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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Editorial: Neuroscience, computing, performance, and benchmarks: Why it matters to neuroscience how fast we can compute

At the turn of the millennium the computational neuroscience community realized that neuroscience was in a software crisis: software development was no longer progressing as expected and reproducibility declined. The International Neuroinformatics Coordinating Facility (INCF) was inaugurated in 2007 as an initiative to improve this situation. The INCF has since pursued its mission to help the development of standards and best practices. In a community paper published this very same year, Brette et al. tried to assess the state of the field and to establish a scientific approach to simulation technology, addressing foundational topics, such as which simulation schemes are best suited for the types of models we see in neuroscience. In 2015, a Frontiers Research Topic “Python in neuroscience” by Muller et al. triggered and documented a revolution in the neuroscience community, namely in the usage of the scripting language Python as a common language for interfacing with simulation codes and connecting between applications. The review by Einevoll et al. documented that simulation tools have since further matured and become reliable research instruments used by many scientific groups for their respective questions. Open source and community standard simulators today allow research groups to focus on their scientific questions and leave the details of the computational work to the community of simulator developers. A parallel development has occurred, which has been barely visible in neuroscientific circles beyond the community of simulator developers: Supercomputers used for large and complex scientific calculations have increased their performance from ~10 TeraFLOPS (10 13 floating point operations per second) in the early 2000s to above 1 ExaFLOPS (10 18 floating point operations per second) in the year 2022. This represents a 100,000-fold increase in our computational capabilities, or almost 17 doublings of computational capability in 22 years. Moore's law (the observation that it is economically viable to double the number of transistors in an integrated circuit every other 18–24 months) explains a part of this; our ability and willingness to build and operate physically larger computers, explains another part. It should be clear, however, that such a technological advancement requires software adaptations and under the hood, simulators had to reinvent themselves and change substantially to embrace this technological opportunity. It actually is quite remarkable that—apart from the change in semantics for the parallelization—this has mostly happened without the users knowing. The current Research Topic was motivated by the wish to assemble an update on the state of neuroscientific software (mostly simulators) in 2022, to assess whether we can see more clearly which scientific questions can (or cannot) be asked due to our increased capability of simulation, and also to anticipate whether and for how long we can expect this increase of computational capabilities to continue.

biophysically detailed models↗
NASA NTRS1981

Benefits of detailed models of muscle activation and mechanics

Recent biophysical and physiological studies identified some of the detailed mechanisms involved in excitation-contraction coupling, muscle contraction, and deactivation. Mathematical models incorporating these mechanisms allow independent estimates of key parameters, direct interplay between basic muscle research and the study of motor control, and realistic model behaviors, some of which are not accessible to previous, simpler, models. The existence of previously unmodeled behaviors has important implications for strategies of motor control and identification of neural signals. New developments in the analysis of differential equations make the more detailed models feasible for simulation in realistic experimental situations.

Lehman, S. L.↗
DOE OSTI2022

Columnar Localization and Laminar Origin of Cortical Surface Electrical Potentials

Electrocorticography (ECoG) methodologically bridges basic neuroscience and understanding of human brains in health and disease. However, the localization of ECoG signals across the surface of the brain and the spatial distribution of their generating neuronal sources are poorly understood. To address this gap, we recorded from rat auditory cortex using customized μECoG, and simulated cortical surface electrical potentials with a full-scale, biophysically detailed cortical column model. Experimentally, μECoG-derived auditory representations were tonotopically organized and signals were anisotropically localized to less than or equal to ±200 μm, that is, a single cortical column. Biophysical simulations reproduce experimental findings and indicate that neurons in cortical layers V and VI contribute ∼85% of evoked high-gamma signal recorded at the surface. Cell number and synchrony were the primary biophysical properties determining laminar contributions to evoked μECoG signals, whereas distance was only a minimal factor. Thus, evoked μECoG signals primarily originate from neurons in the infragranular layers of a single cortical column. SIGNIFICANCE STATEMENT ECoG methodologically bridges basic neuroscience and understanding of human brains in health and disease. However, the localization of ECoG signals across the surface of the brain and the spatial distribution of their generating neuronal sources are poorly understood. We investigated the localization and origins of sensory-evoked ECoG responses. We experimentally found that ECoG responses were anisotropically localized to a cortical column. Biophysically detailed simulations revealed that neurons in layers V and VI were the primary sources of evoked ECoG responses. These results indicate that evoked ECoG high-gamma responses are primarily generated by the population spike rate of pyramidal neurons in layers V and VI of single cortical columns and highlight the possibility of understanding how microscopic sources produce mesoscale signals.

