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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Nanoscale Turing patterns in a bismuth monolayer

Turing’s reaction–diffusion theory of morphogenesis has been very successful for understanding macroscopic patterns within complex objects ranging from biological systems to sand dunes. However, Turing patterns on microscopic length scales are extremely rare. Here we show that a strained atomic bismuth monolayer assembled on the surface of NbSe 2 —and subject to interatomic interactions and kinetics—displays Turing patterns. Our reaction–diffusion model produces stripe patterns with a period of five atoms (approximately 2 nm) and domain walls with Y-shaped junctions that bear a striking resemblance to what has been experimentally observed. Our work establishes that Turing patterns can occur at the atomic scale in a hard condensed-matter setting.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Controlled patterning of crystalline domains by frontal polymerization

Materials with hierarchical architectures that combine soft and hard material domains with coalesced interfaces possess superior properties compared with their homogeneous counterparts. These architectures in synthetic materials have been achieved through deterministic manufacturing strategies such as 3D printing, which require an a priori design and active intervention throughout the process to achieve architectures spanning multiple length scales. Here we harness frontal polymerization spin mode dynamics to autonomously fabricate patterned crystalline domains in poly(cyclooctadiene) with multiscale organization. This rapid, dissipative processing method leads to the formation of amorphous and semi-crystalline domains emerging from the internal interfaces generated between the solid polymer and the propagating cure front. The size, spacing and arrangement of the domains are controlled by the interplay between the reaction kinetics, thermochemistry and boundary conditions. Small perturbations in the fabrication conditions reproducibly lead to remarkable changes in the patterned microstructure and the resulting strength, elastic modulus and toughness of the polymer. Furthermore, this ability to control mechanical properties and performance solely through the initial conditions and the mode of front propagation represents a marked advancement in the design and manufacturing of advanced multiscale materials. Drawing inspiration from biological systems in which structural complexity develops through dissipative reaction–diffusion processes, this study explores a transformative synthetic manufacturing strategy aimed at harnessing the principles underpinning morphogenic growth, unlocking new avenues for advanced materials design and fabrication. Synthetic coupled reaction-transport processes offer a versatile yet relatively underexplored method to manipulate the spatial attributes of synthetic materials10. Here we introduce an innovative manufacturing approach based on frontal ring-opening metathesis polymerization (FROMP) that draws parallels with morphogenic growth and development, enabling the formation of patterned microstructures within polymeric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Incorporating the molecular-scale into a hydrodynamic description of confined aqueous systems

Hydrodynamics provides a continuum-level description of fluid motion, but its applicability at the nanoscale becomes uncertain due to the emerging importance of molecular-level effects such as spatial heterogeneity. Hydrodynamic boundary conditions that incorporate molecular details allow us to partition the system into a near-wall region and a bulk fluid region. We identify a hydrodynamic wall located inside the fluid that determines where slip begins. By extending the hydrodynamic wall with the slip length, the position of the extrapolated wall is established. This offers a unified description of both slip and stagnant flow behaviors, with wall hydrophobicity characterized by the relative location of the extrapolated wall with respect to the physical wall. Employing this concept in analyses of equilibrium molecular dynamics (MD) and non-equilibrium MD simulations of Couette and Poiseuille flows, our results demonstrate consistency between equilibrium and non-equilibrium approaches across different flow types and confinement levels. This demonstrates the robust nature of linear response theory. We then explore the effects of fluid-wall and bulk fluid interactions on the hydrodynamic properties. These findings enhance the effectiveness of molecular-based simulations for investigating complex confined systems in nanofluidics, biology, and colloidal science, offering a complementary molecular-scale perspective to traditional continuum approaches.

