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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Multi-scale organization in communicating active matter

The emergence of collective motion among interacting, self-propelled agents is a central paradigm in non-equilibrium physics. Examples of such active matter range from swimming bacteria and cytoskeletal motility assays to synthetic self-propelled colloids and swarming microrobots. Remarkably, the aggregation capabilities of many of these systems rely on a theme as fundamental as it is ubiquitous in nature: communication. Despite its eminent importance, the role of communication in the collective organization of active systems is not yet fully understood. Here we report on the multi-scale self-organization of interacting self-propelled agents that locally process information transmitted by chemical signals. We show that this communication capacity dramatically expands their ability to form complex structures, allowing them to self-organize through a series of collective dynamical states at multiple hierarchical levels. Our findings provide insights into the role of self-sustained signal processing for self-organization in biological systems and open routes to applications using chemically driven colloids or microrobots.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

ExaCA grain structure predictions for laser powder bed fusion processing

This dataset contains simulated cross-sections of laser powder bed fusion grain structures produced using the microstructure model ExaCA, in turn using time-temperature history data produced using the heat transport model AdditiveFOAM. These predictions show the grain structure using various permutations of hatch spacing and nucleation density. Also contained in the dataset are the input files necessary to reproduce the results. AdditiveFOAM (https://github.com/ORNL/AdditiveFOAM) and ExaCA (https://github.com/LLNL/ExaCA), both open source software, are required to reproduce the results in this dataset using the given input files. This DOI was updated 12/09/2025.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗

DOE OSTI2022

Knowledge-matching based computational framework for genome-scale metabolic model refinement

Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β -Sheet Conformations on Time of SIV mac251 Acquisition

The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vacci nated macaque that was protected from multiple simian immunodeficiency virus (SIV) chal lenges, both target an overlapping, conformationally dynamic epitope in SIV envelope vari able region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a b-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIV mac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIV mac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1996

Human physiology in space

The universality of gravity (1 g) in our daily lives makes it difficult to appreciate its importance in morphology and physiology. Bone and muscle support systems were created, cellular pumps developed, neurons organised and receptors and transducers of gravitational force to biologically relevant signals evolved under 1g gravity. Spaceflight provides the only microgravity environment where systematic experimentation can expand our basic understanding of gravitational physiology and perhaps provide new insights into normal physiology and disease processes. These include the surprising extent of our body's dependence on perceptual information, and understanding the effect and importance of forces generated within the body's weightbearing structures such as muscle and bones. Beyond this exciting prospect is the importance of this work towards opening the solar system for human exploration. Although both appear promising, we are only just beginning to taste what lies ahead.

NASA Center HQS↗

DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗

NASA NTRSDate not supplied

High School Citizen Scientists Use AI/ML to Predict Intra-Ocular Pressure From Gene Expression Data for Spaceflown Mice

Artificial Intelligence (AI) and Machine Learning (ML) have increasingly become pivotal in biological and biomedical research, largely due to the culture of open data sharing and its associated benefits. The methodologies inherent in AI/ML are particularly adept at identifying and forecasting biological phenotypes from the vast amounts of data generated by next-generation sequencing technologies. These techniques offer substantial promise for advancing research in space biosciences and for the development of automated systems for monitoring space health. Nevertheless, there are crucial aspects to consider when training, validating, and testing machine learning models in both biological research and clinical contexts. It is essential that Open Science principles, including data sharing and the availability of open-source code, are complemented by high-quality, publicly accessible training resources. These resources should focus on best practices and include modules based on real-world scientific cases and data to ensure that future AI/ML practitioners gain practical experience with genuine problems. Addressing this knowledge gap, we have designed, developed, and delivered both interactive and self-paced training programs for citizen scientists worldwide, enabling them to utilize AI/ML for space biology research. This initiative was made possible through generous funding from a Transformation to Open Science Training grant. The interactive training sessions, conducted this summer, utilized AI/ML techniques to analyze data from the Open Science Data Repository, specifically targeting the effects of spaceflight on ocular structure and function. The dataset OSD-583, from the Rodent Research 9 mission, provides experimental data detailing the ocular responses of mice subjected to a 35-day spaceflight, compared with ground control counterparts. Using OSD-583 as observational data, our summer training participants applied AI/ML methods to predict intraocular pressure from RNA-seq data and identify the genes most predictive of the observed responses. Further analysis through pathway enrichment and gene set enrichment revealed that these genes are involved in molecular and cellular processes contributing to retinal degeneration.

