAD – ADP-ribosylation donor) consumption assay and an enzyme-linked immunosorbent assay (ELISA) to measure ADP-ribosyltransferase activity. Testing these assays with the insulin mRNA confirmed that this transcript is ADP-ribosylated. These assays will not only enable studying the function of ADP-ribosylation but can be easily adapted for studying other RNA modifications. This will open opportunities to study RNA modifications in different model systems from bacteria to viruses to plants, bringing insights into their cellular functions and the possibility of targeting them for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2007

NanoSIMS opens a New Window for Deciphering Organic Matter in Terrestrial and Extraterrestrial Samples

Recognition of the earliest morphological or chemical evidence of terrestrial life has proved to be challenging, as organic matter in ancient rocks is commonly fragmentary and difficult to distinguish from abiotically-produced materials (Schopf, 1993; Van Zuilen et al., 2002; Altermann & Kazmierczak, 2003; Cady et al., 2003; Brasier et al., 2002, 2004, 2005; Hofmann, 2004; Skrzypczak et al., 2004, 2005). Yet, the ability to identify remnants of earliest life is critical to our understanding of the timing of life's origin on earth, the nature of earliest terrestrial life, and recognition of potential remnants of microbial life that might occur in extraterrestrial materials. The search for earliest life on Earth now extends to early Archean organic remains; these tend to be very poorly preserved and considerably more difficult to interpret than the delicately permineralized microfossils known from many Proterozoic deposits. Thus, recent efforts have been directed toward finding biosignatures that can help distinguish fragmentary remnants of ancient microbes from either pseudofossils or abiotic organic materials that may have formed hydrothermally or in extraterrestrial processes (House et al., 2000; Boyce et al., 2001; Kudryavtsev et al., 2001; Schopf, 2002; Schopf et al., 2002, 2005a,b; Cady et al., 2003; Garc a-Ruiz et al., 2003; Hofmann, 2004; Brasier et al., 2005; Rushdi and Simoneit, 2005; Skrzypczak et al., 2005). An exciting area of biosignature research involves the developing technology of NanoSIMS. NanoSIMS is secondary ion mass spectrometry (SIMS) for ultrafine feature, elemental and isotopic analysis. Its resolution approaches 0.05 micrometers for element mapping, which is 10-50 times finer than that attainable with conventional SIMS or electron microprobes. Consequently, NanoSIMS has the potential to reveal previously unknown, chemical and structural characteristics of organic matter preserved in geologic materials. Robert et al. (2005) were the first to combine NanoSIMS element maps with optical microscopic imagery in an effort to develop a new method for assessing biogenicity. They showed that the ability to simultaneously map the distribution of organic elements [such as carbon (C), nitrogen (N), and sulfur (S)] and compare those element distributions with optically recognizable, cellularly preserved fossils could provide significant new insights into the origin of organic materials in ancient sediments. This chapter details a recent NanoSIMS study which was designed to acquire new data relevant to establishing critical biosignatures (Oehler et al., 2006a-c). In this study, NanoSIMS was used to characterize element distributions of spheroidal and filamentous microfossils and associated organic laminae in chert from the approx. 0.85 billion year old (Ga) Bitter Springs Formation of Australia. Previous work established preservation of a diverse microbiota in the Bitter Springs Formation (Schopf, 1968; Schopf and Blacic, 1971), and there is no dispute within the scientific community regarding the biogenicity of any of the Bitter Springs structures evaluated in this new study. Thus, the NanoSIMS results described below provide new insight into - and can be used as a guide for assessing - the origin of less well understood organic materials that may occur in early Archean samples and in meteorites or other extraterrestrial samples.