Baratham, Vyassa L.↗
NASA NTRS1992

Testing a detailed biophysical parameterization for land-air exchange in a high-resolution boundary-layer model

This study modifies the 1D PBL model of Zhang and Anthes (1982) to account more explicitly for the effects of a vegetation layer. New equations for the latent, sensible, and ground heat fluxes, reformulated in terms of vegetation parameters are substituted into the model. The model produces good agreement with observations over a wide range of conditions: for wet, high-vegetation conditions, and for dry, low-vegetation conditions in both the winter and the summer.

Argentini, S.↗
DOE OSTI2023

Assembly of JAZ–JAZ and JAZ–NINJA complexes in jasmonate signaling

Jasmonates (JAs) are plant hormones with crucial roles in development and stress resilience. They activate MYC transcription factors by mediating the proteolysis of MYC inhibitors called JAZ proteins. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC–JAZ–Novel Interactor of JAZ (NINJA)–TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which has precluded their experimental structure determination. Through a combination of biochemical, mutational, and biophysical analyses and AlphaFold-derived ColabFold modeling, we characterized JAZ–JAZ and JAZ–NINJA interactions and generated models with detailed, high-confidence domain interfaces. We demonstrate that JAZ, NINJA, and MYC interface domains are dynamic in isolation and become stabilized in a stepwise order upon complex assembly. By contrast, most JAZ and NINJA regions outside of the interfaces remain highly dynamic and cannot be modeled in a single conformation. Our data indicate that the small JAZ Zinc finger expressed in Inflorescence Meristem (ZIM) motif mediates JAZ–JAZ and JAZ–NINJA interactions through separate surfaces, and our data further suggest that NINJA modulates JAZ dimerization. This study advances our understanding of JA signaling by providing insights into the dynamics, interactions, and structure of the JAZ–NINJA core of the JA repressor complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A novel approach to increase accuracy in remotely sensed evapotranspiration through basin water balance and flux tower constraints

Remote sensing-derived evapotranspiration (RSET) products capture the spatiotemporal variations of evapotranspiration (ET) from field to basin scales with unprecedented details. However, their accuracy varies across RSET estimation methods and diverse hydroclimate regions. While ET modeling efforts to account for biophysical processes and controlling parameters have made good progress in recent years, a parallel approach of integrating in-situ ET with RSET could reduce biases in RSET products. Basin water balance ET (WBET) and flux tower ET are widely applied to evaluate RSET accuracy, yet such ET measurements are rarely used for RSET bias corrections, especially for large area applications. To address this issue, we propose a novel approach: the water balance equivalence (WABE) method, which generates spatially continuous WBET for correcting biases in RSET products. The WABE method computes synthetic WBET by integrating observed WBET and flux tower-derived FLUXCOM ET, which fills the spatial gaps of observed WBET and generates a spatially continuous WBET dataset. Synthetic WBET (2002–2015 annual average) of eight-digit hydrologic unit code (HUC8) basins across the conterminous United States (CONUS), constituting 44 % (887 out of 2035 basins) of CONUS basins, was determined within 2.0 % (RMSE = 12 %) of observed WBET at CONUS and between 1–12 % (RMSE = 3–33 %) across 18 regions in CONUS. With WABE-based bias corrections, the overall annual bias of RSET decreased from 10 % (RMSE = 34 %) to 6 % (RMSE = 26 %) across 37 flux tower sites. The WABE method offers a new approach for RSET accuracy improvement and shows great promise for large area implementations with a potential to yield substantial benefits for building accurate basin water budgets and water management decisions.

