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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 OSTI2022

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2000

Dietary Sodium Effects on Bone Loss and Calcium Metabolism During Bed Rest

The acceleration of age-related bone loss is one of the most detrimental effects of space flight. The ability to understand and counteract this loss will be critical for crew health and safety during and after long-duration missions. Studies in healthy ambulatory individuals have linked high salt (sodium) diets, hypercalciuria, and increased renal stone risk. Dietary salt may modulate bone loss through changes in calcium metabolism and the calcium endocrine system. The research proposed here will determine the role of dietary salt in the loss of bone during simulated space flight. Calcium metabolism will be determined through calcium kinetics studies, endocrine and biochemical measurements; and estimates of the mass, distribution and mechanical properties of bone, in subjects fed low (100 mmol sodium/day) or high (250 mmol sodium/day) levels of dietary salt during 28 days of headdown tilt bedrest. This research addresses the role of dietary salt in the loss of bone and calcium in space flight, and integrates the changes in calcium metabolism with those occurring in other physiologic systems. These data will be critical for both countermeasure development, and in determination of nutritional requirements for extended-duration space flight. The potential countermeasures resulting from this research will reduce health risks due to acceleration of age-related osteoporosis and increased risk of renal stone formation..

Smith, Scott M.↗
NASA NTRS1993

Design and testing of a unique randomized gravity, continuous flow bioreactor

A rotating, null gravity simulator, or Couette bioreactor was successfully used for the culture of mammalian cells in a simulated microgravity environment. Two limited studies using Lipomyces starkeyi and Streptomyces clavuligerus were also conducted under conditions of simulated weightlessness. Although these studies with microorganisms showed promising preliminary results, oxygen limitations presented significant limitations in studying the biochemical and cultural characteristics of these cell types. Microbial cell systems such as bacteria and yeast promise significant potential as investigative models to study the effects of microgravity on membrane transport, as well as substrate induction of inactive enzyme systems. Additionally, the smaller size of the microorganisms should further reduce the gravity induced oscillatory particle motion and thereby improve the microgravity simulation on earth. Focus is on the unique conceptual design, and subsequent development of a rotating bioreactor that is compatible with the culture and investigation of microgravity effects on microbial systems. The new reactor design will allow testing of highly aerobic cell types under simulated microgravity conditions. The described reactor affords a mechanism for investigating the long term effects of reduced gravity on cellular respiration, membrane transfer, ion exchange, and substrate conversions. It offers the capability of dynamically altering nutrients, oxygenation, pH, carbon dioxide, and substrate concentration without disturbing the microgravity simulation, or Couette flow, of the reactor. All progeny of the original cell inoculum may be acclimated to the simulated microgravity in the absence of a substrate or nutrient. The reactor has the promise of allowing scientists to probe the long term effects of weightlessness on cell interactions in plants, bacteria, yeast, and fungi. The reactor is designed to have a flow field growth chamber with uniform shear stress, yet transfer high concentrations of oxygen into the culture medium. The system described allows for continuous, on line sampling for production of product without disturbing fluid and particle dynamics in the reaction chamber. It provides for the introduction of substrate, or control substances after cell adaptation to simulated microgravity has been accomplished. The reactor system provides for the nondisruptive, continuous flow replacement of nutrient and removal of product. On line monitoring and control of growth conditions such as pH and nutrient status are provided. A rotating distribution valve allows cessation of growth chamber rotation, thereby preserving the simulated microgravity conditions over longer periods of time.