Oehler, Dorothy ZS.↗
DOE OSTI2021

The Role of Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology: Proceedings of a Workshop

Quantum concepts hold the potential to enable significant advances in sensing and imaging technologies that could be vital to the study of biological systems. The workshop Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology, held online March 8–10, 2021, was organized to examine the research and development needs to advance biological applications of quantum technology. Hosted by the National Academies of Sciences, Engineering, and Medicine, the event brought together experts working on state-of-the-art, quantum-enabled technologies and scientists who are interested in applying these technologies to biological systems. Through talks, panels, and discussions, the workshop facilitated a better understanding of the current and future biological applications of quantum-enabled technologies in fields such as microbiology, molecular biology, cell biology, plant science, mycology, and many others. The workshop was organized around three main themes. The first, quantum in biology, examined quantum concepts that are hypothesized to be important for life processes and that researchers are working to observe through biological imaging and sensing. The second, quantum for biology, addressed ways to use quantum concepts to enhance technologies for biological imaging and sensing. The third, biology for quantum, offered a wider discussion of how the frontiers of biological imaging and sensing could enable future study using quantum concepts, tools, or technologies. Throughout the workshop, participants identified a wide range of emerging approaches and opportunities at the intersection of quantum physics and biological sensing and imaging. During the workshop, there were some differences in how each speaker defined the term quantum. During one of the panels, Prem Kumar offered thoughts on what phenomena are classical versus quantum, explaining that techniques get progressively more quantum as you move from just having superposition to having superposition with measurement and entanglement. Another explanation from Clarice Aiello delineates the definition into several levels. This includes a base level of “quantum-ness,” which reflects that all matter is made of atoms, and when these particles are isolated they behave based on quantum mechanical principles. A second level is related to quantum coherence, where a single quantum object might be found in a coherent superposition state. A final level, which she described as the quantum-entangled level, involves multiple quantum systems which are entangled among themselves. Overall, the workshop touched on concepts such as superposition, entanglement, and squeezing and their potential implications for communication, computing, and simulation, in addition to the workshop’s main focal area, biological sensing and imaging. At the opening of the workshop, Thorsten Ritz of the University of California, Irvine, identified two questions at the heart of quantum biology: Is the machinery of life quantum mechanical, and can quantum mechanics be used to study the machinery of life in new ways? Participants highlighted systems in which researchers have explored these questions, from the vast array of molecular interactions involved in biological processes such as photosynthesis, to the mechanics involved in cellular functions such as differentiation and aggregation, to the role of oscillating magnetic fields in flight orientation among birds. Sensing and imaging technologies are crucial to biological research; these technologies could both enhance the study of quantum effects and be enhanced by quantum concepts. A critical challenge in biological research is to develop imaging and sensing tools that do not damage or interfere with the often fragile and fleeting systems being studied. Attendees discussed a variety of established and emerging technologies that could enhance noninvasive biological imaging, including single- and two-photon spectroscopy, single-molecule spectroscopy, quantum illumination, ghost imaging, and cryo-electron microscopy. One example came from Marlan Scully who gave a keynote address on the first day of the workshop. Scully emphasized the use of different laser technologies, which exhibit coherence and other quantum properties, in moving toward real-world biological applications, such as the detection of SARS-CoV-2. Both tools and theory will play an important role in advancing quantum biology research and applications. Several participants suggested theorists and experimentalists should work in tandem to understand and model biological processes. While physics often reduces systems to their simplest forms for fundamental insights, participants also noted the value of observing and understanding biological systems in all their “messiness,” capturing both the inner workings of biological systems and the complex interactions that occur within and between organisms. In discussions among participants, several attendees stressed the need to match emerging tools with the right scientific questions. Rather than developing quantum technologies as “a hammer looking for a nail,” participants emphasized a focus on exploring the problems these technologies are best suited to address. For example, it is important to consider the size of the phenomenon being studied, the timescales that are important in answering the scientific question, and other relevant considerations. Every tool along the spectrum from classical to quantum involves its own set of trade-offs. For example, Ted Laurence of the Lawrence Livermore National Laboratory said that quantum measurements, such as single photon counting, fluorescence transitions, and lasers, can take longer to produce the same results as classical measurements. These quantum measurements, however, do not require calibration and can enable new research questions to be answered. Prem Kumar, Northwestern University, noted that, despite their promise, quantum approaches should not be used simply for the sake of using quantum, especially in situations where classical approaches better meet the needs of the researcher. Understanding and applying quantum concepts could enable advances in a wide range of application areas including energy, synthetic biology, medicine, and sustainability. For example, Michelle O’Malley, University of California, Santa Barbara, described how improved noninvasive imaging approaches could help capture the complex interactions and functions involved in the breakdown of organic matter by microbial communities and lead to new technologies for capturing valuable products from plant waste. Several other participants discussed needs in tracking the movement of metabolites and molecules in microbial communities for insights into nutrient cycling in environments such as soil. Margaret Ahmad, Sorbonne University, discussed potential opportunities to leverage the magnetic properties of cryptochromes to advance new treatment approaches for diseases such as COVID-19 and cancer. Looking toward the future development of the field, participants discussed challenges to advancing quantum biology that arise from disciplinary disconnects between physicists and biologists. The siloing of academic research disciplines represents a significant barrier to progress. Disconnects in terminology, motivations and priorities, and structural barriers to collaborative work underscore the need for concerted efforts to bridge these divides. Attendees and speakers offered suggestions for resolving these divergences, establishing a shared language, moving the field forward, and fostering meaningful feedback between disciplines. Overall, participants stressed a need for balance, open communication, collaboration, unity, and clear dialogue on trade-offs between quantum and classical approaches. Keiko Torii, The University of Texas at Austin, said that the best collaborations happen when the project provides mutual advantages that can show off everyone’s talents, each team finds the work interesting, and partners develop a camaraderie to pursue new knowledge. To enable near- and long-term opportunities in this space, participants suggested that exploratory, high-risk funding could improve existing instrumentation to explore quantum enhancement collaboratively. They also emphasized the need for collaboration between quantum physicists and sensing/imaging scientists, which could be advanced through a dedicated quantum biology investigator program. People, even more than technology, will be crucial to the future of quantum biology. Participants explored training, education, and workforce needs to further develop this burgeoning field and cultivate the next generation of scientists. While many programs are still in their nascent stages, participants highlighted examples of approaches and programs being developed at various types of institutions to engage students and professional scientists in quantum biology research. Several participants stressed the need for an inclusive approach, spanning disciplines as well as communities to foster a diverse field fueled by the intellectual contributions of a wide range of people, including historically under-resourced schools and students. To increase awareness and excitement about quantum physics and related areas of biology, attendees suggested capitalizing on the “buzz” around quantum. Several participants emphasized the need to start early, introducing students to quantum concepts and their appealing “weirdness” in K–12 education. Engaging students early—before they become entrenched in traditional disciplinary siloes as typically happens in graduate school—could help to galvanize interest in the area and foster a generation of scientists with the interdisciplinary mindset and skills needed to advance this interdisciplinary field. While these efforts could be advanced at many levels and across multiple sectors, several participants suggested a national quantum biology center could be a valuable hub to coordinate and support quantum biology education and workforce development across academia, industry, and government.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Uncovering grain and subgrain microstructure at the scale of additive manufacturing melt tracks with a scalable cellular automaton solidification model