Khand, Kul↗
DOE OSTI2025

U-Surf: a global 1 km spatially continuous urban surface property dataset for kilometer-scale urban-resolving Earth system modeling

High-resolution urban climate modeling has faced substantial challenges due to the absence of a globally consistent, spatially continuous, and accurate dataset to represent the spatial heterogeneity of urban surfaces and their biophysical properties. This deficiency has long obstructed the development of urban-resolving Earth system models (ESMs) and ultra-high-resolution urban climate modeling, over large domains. Here, we present U-Surf, a first-of-its-kind 1 km resolution present-day (circa 2020) global continuous urban surface parameter dataset. Using the urban canopy model (UCM) in the Community Earth System Model as a base model for satisfying dataset requirements, U-Surf leverages the latest advances in remote sensing, machine learning, and cloud computing to provide the most relevant urban surface biophysical parameters, including radiative, morphological, and thermal properties, for UCMs at the facet and canopy level. Generated using a systematically unified workflow, U-Surf ensures internal consistency among key parameters, making it the first globally coherent urban canopy surface dataset. U-Surf significantly improves the representation of the urban land heterogeneity both within and across cities globally; provides essential, high-fidelity surface biophysical constraints to urban-resolving ESMs; enables detailed city-to-city comparisons across the globe; and supports next-generation kilometer-resolution Earth system modeling across scales. U-Surf parameters can be easily converted or adapted to various types of UCMs, such as those embedded in weather and regional climate models, as well as air quality models. The fundamental urban surface constraints provided by U-Surf can also be used as features for machine learning models and can have other broad-scale applications for socioeconomic, public health, and urban planning contexts. We expect U-Surf to advance the research frontier of urban system science, climate-sensitive urban design, and coupled human–Earth systems in the future. The dataset is publicly available at https://doi.org/10.5281/zenodo.11247598 (Cheng et al., 2024).

Cheng, Yifan [Univ. of Illinois at Urbana-Champaig↗
NASA NTRS1974

Silverton Conference on Applications of the Zero Gravity Space Shuttle Environment to Problems in Fluid Dynamics

The possible utilization of the zero gravity resource for studies in a variety of fluid dynamics and fluid-dynamic related problems was investigated. A group of experiments are discussed and described in detail; these include experiments in the areas of geophysical fluid models, fluid dynamics, mass transfer processes, electrokinetic separation of large particles, and biophysical and physiological areas.

Eisner, M.↗
NASA NTRS2026

LAI Assimilation Schedules to Constrain Uncertain Cultivars and Soils in CERES-Maize

In anticipation of large-domain crop model applications where precise local configuration and calibration is not possible, we describe benefits and potential drawbacks of employing a crop pest module to achieve leaf area index (LAI) assimilation into a high performing CERES-Maize crop model configuration at a field experiment site in Perry, Iowa. Simulation experiments explore the use of MODIS satellite-derived LAI to constrain and adjust LAI to counter imprecise cultivar and soil configurations often occurring in the absence of high-quality local information. Simulations using single-day, window, and continuous LAI replacement across 5 cultivars and 2 soil calibration approaches for nine corn rotation years from 2004 to 2020 led to different yield outcomes and reverberations throughout the field environment. Evaluating variance and mean bias, results indicate minimal interventions in early vegetative and grain-filling stages were more beneficial than use of continuous LAI adjustments, as they minimized disruptions to the internal resource balances governing plant stresses and grain production. LAI adjustment was particularly helpful in constraining growth related to uncertain thermal unit requirements and leaf tip appearance rates (P1 and PHINT cultivar parameters, respectively). Findings underscore the need to assimilate additional state variables to ensure internal biophysical coherence. This approach shows promise for applications spanning wider domains with prediction time pressure where detailed configuration, more complex assimilation methods, or recalibration of crop model parameters may not be practical.