flow simulations↗
DOE OSTI2020

ARM Aerial Instrument Workshop Report

The mission of the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program is to “support transformative science and scientific user facilities to achieve a predictive understanding of complex biological, earth, and environmental systems for energy and infrastructure security, independence, and prosperity.” (https://science.osti.gov/ber) Aligned with the BER central mission, the Earth and Environmental Systems Sciences Division (EESSD) plays a vital role in supporting the fundamental research to understand and predict Earth’s climate and environmental systems, and is also in a unique position to inform the development of sustainable solutions to the nation’s energy and environmental challenges. Specifically, EESSD manages two scientific user facilities: the Atmospheric Radiation Measurement (ARM) user facility and the Environmental Molecular Sciences Laboratory (EMSL). These facilities provide the broader scientific community with scientific expertise, technical capabilities, and unique data sets to facilitate science in areas of importance to DOE. As a multi-platform scientific user facility, ARM aims to fulfill the needs predominantly within the EESSD Atmospheric System Research (ASR) and the Earth and Environmental System Modeling (EESM) mission areas, and provide the critical measurements required to improve understanding of aerosol and cloud life cycles and their interactions, and their coupling with the Earth’s surface. Over the years, ARM has carried out piloted and unmanned aircraft campaigns under different organizational and operational paradigms (Schmid et al. 2014, 2016). Building on its success, the ARM Aerial Facility (AAF) continues to complement the ground-based observations with airborne in situ cloud, aerosol, and trace gas observations as well as measurements of atmospheric state and atmospheric radiation. During the past three years, ARM has managed field campaigns using unmanned aerial systems (UAS) and tethered balloon systems (TBS) at Oliktok Point in Alaska to improve understanding of atmospheric processes in the Arctic. In 2019, following a careful evaluation of scientific community needs, ARM acquired a Bombardier Challenger 850 regional jet to replace the vintage Grumman Gulfstream-159 turboprop aircraft previously used by AAF. With this new “laboratory in the sky”, AAF is evaluating its current and future aerial observation capabilities to continue satisfying the needs of the research community.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Ultra-high Information-content Chemical Imaging with Broadband Coherent Anti-Stokes Raman and Two-photon Fluorescence Lifetime Microscopy

Raman fingerprint spectroscopy and fluorescence lifetime imaging are emerging tools for studying metabolic profiles of biological specimens. While Raman fingerprint spectroscopy detects intrinsic molecular vibrations that reflect the molecular composition and chemical environment of a sample, fluorescence lifetime imaging measures changes in the excited-state lifetime of fluorophores that are sensitive to their microenvironments. Here, we present a multimodal imaging platform combining broadband coherent anti-Stokes Raman scattering (BCARS) and two-photon fluorescence lifetime imaging (2p-FLIM) microscopy that can acquire biologically relevant Raman fingerprint spectra and fluorescence lifetime signals in vivo and simultaneously. The tremendous chemical information obtained from spatially co-registered BCARS and 2p-FLIM images allows us to characterize the subtle differences between sub-cellular compartments and verify the potential false-positive results generated by fluorescence imaging alone. This is demonstrated by directly comparing the BCARS, 2p-FLIM, and two-photon excitation fluorescence(TPEF) signals simultaneously obtained from the same dye-stained organelle in the live, intact C. elegans expressing a green fluorescent protein (GFP) marker. In this work, we introduce the BCARS/2p-FLIM/TPEF setup scheme, the image acquisition steps, data processing, and representative results showing that the cross-modality imaging method enables rigorous characterization and in vivo detection at sub-cellular resolution. Furthermore, this protocol provides a framework for simultaneous chemical and fluorescence lifetime imaging to improve the accuracy of biological interpretation in complex living systems.

Xu, Haoyu [Georgia Institute of Technology, Atlant↗
NASA NTRS2000

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik↗
NASA NTRS2017

Developing Model Benchtop Systems for Microbial Experimental Evolution

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Developing↗
DOE OSTI2023

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Open Science for Plants in Space: Improvements in NASA's Open Science Data Repository

Upcoming deep space missions will rely on plants for crew and ecosystem health. Open access space biology data enables scientists to examine the biological responses of plants to ionizing radiation, altered gravity, elevated CO2, and many other abiotic stressors. NASA has declared 2023 as the ‘Year of Open Science’ and created a 5-year Transform to Open Science (TOPS) initiative designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. Current OSDR standards include the ISA (Investigation-Study-Assay) experiment model, assay metadata configurations, and standardized terminology and ontologies. In 2024 OSDR will include a new suite of features for improved FAIR compliance including downloadable plant metadata templates, data submission tools and overall improved AI-readiness of plant datasets. AI/ML methods can be helpful tools to overcome the inherent challenges of space biology research (small sample size, sparse and heterogeneous data etc.). However these methods are built on an assumption of normalized and well-curated data. OSDR’s new curation tools will improve users ability to leverage ML and AI methods to model space biology data and better understand the complex effects of spaceflight on living systems across hierarchical biological levels. We look forward to sharing our advances with the spaceflight community.