Lassiter, Carroll B.↗
DOE OSTI2021

Supply analysis of preferential market incentive for energy crops

This analysis explores the valuation of feedstock quality attributes of switchgrass and miscanthus – two energy crops poised for future expansion – and compares the relative economic availability of these two crops under two scenarios: (i) uniform price assumptions (i.e., no incentive for quality), and (ii) a scenario of a price premium based on convertibility (i.e., an incentive for quality). Given data on cellulose content, hemicellulose content, and their relative convertibility, miscanthus is expected to be 11% more efficient at conversion to biofuels than switchgrass under the biochemical conversion route. Based on this scenario of improved conversion efficiency and associated profit, we simulate an 11% price premium for miscanthus over other feedstocks in a base-case scenario. By adding this price premium, supplies of miscanthus increase over the base case by about 4 million (44%), 94 million (64%), and 166 million (94%) tons in year 0, 10, and 20 after simulated contracts for production are initiated respectively. These results emphasize that custom simulations are needed to quantify feedstock availability if supplies are intended to reflect grower response to industry demands for feedstock quality specifications. Farmers can grow ‘peas or carrots’, and price signals from biorefineries will influence what energy crops they produce. Recognizing that the energy crop mix is tractable according to quality characteristics is relevant both for near-term and long-term biofuels research and development. Here, we recommend accounting for market preferences for quality attributes when estimating potential future supplies of energy crops.

09 BIOMASS FUELS↗
NASA NTRS1992

The 1991 AVIRIS/POLDER experiment in Camargue, France

Airborne campaigns during the eighties provided high spectral resolution data, collected with imaging instruments such as AIS, AVIRIS, FLI, CAESI, and ISM, in order to investigate the relationship with canopy biophysical characteristics. The statistical approaches used to analyze these data do not allow investigation of the causality and the applicability of the observed correlations. Further, statistical studies demonstrated the high degree of redundancy of the spectral information amongst many others. And for retrieving vegetation biophysical characteristics, few results demonstrate the real information gain attributable to the high spectral resolution capability as compared to the use of a few wide wavelength bands. With several new imaging spectrophotometers scheduled for launch during the next 10 years (MERIS, MODIS, HIRIS), progress in the description and understanding of the mechanisms that drive the spectral variation of canopy reflectance is required. Most of these new sensor systems will also have the capability to observe the target under differing view directions. The problem of the combination and the use of the synergy between both the spectral and the directional sources of canopy reflectance variations has to be addressed. Apart from the atmospheric effects, the spectral variation of the light reflected by canopies originates from the leaves, the soil or the other vegetation elements such as branches and fruits. At leaf level, both diffuse reflectance and transmittance may be simulated by simple models, although no accurate information exists on the absorption features of the biochemicals (except water) in the 900-2500nm wavelength range. Many models mimic the directional variability of canopy reflectance at a given wavelength. Combining a leaf spectral model with a canopy directional model provides a powerful tool to analyze this problem. Some of us have initiated such a study, but our approach and theory remain to be tested using canopy data with their complexity, associated experimental error, and atmospheric effects. The main objective of the 1990 POLDER/AVIRIS experiment in Camargue was to provide a consistent data set over various canopies in order to test the applicability of the theory. The experiment, part of the 1991 MAC Europe experiment, involved simultaneous data collection using two sensors: AVIRIS and POLDER which measures the bidirectional and polarization properties of the targets at 670 and 880nm wavebands.

Baret, F.↗
NASA NTRS2016

EVA Health and Human Performance Benchmarking Study

Multiple HRP Risks and Gaps require detailed characterization of human health and performance during exploration extravehicular activity (EVA) tasks; however, a rigorous and comprehensive methodology for characterizing and comparing the health and human performance implications of current and future EVA spacesuit designs does not exist. This study will identify and implement functional tasks and metrics, both objective and subjective, that are relevant to health and human performance, such as metabolic expenditure, suit fit, discomfort, suited postural stability, cognitive performance, and potentially biochemical responses for humans working inside different EVA suits doing functional tasks under the appropriate simulated reduced gravity environments. This study will provide health and human performance benchmark data for humans working in current EVA suits (EMU, Mark III, and Z2) as well as shirtsleeves using a standard set of tasks and metrics with quantified reliability. Results and methodologies developed during this test will provide benchmark data against which future EVA suits, and different suit configurations (eg, varied pressure, mass, CG) may be reliably compared in subsequent tests. Results will also inform fitness for duty standards as well as design requirements and operations concepts for future EVA suits and other exploration systems.