Phenology↗
DOE OSTI2022

Economic and biophysical limits to seaweed farming for climate change mitigation

Net-zero greenhouse gas (GHG) emissions targets are driving interest in opportunities for biomass-based negative emissions and bioenergy, including from marine sources such as seaweed. Yet the biophysical and economic limits to farming seaweed at scales relevant to the global carbon budget have not been assessed in detail. We use coupled seaweed growth and technoeconomic models to estimate the costs of global seaweed production and related climate benefits, systematically testing the relative importance of model parameters. Under our most optimistic assumptions, sinking farmed seaweed to the deep sea to sequester a gigaton of CO 2 per year costs as little as US$\$$480 per tCO 2 on average, while using farmed seaweed for products that avoid a gigaton of CO 2 -equivalent GHG emissions annually could return a profit of $\$$50 per tCO 2 -eq. However, these costs depend on low farming costs, high seaweed yields, and assumptions that almost all carbon in seaweed is removed from the atmosphere (that is, competition between phytoplankton and seaweed is negligible) and that seaweed products can displace products with substantial embodied non-CO 2 GHG emissions. Moreover, the gigaton-scale climate benefits we model would require farming very large areas (>90,000 km 2 )—a >30-fold increase in the area currently farmed. Our results therefore suggest that seaweed-based climate benefits may be feasible, but targeted research and demonstrations are needed to further reduce economic and biophysical uncertainties.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2003

Mechanosensitive Ion Channels in Bacteria: Functional Domains and Mechanisms of Gating

The past funding period was productive for the group. The progress in the mechanosensitive channel field was critically affected in the end of 1998 by the solution of the crystal structure of the mycobacterial homolog of MscL by our colleagues from Caltech. Having the structure of TbMscL in the closed state, we developed a detailed homology model of EcoMscL, and related the structural model with the wealth of functional phenomenology available for the E. coli version of the channel (EcoMscL). The biophysical properties of the open MscL helped to model the open conformation and infer the pathway for the entire gating transition. The following experiments provided strong support to the atomic model of the gating process, and allowed to make further predictions. The work has advanced our understanding of tension-driven conformational transitions in membrane-embedded mechanosensory proteins, determine major energetic contributions and set the stage for further exploration of the whole family of mechanosensitive channels. The results have been published in seven experimental and theoretical papers, with three other papers currently in press or in preparation.

Sukharev, Sergei↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nanoscopic lipid domains determined by microscopy and neutron scattering

Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. Here, in this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Challenges in simulating economic effects of climate change on global agricultural markets

Abstract Many approaches have been used to investigate climate change impacts on agriculture. However, several caveats remain in this field: (i) analyses focus only on a few major crops, (ii) large differences in yield impacts are observed between projections from site-based crops models and Global Gridded Crop Models (GGCMs), (iii) climate change impacts on livestock are rarely quantified, and (iv) several causal relations among biophysical, environmental, and socioeconomic aspects are usually not taken into account. We investigate how assumptions about these four aspects affect agricultural markets, food supply, consumer well-being, and land use at global level by deploying a large-scale socioeconomic model of the global economy with detailed representation of the agricultural sector. We find global welfare impacts several times larger when climate impacts all crops and all livestock compared to a scenario with impacts limited to major crops. At the regional level, food budget can decrease by 10 to 25% in developing countries, challenging food security. The role of land area expansion as a major source of adaptation is highlighted. Climate impacts on crop yields from site-based process crop models generate more challenging socioeconomic outcomes than those from GGCMs. We conclude that the agricultural research community should expand efforts to estimate climate impacts on many more crops and livestock. Also, careful comparison of the GGCMs and traditional site-based process crop models is needed to understand their major implications for agricultural and food markets.