FAIR↗
DOE OSTI2025

Poplar: a phylogenomics pipeline

Motivation Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist. Results We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline. Availability and implementation Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Koning, Elizabeth [Sandia National Laboratories (S↗
NASA NTRS1999

Hydroponics Database and Handbook for the Advanced Life Support Test Bed

During the summer 1998, I did student assistance to Dr. Daniel J. Barta, chief plant growth expert at Johnson Space Center - NASA. We established the preliminary stages of a hydroponic crop growth database for the Advanced Life Support Systems Integration Test Bed, otherwise referred to as BIO-Plex (Biological Planetary Life Support Systems Test Complex). The database summarizes information from published technical papers by plant growth experts, and it includes bibliographical, environmental and harvest information based on plant growth under varying environmental conditions. I collected 84 lettuce entries, 14 soybean, 49 sweet potato, 16 wheat, 237 white potato, and 26 mix crop entries. The list will grow with the publication of new research. This database will be integrated with a search and systems analysis computer program that will cross-reference multiple parameters to determine optimum edible yield under varying parameters. Also, we have made preliminary effort to put together a crop handbook for BIO-Plex plant growth management. It will be a collection of information obtained from experts who provided recommendations on a particular crop's growing conditions. It includes bibliographic, environmental, nutrient solution, potential yield, harvest nutritional, and propagation procedure information. This handbook will stand as the baseline growth conditions for the first set of experiments in the BIO-Plex facility.

Allen J Nasb↗
DOE OSTI2020

Functional, Hierarchical Colloidal Liquid Crystal Gels and Liquid Crystal Elastomers Nanocomposites. Final Report

Biological systems rely on a hierarchy of dynamic, complex and reconfigurable compartments to carry out functions essential for life. This hierarchical organization serves as an amplifier that allows highly localized, molecular events to propagate into the mesoscale, resulting in dynamic functional properties of biological systems that have not yet been fully realized in synthetic material designs. We pursued a program of research in which we recreated such principles using synthetic liquid crystals (LC) as a versatile platform. We elucidated new hierarchical design strategies that heavily leverage surface anchoring, coexisting phases and interfacial tension gradient to realize equilibrium and non-equilibrium, dynamic mesoscale phenomena in the context of micrometer-sized LC droplets containing multiple compartments. Specifically, we unmasked how equilibrium and dynamical phenomena emerged from hierarchical organizations in reconfigurable, thermotropic liquid crystalline assemblies. The long-term impact of the project is to advance new hierarchical designs of complex soft matter systems in which biomimetic principles, including the propagation of events or information over multiple temporal and spatial scales, are enacted in a facile manner.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. Here, the spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.

42 ENGINEERING↗
DOE OSTI2023

KBase Narrative - SOMATA - Motivating Example

A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.

Cashman, Mikaela↗
DOE OSTI2023

Multi-scale models of whole cells: progress and challenges

Whole-cell modeling is “the ultimate goal” of computational systems biology and “a grand challenge for 21st century”. These complex, highly detailed models account for the activity of every molecule in a cell and serve as comprehensive knowledgebases for the modeled system. Their scope and utility far surpass those of other systems models. In fact, whole-cell models (WCMs) are an amalgam of several types of “system” models. The models are simulated using a hybrid modeling method where the appropriate mathematical methods for each biological process are used to simulate their behavior. Given the complexity of the models, the process of developing and curating these models is labor-intensive and to date only a handful of these models have been developed. While whole-cell models provide valuable and novel biological insights, and to date have identified some novel biological phenomena, their most important contribution has been to highlight the discrepancy between available data and observations that are used for the parametrization and validation of complex biological models. Another realization has been that current whole-cell modeling simulators are slow and to run models that mimic more complex (e.g., multi-cellular) biosystems, those need to be executed in an accelerated fashion on high-performance computing platforms. In this manuscript, we review the progress of whole-cell modeling to date and discuss some of the ways that they can be improved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Challenges in cybersecurity: Lessons from biological defense systems

Defending against novel, repeated, or unpredictable attacks, while avoiding attacks on the ‘self’, are the central problems of both mammalian immune systems and computer systems. Both systems have been studied in great detail, but with little exchange of information across the different disciplines. Here, we present a conceptual framework for structured comparisons across the fields of biological immunity and cybersecurity, by framing the context of defense, considering different (combinations of) defensive strategies, and evaluating defensive performance. Throughout this paper, we pose open questions for further exploration. In this work we hope to spark the interdisciplinary discovery of general principles of optimal defense, which can be understood and applied in biological immunity, cybersecurity, and other defensive realms.

59 BASIC BIOLOGICAL SCIENCES↗