James Casaletto↗

DOE OSTI2023

Insights into the relation between vertical cloud structure and dynamics of three polar lows: Observations from COMBLE

The vertical structure of three polar lows is described using profiling radar, lidar, and passive remote sensors deployed at a coastal site in northern Norway. The data were collected as part of the Cold-air Outbreaks in the Marine Boundary Layer Experiment (COMBLE). These data are examined in the context of satellite imagery, operational weather radar reflectivity imagery, and output from the AROME-Arctic model. A comparison to satellite images shows that AROME-Arctic captured the polar lows well. All three polar lows form in marine cold-air outbreaks and are surrounded by open-cellular convection typical of such outbreaks. Two of the lows form in a forward shear environment, and one under reverse shear. Initially, the three polar lows are comma-shaped; two of them transition to be more spirali-form at their mature stage and have mostly cloud-free warm cores. The warm cores are the result of a warm-seclusion process. All three lows have stratiform precipitation bands, marked by little cloud liquid water, and rather high surface precipitation rate. The vertical drafts and turbulence in these stratiform clouds are generally weak. In conclusion, all three lows also have convective clouds, which have stronger vertical drafts, stronger turbulence, and pockets of high liquid water content.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes

Background Processing of archaeal 16S and 23S rRNAs is believed to involve excision of individual rRNAs from polycistronic precursors, circularization of excised rRNAs, and re-linearization before the incorporation into ribosomes. However, all the knowledge is derived from several isolated species, leaving open the possibility that different processes may occur in other archaeal groups. Results Here, we investigate rRNAs from diverse and mostly uncultivated archaea. Sequencing of total cellular RNA from eight phylum-level lineages indicates that archaeal circular 23S rRNA transcript abundances vastly exceed those of linear counterparts, and linear versions are often undetectable. As the majority of rRNAs derive from mature ribosomes, the data suggest that ribosomes contain circular 23S rRNAs. Thus, we directly sequence RNA extracted from isolated ribosomes of a model archaeon, Methanosarcina acetivorans, and confirm that the 23S rRNAs in the ribosomes are circular. Structural modeling places the 5′ and 3′ ends of the linear precursors of archaeal 23S rRNAs in close proximity to form a GNRA tetraloop (in which N is A, C, G, or U and R is A or G), consistent with their existence as circular molecules. We also confirm the existence of circular 16S rRNA intermediates in transcriptomes of most archaea, yet a circular form is not evident in some distinct archaeal groups, suggesting that certain archaea do not circularize 16S rRNA during processing. Conclusions Our findings uncover unexpected variations in the processing required to generate mature rRNAs and the conformation of functional molecules in archaeal ribosomes.

Archaea↗

DOE OSTI2025

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

Recent advancements in RNA structural biology have focused on unraveling the complexities of non-coding mRNA elements like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up or downregulation of downstream genes. The purine riboswitch family regulates many prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a 3-way helical junction, where ligand encapsulation occurs at the junctional core. In our study, we chemically probed the aptamer domain of the 2’-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg²⁺ and 2’-dG influence riboswitch folding. Here, we find that efficient 2’-dG binding strongly depends on Mg²⁺, indicating that Mg²⁺ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5’ tail of dGsw that is complementary to a conserved helix. The inclusion of this region in a construct led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that 5’ flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may, therefore, facilitate the formation of an anti-terminator helix by opening the 3-way junction surrounding the 2’-dG binding site. Our study further establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt may fine-tune downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.