Metal additive manufacturing, characterized by rapid solidification, yields refined grains with a distinctive cellular subgrain microstructure that plays a pivotal role in determining material properties. Due to the significant computational expense demanded to simulate the required physics with submicron spatial resolution, their numerical simulations have been limited to proof-of-concept studies to either 2D or small subregions of a melt pool. In this study, an open-source, scalable, solidification code, muMatScale, based on the cellular automaton method, has been developed to predict the grain and the underlying subgrain microstructure over an entire melt pool. The model incorporates flexible parallelization schemes, utilizing MPI and OpenMP GPU Offloading, in addition to appropriate multi-physics specific to non-equilibrium rapid solidification in AM. The impact of nucleation parameters on grain microstructures was investigated with a focus on grain size variations and morphology transitions. With selected nucleation parameters, the simulation predicted the grain size, subgrain morphology, crystallographic orientation, and microsegregation aligned with experimental measurements. The model demonstrates that epitaxial grain growth is a dominant factor at the melt pool boundary, influencing grain size variation under different grain sizes in the build plate while maintaining consistent primary dendrite arm spacing under identical thermal conditions. Here, the highly efficient numerical model enables large-scale simulations with a spatial resolution of 100 nm or less, unveiling unprecedented insights into thermal and solutal diffusion driven grain growth, and the subgrains with microsegregation within grains in 3D across scales. muMatScale will enable the linking of submicron length-scale microstructure to part-level material behavior by investigating fundamental solidification problems at the intercellular scale in many-track and many-layer builds.