Abercromby, A. F.↗
NASA NTRSDate not supplied

Quantum Hardware-Enabled Molecular Dynamics via Transfer Learning

The ability to perform ab initio molecular dynamics simulations using potential energy surfaces provided by quantum computers would open the door to virtually exact dynamics for a variety of chemical and biochemical systems, with impacts on catalysis and biophysics. Nonetheless, performing molecular dynamics on surfaces produced by quantum hardware has been hampered by the noisy energies typically produced by quantum computers and challenges associated with computing gradients and scaling to large systems interest. A recent set of advances in machine learning, known as transfer learning, provides a new path forward for molecular dynamics simulations on quantum hardware. Transfer learning offers a workaround, where one first trains models on larger, less accurate classical datasets and then refines them on smaller, more accurate quantum datasets. We explore this approach by training machine learning models to predict a molecule's potential energy based on its geometric structure using Behler-Parrinello neural networks. When successfully trained, the model enables energy gradient predictions necessary for dynamic simulations. To reduce the quantum resources needed, the model is initially trained with data derived from classical density functional theory and subsequently refined with a smaller dataset obtained from a variational quantum eigensolver optimization of the unitary coupled cluster ansatz. We show that this approach significantly reduces the size of the needed quantum training dataset while capturing the high accuracies needed within quantum chemistry simulations. The success of this two-step training method opens more opportunities to apply machine learning models on quantum data, a significant stride towards efficient quantum-classical hybrid computational models.

quantum computing↗
DOE OSTI2023

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization

Abstract HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA NTD -CA NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A a α9-helices compared to WT, E45A/R132T, WT PF74 , WT Nup153 , and WT CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon-climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool-based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool-based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. In this study, we propose a novel conceptual framework to explore controls on belowground carbon cycling: Probabilistic Representation of Organic Matter Interactions within the Soil Environment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1997

Advanced Technologies for Space Life Science Payloads on the International Space Station

SENSORS 2000! (S2K!) is a specialized, high-performance work group organized to provide advanced engineering and technology support for NASA's Life Sciences spaceflight and ground-based research and development programs. In support of these objectives, S2K! manages NASA's Advanced Technology Development Program for Biosensor and Biotelemetry Systems (ATD-B), with particular emphasis on technologies suitable for Gravitational Biology, Human Health and Performance, and Information Technology and Systems Management. A concurrent objective is to apply and transition ATD-B developed technologies to external, non-NASA humanitarian (medical, clinical, surgical, and emergency) situations and to stimulate partnering and leveraging with other government agencies, academia, and the commercial/industrial sectors. A phased long-term program has been implemented to support science disciplines and programs requiring specific biosensor (i.e., biopotential, biophysical, biochemical, and biological) measurements from humans, animals (mainly primates and rodents), and cells under controlled laboratory and simulated microgravity situations. In addition to the technology programs described above, NASA's Life and Microgravity Sciences and Applications Office has initiated a Technology Infusion process to identify and coordinate the utilization and integration of advanced technologies into its International Space Station Facilities. This project has recently identified a series of technologies, tasks, and products which, if implemented, would significantly increase the science return, decrease costs, and provide improved technological capability. This presentation will review the programs described above and discuss opportunities for collaboration, leveraging, and partnering with NASA.