Biochemistry & Molecular Biology↗

NASA NTRS2002

The cytoskeleton and gravitropism in higher plants

The cellular and molecular mechanisms underlying the gravitropic response of plants have continued to elude plant biologists despite more than a century of research. Lately there has been increased attention on the role of the cytoskeleton in plant gravitropism, but several controversies and major gaps in our understanding of cytoskeletal involvement in gravitropism remain. A major question in the study of plant gravitropism is how the cytoskeleton mediates early sensing and signal transduction events in plants. Much has been made of the actin cytoskeleton as the cellular structure that sedimenting amyloplasts impinge upon to trigger the downstream signaling events leading to the bending response. There is also strong molecular and biochemical evidence that the transport of auxin, an important player in gravitropism, is regulated by actin. Organizational changes in microtubules during the growth response phase of gravitropism have also been well documented, but the significance of such reorientations in controlling differential cellular growth is unclear. Studies employing pharmacological approaches to dissect cytoskeletal involvement in gravitropism have led to conflicting results and therefore need to be interpreted with caution. Despite the current controversies, the revolutionary advances in molecular, biochemical, and cell biological techniques have opened up several possibilities for further research into this difficult area. The myriad proteins associated with the plant cytoskeleton that are being rapidly characterized provide a rich assortment of candidate regulators that could be targets of the gravity signal transduction chain. Cytoskeletal and ion imaging in real time combined with mutant analysis promises to provide a fresh start into this controversial area of research.

Review↗

DOE OSTI2024

Simple Scattering: Lipid nanoparticle structural data repository

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Microchemomechanical devices using DNA hybridization

Significance With simple DNA origami lever arms arranged in hinges and accordion structures, we amplify the nanometer displacements from DNA hairpin zippers to 4-μm motion, easily observable and quantified in real space and real time with conventional optical microscopy. Mechanically pulling a bead tethered on the accordion end, we measure high-energy recovery and retraction speeds up to 50 μm/s. On longer time scales, we have also opened and closed the hinges with light and heat. DNA nanotechnology, and particularly DNA origami, combined with colloids and emulsions can provide powerful architectures. The present study is a step toward activating such colloidal/cellular scale devices using DNA as a power source/fuel. We envision artificial active flagella, cilia, micropumps, and other cellular scale devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Mesoscale Cellular Convection Detection and Classification Using Convolutional Neural Networks: Insights From Long-Term Observations at ARM Eastern North Atlantic Site

Marine boundary layer clouds are crucial in Earth's climate system. They frequently manifest as closed or open cell mesoscale cellular convection (MCC). MCC clouds are challenging to represent accurately in current climate models, highlighting the need for detailed observational data sets and in-depth analyses. This study utilizes over 8 years of observations from the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) User Facility Eastern North Atlantic (ENA) site at Graciosa Island, Azores, to investigate these clouds. We first apply a convolutional neural network with a U-Net architecture to classify open and closed cells, marking the first application of such an approach for automatically detecting MCC patterns from ground-based radar measurements. This method addresses some observational gaps in satellite data related to low temporal resolution, nighttime challenges, and limited vertical structure capture. The analysis of the MCC cases shows clear differences between closed and open MCCs: Closed MCC clouds are characterized by lower cloud tops and bases, shallower cloud geometrical depth, weaker horizontal wind speeds, stronger atmospheric stability, and a more homogeneous liquid water path than open MCCs. Finally, we demonstrate two potential applications of our radar-based MCC classifications: (a) facilitating the investigation of aerosol-cloud interactions and (b) exploring meteorological factors along with MCC's evolution by integrating satellite imagery and back-trajectory analysis. The identified MCC cases offer a valuable resource for the scientific community to study MCC processes further and improve climate model accuracy.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Characterization of Caenorhabditis elegans sphingomyelin synthases through heterologous expression

Sphingomyelin (SM) is a major component of mammalian cell membranes and particularly abundant in the myelin sheath that surrounds nerve fibers. Its production is catalyzed by SM synthases SMS1 and SMS2, which interconvert phosphatidylcholine and ceramide to diacylglycerol and SM in the Golgi and at the plasma membrane, respectively. As the lipids participating in this reaction fulfill both structural and signaling functions, SMS enzymes have considerable potential to influence diverse important cellular processes. The nematode Caenorhabditis elegans is an attractive model for studying both animal development and human disease. The organism contains five SMS homologues but none of these have been characterized in any detail. Here, we carried out the first systematic analysis of SMS family members in C. elegans . Using heterologous expression systems, genetic ablation, metabolic labeling and lipidome analyses, we show that C. elegans harbors at least three distinct SM synthases and one ceramide phosphoethanolamine (CPE) synthase. Moreover, C. elegans SMS family members have partially overlapping but also unique sub-cellular distributions and together occupy all principal compartments of the secretory pathway. Our findings shed light on crucial aspects of sphingolipid metabolism in a valuable animal model and opens avenues for exploring the role of SM and its metabolic intermediates in organismal development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