36 MATERIALS SCIENCE↗
NASA NTRS2012

Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106 above background was evolved in vitro. This enzyme does not look like any contemporary protein. It is very flexible and its structure is kept together just by a single salt bridge between a charged residue and a coordinating zinc. A similar picture emerges from studies of simple transmembrane channels that mimic those in ancestral cells. Again, they are extremely flexible and do not form a conventional pore. Yet, they efficiently mediate ion transport. Studies on simple proteins that are on-going in several laboratories hold promise of revealing crucial links between chemical and biological catalysis and other ubiquitous cell functions. Interaction between composition, growth and division of protobiologically relevant vesicles and metabolic reactions that they encapsulate is an example of coupling between simple functions that promotes reproduction and evolution. Recent studies have demonstrated possible mechanisms by which vesicles might have evolved their composition from fatty acids to phospholipids, thus facilitating a number of new cellular functions. Conversely, it has been also demonstrated that an encapsulated metabolism might drive vesicle division. These are, again, examples of processes that might have driven the transition from chemistry to biology.

Pohorille, Andrew↗
NASA NTRS2001

Proton Transport

The transport of protons across membranes is an essential process for both bioenergetics of modern cells and the origins of cellular life. All living systems make use of proton gradients across cell walls to convert environmental energy into a high-energy chemical compound, adenosine triphosphate (ATP), synthesized from adenosine diphosphate. ATP, in turn, is used as a source of energy to drive many cellular reactions. The ubiquity of this process in biology suggests that even the earliest cellular systems were relying on proton gradient for harvesting environmental energy needed to support their survival and growth. In contemporary cells, proton transfer is assisted by large, complex proteins embedded in membranes. The issue addressed in this Study was: how the same process can be accomplished with the aid of similar but much simpler molecules that could have existed in the protobiological milieu? The model system used in the study contained a bilayer membrane made of phospholipid, dimyristoylphosphatidylcholine (DMPC) which is a good model of the biological membranes forming cellular boundaries. Both sides of the bilayer were surrounded by water which simulated the environment inside and outside the cell. Embedded in the membrane was a fragment of the Influenza-A M$_2$ protein and enough sodium counterions to maintain system neutrality. This protein has been shown to exhibit remarkably high rates of proton transport and, therefore, is an excellent model to study the formation of proton gradients across membranes. The Influenza M$_2$ protein is 97 amino acids in length, but a fragment 25 amino acids long. which contains a transmembrane domain of 19 amino acids flanked by three amino acids on each side. is sufficient to transport protons. Four identical protein fragments, each folded into a helix, aggregate to form small channels spanning the membrane. Protons are conducted through a narrow pore in the middle of the channel in response to applied voltage. This channel is large enough to contain water molecules. and is normally filled with water. In analogy to the mechanism of proton transfer in some other channels, it has been postulated that protons are translocated along the network of water molecules filling the pore of the channel. This mechanism, however, must involve an additional important step because the channel contains four histidine amino acid residues, one from each of the helices, which are sufficiently large to occlude the pore and interrupt the water network. The histidine residues ensure channel selectivity by blocking transport of small ions, such as sodium or potassium. They have been also implicated in gating protons due to the ability of each histidine to become positively charged by accepting an additional proton. Two mechanisms of gating have been proposed. In one mechanism, all four histidines acquire an additional proton and, due to repulsion between their positive charges, move away from one another, thus opening the channel. The alternative mechanism relies of the ability of protons to move between different atoms in a molecule (tautomerization). Thus, a proton is captured on one side of the gate while another proton is released from the opposite side, and the molecule returns to the initial state through tautomerization. The simulations were designed to test these two mechanisms. Large-scale, atomic-level molecular dynamics simulations of the channel with the histidine residues in different protonation states revealed that all intermediate states of the system involved in the tautomerization mechanism are structurally stable and the arrangement of water molecules in the channel is conducive to the proton transport. In contrast, in the four-protonated state, postulated to exist in the gate-opening mechanism, the electrostatic repulsion between the histidine residues appears to be so large that the channel loses its structural integrity and one helix moves away from the remaining three. Additional information is contained within the original extended abstract.

Pohorille, Andrew↗