Hines, John W.↗
NASA NTRS2003

Growth and Metabolism of the Green Alga, Chlorella Pyrenoidosa, in Simulated Microgravity

The effect of microgravity on living organisms during space flight has been a topic of interest for some time, and a substantial body of knowledge on the subject has accumulated. Despite this, comparatively little information is available regarding the influence of microgravity on algae, even though it has been suggested for long duration flight or occupancy in space that plant growth systems, including both higher plants and algae, are likely to be necessary for bioregenerative life support systems. High-Aspect-Ratio Rotating-Wall Vessel or HARV bioreactors developed at Johnson Space Center provide a laboratory-based approach to investigating the effects of microgravity on cellular reactions. In this study, the HARV bioreactor was used to examine the influence of simulated microgravity on the growth and metabolism of the green alga, Chlorella pyrenoidosa. After the first 2 days of culture, cell numbers increased more slowly in simulated microgravity than in the HARV gravity control; after 7 days, growth in simulated microgravity was just over half (58%) that of the gravity control and at 14 days it was less than half (42%). Chlorophyll and protein were also followed as indices of cell competence and function; as with growth, after 2-3 days, protein and chlorophyll levels were reduced in modeled microgravity compared to gravity controls. Photosynthesis is a sensitive biochemical index of the fitness of photosynthetic organisms; thus, CO2-dependent O2 evolution was tested as a measure of photosynthetic capacity of cells grown in simulated microgravity. When data were expressed with respect to cell number, modeled microgravity appeared to have little effect on CO2 fixation. Thus, even though the overall growth rate was lower for cells cultured in microgravity, the photosynthetic capacity of the cells appears to be unaffected. Cells grown in simulated microgravity formed loose clumps or aggregates within about 2 days of culture, with aggregation increasing over time. Presently, the basis for, or significance of, the cell aggregation is unknown. The results from this study suggest that cell growth and morphological characteristics of green algae may be altered by culture in simulated microgravity. The data obtained to date should provide a solid basis for additional experimentation regarding the influence of modeled microgravity on cell morphology, physiological activity, protein production and possibly gene expression in algal and plant cell systems. The final aim of the study is to provide useful information to elucidate the underlying mechanism for the biological effects of microgravity on cells.

Mills, W. Ronald↗
NASA NTRS1997

Integration of CELSS Simulation with Long-Term Crop Scheduling

This project presents guidelines for the integration of the Intelligent Crop Scheduler (ICS) developed by Leon (1995) with a version of the Biological Life Support System (BLSS) simulation based on the work by Volk and Rummel (1987). These guidelines will also aid in defining the appropriate model detail of simulation-based schedulers. ICS determines what, when and how much to plant of different crops. These decisions are made such that the critical reservoir levels are maintained close to their nominal or desired settings during the duration of the mission. Initial feasibility of the approach has been demonstrated using simplified implementations of the scheduling approach and CELSS 'world' model developed by the investigator at JSC in the Summer of 1995. The BLSS model incorporates more detail. The increased fidelity is in terms of added mass-regeneration formalism (biochemical stoichiometry), more plants, and more accurate modeling of the mechanical system. This report describes the main features of the Crop scheduler and CELSS simulator, discusses integration issues, and provides with detailed guidelines for the integration of these two applications.

Leon, V. Jorge↗
NASA NTRS2002

Mechanotransduction through Cytoskeleton

The goal of this project was to characterize the molecular mechanism by which cells recognize and respond to physical forces in their local environment. The project was based on the working hypothesis that cells sense mechanical stresses, such as those due to gravity, through their cell surface adhesion receptors (e.g., integrins) and that they respond as a result of structural arrangements with their internal cytoskeleton (CSK) which are orchestrated through use of tensegrity architecture. In this project, we carried out studies to define the architectural and molecular basis of cellular mechanotransduction. Our major goal was to define the molecular pathway that mediates mechanical force transfer between integrins and the CSK and to determine how mechanical deformation of integrin-CSK linkages is transduced into a biochemical response. Elucidation of the mechanism by which cells sense mechanical stresses through integrins and translate them into a biochemical response should help us to understand the molecular basis of the cellular response to gravity as well as many other forms of mechanosensation and tissue regulation. The specific aims of this proposal were: 1. To define the molecular basis of mechanical coupling between integrins, vinculin, and the actin CSK; 2. To develop a computer simulation of how mechanical stresses alter CSK structure and test this model in living cells; 3. To determine how mechanical deformation of integrin-CSK linkages is transduced into a biochemical response.