Gurgel, Angelo C. (ORCID:0000000183319508)↗
NASA NTRS2007

Reconstructed Historical Land Cover and Biophysical Parameters for Studies of Land-Atmosphere Interactions within the Eastern United States

The local environment where we live within the Earth's biosphere is often taken for granted. This environment can vary depending on whether the land cover is a forest, grassland, wetland, water body, bare soil, pastureland, agricultural field, village, residential suburb, or an urban complex with concrete, asphalt, and large buildings. In general, the type and characteristics of land cover influence surface temperatures, sunlight exposure and duration, relative humidity, wind speed and direction, soil moisture amount, plant life, birds, and other wildlife in our backyards. The physical and biological properties (biophysical characteristics) of land cover help to determine our surface environment because they directly affect surface radiation, heat, and soil moisture processes, and also feedback to regional weather and climate. Depending on the spatial scale and land use intensity, land cover changes can have profound impacts on our local and regional environment. Over the past 350 years, the eastern half of the United States, an area extending from the grassland prairies of the Great Plains to the Gulf and Atlantic coasts, has experienced extensive land cover and land use changes that began with land clearing in the 1600s, led to extensive deforestation and intensive land use practices by 1920, and then evolved to the present-day landscape. Determining the consequences of such land cover changes on regional and global climate is a major research issue. Such research requires detailed historical land cover data and modeling experiments simulating historical climates. Given the need to understand the effects of historical land cover changes in the eastern United States, some questions include: - What were the most important land cover transformations and how did they alter biophysical characteristics of the land cover at key points in time since the mid-1600s? - How have land cover and land use changes over the past 350 years affected the land surface environment including surface weather, hydrologic, and climatic variability? - How do the potential effects of regional human-induced land cover change on the environment compare to similar changes that are caused by the natural variations of the Earth's climate system? To help answer these questions, we reconstructed a fractional land cover and biophysical parameter dataset for the eastern United States at 1650, 1850, 1920, and 1992 time-slices. Each land cover fraction is associated with a biophysical parameter class, a suite of parameters defining the biophysical characteristics of that kind of land cover. This new dataset is designed for use in computer models of land-atmosphere interactions, to understand and quantify the effects of historical land cover changes on the water, energy, and carbon cycles

Steyaert, Louis T.↗
DOE OSTI2025

ITreeForeCast: An integrated modeling software to simulate tree level growth and forest carbon storage

Healthy trees in forest act as a natural carbon sink, capturing carbon. As they grow, they store carbon in their trunks, leaves and roots. Not all trees store carbon at the same rate, or in the same quantities, as it depends on a variety of biophysical and climatic factors. Furthermore, although carbon estimation in trees can be complex, the precision of estimates is tightly linked to trees growth, both in diameter and height. However, the simulation of carbon uptake by forest and forest growth has each been modeled separately, and independently at differing levels of detail and spatial resolution. In this paper, we introduce ITreeForeCast, a simulation model combining the two types of modeling on a unified platform, enabling the investigation of impacts of management strategies on carbon sequestration and wood products. ITreeForeCast is a user-extendable framework that offers new opportunities to model, simulate, and visualize the dynamics of individual trees in a forest, simulate management strategies over time, and carbon uptake.

09 - BIOMASS FUELS↗
NASA NTRS2015

AgMIP's Transdisciplinary Agricultural Systems Approach to Regional Integrated Assessment of Climate Impacts, Vulnerability, and Adaptation

This chapter describes methods developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) to implement a transdisciplinary, systems-based approach for regional-scale (local to national) integrated assessment of agricultural systems under future climate, biophysical, and socio-economic conditions. These methods were used by the AgMIP regional research teams in Sub-Saharan Africa and South Asia to implement the analyses reported in their respective chapters of this book. Additional technical details are provided in Appendix 1.The principal goal that motivates AgMIP's regional integrated assessment (RIA) methodology is to provide scientifically rigorous information needed to support improved decision-making by various stakeholders, ranging from local to national and international non-governmental and governmental organizations.

agriculture↗