Ingber, Donald↗
DOE OSTI2024

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2009

Simulating Bone Loss in Microgravity Using Mathematical Formulations of Bone Remodeling

Most mathematical models of bone remodeling are used to simulate a specific bone disease, by disrupting the steady state or balance in the normal remodeling process, and to simulate a therapeutic strategy. In this work, the ability of a mathematical model of bone remodeling to simulate bone loss as a function of time under the conditions of microgravity is investigated. The model is formed by combining a previously developed set of biochemical, cellular dynamics, and mechanical stimulus equations in the literature with two newly proposed equations; one governing the rate of change of the area of cortical bone tissue in a cross section of a cylindrical section of bone and one governing the rate of change of calcium in the bone fluid. The mechanical stimulus comes from a simple model of stress due to a compressive force on a cylindrical section of bone which can be reduced to zero to mimic the effects of skeletal unloading in microgravity. The complete set of equations formed is a system of first order ordinary differential equations. The results of selected simulations are displayed and discussed. Limitations and deficiencies of the model are also discussed as well as suggestions for further research.

Pennline, James A.↗
NASA NTRS1992

The role of pyridoxine as a countermeasure for in-flight loss of lean body mass

Ground based and in flight research has shown that humans, under conditions of microgravity, sustain a loss of lean body tissue (protein) and changes in several biological processes including, reductions in red blood cell mass, and neurotransmitters. The maintenance of muscle mass, the major component of lean body mass, is required to meet the needs of space station EVAs. Central to the biosynthesis of amino acids, the building blocks of protein, is pyridoxine (vitamin B-6). Muscle mass integrity requires the availability of vitamin B-6 for protein metabolism and neurotransmitter synthesis. Furthermore, the formation of red blood cells require pyridoxine as a cofactor in the biosynthesis of hemoglobin, a protein that carries oxygen to tissues. In its active form, pyridoxal-5'-phosphate (PLP), vitamin B-6 serves as a link between amino acid and carbohydrate metabolism through intermediates of glycolysis and the tricarboxylic acid cycle. In addition to its role in energy metabolism, PLP is involved in the biosynthesis of hemoglobin and neurotransmitter which are necessary for neurological functions. Alterations in pyridoxine metabolism may affect countermeasures designed to overcome some of these biochemical changes. The focus of this research is to determine the effects of microgravity on the metabolic utilization of vitamin B-6, integrating nutrition as an integral component of the countermeasure (exercise) to maintain lean body mass and muscle strength. The objectives are: 1) to determine whether microgravity effects the metabolic utilization of pyridoxine and 2) to quantitate changes in B-6 vitamer distribution in tissue and excreta relative to loss of lean body tissue. The rationale for this study encompasses the unique challenge to control biochemical mechanisms effected during space travel and the significance of pyridoxine to maintain and counter muscle integrity for EVA activities. This experiment will begin to elucidate the importance of biochemical interactions between micronutrients and the homeostasis condition of biological processes in the space environment. To address this research topic a simulated microgravity model has been developed. The experiment uses radioisotopically labelled pyridoxine administered as an oral dose to rats which are maintained by tail suspension to simulate a microgravity environment. At the termination of the study, liver, muscle, blood and urine are collected and analyzed by reverse phase high pressure liquid chromatography to determine the quantity and distribution of the B-6 vitamers in tissue and excreta relative to lean body tissue loss. Earlier studies, published by this investigator, have shown that differences in vitamer distribution among samples from experimental versus control subjects indicate changes in metabolic utilization and storage of vitamin B-6.

Gilbert, Joyce A.↗
DOE OSTI2024

Spatial modeling algorithms for reactions and transport in biological cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