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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2001

Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

Beard, Daniel A.↗
NASA NTRS2003

Second Law of Thermodynamics Applied to Metabolic Networks

We present a simple algorithm based on linear programming, that combines Kirchoff's flux and potential laws and applies them to metabolic networks to predict thermodynamically feasible reaction fluxes. These law's represent mass conservation and energy feasibility that are widely used in electrical circuit analysis. Formulating the Kirchoff's potential law around a reaction loop in terms of the null space of the stoichiometric matrix leads to a simple representation of the law of entropy that can be readily incorporated into the traditional flux balance analysis without resorting to non-linear optimization. Our technique is new as it can easily check the fluxes got by applying flux balance analysis for thermodynamic feasibility and modify them if they are infeasible so that they satisfy the law of entropy. We illustrate our method by applying it to the network dealing with the central metabolism of Escherichia coli. Due to its simplicity this algorithm will be useful in studying large scale complex metabolic networks in the cell of different organisms.

Nigam, R.↗
NASA NTRSDate not supplied

Bioreactor Development for CO2-Based In Situ Resource Utilization Manufacturing

Sustainable long-duration manned missions on both the Moon and Mars will require in situ resource utilization (ISRU). Carbon dioxide (CO2) has great potential as a harvestable resource, making up 95% of the atmosphere on Mars and being produced as respiratory waste in spacecraft and future planetary habitats. Through ISRU, biomanufacturing has the capability to produce a near limitless array of products from local space resources. Here, a CO2-based ISRU recombinant protein producing bioreactor and associated biomanufacturing organisms were designed to produce a highly stable carbonic anhydrase (CA). Candidate organisms were selected by growth characterization on acetate and formic acid, carbon substrates that are synthesized via electrochemical conversion of CO2. To improve growth on the CO2 producing substrate formic acid and for direct integration of ISRU CO2, a synthetic Calvin-Benson-Bassam cycle was designed for use in Escherichia coli. Multiplex genetic modification in E. coli was facilitated by a tailored CRISPR/Cas9 and λ red recombineering two-vector system. For expression of CA, a blue light regulated T7 promoter was employed for dynamic and small molecule free induction. Efficient bioproduction through a fed-batch exponential feeding strategy was determined via mass balance analysis from ISRU substrates to biomass and CA yield. Flux balance analysis was used to model ISRU substrate metabolism and metabolic pathway engineering in candidate organisms under cultivation strategy conditions for both metabolism reconstruction and pathway design optimization. Finally, a small-scale, disposable bag bioreactor for use in the NASA Bioculture System infrastructure was designed to enable CO2-based CA biomanufacturing in reduced-gravity environments.

biomanufacturing↗
NASA NTRSDate not supplied

Bioreactor Development for CO2-Based In Situ Resource Utilization Manufacturing

Sustainable long-duration manned missions on both the Moon and Mars will require in situ resource utilization (ISRU). Carbon dioxide (CO2) has great potential as a harvestable resource, making up 95% of the atmosphere on Mars and being produced as respiratory waste in spacecraft and future planetary habitats. Through ISRU, biomanufacturing has the capability to produce a near limitless array of products from local space resources, which include pharmaceuticals, bioplastics, chemical feedstocks, and industrial enzymes. Here, a CO2-based ISRU recombinant protein bioreactor and associated biomanufacturing organisms were designed to produce a highly stable carbonic anhydrase (CA). Initial work characterized candidate organisms for growth on acetate and formic acid, carbon substrates that can be synthesized via electrochemical conversion of CO2. To improve growth on the CO2 producing substrate formic acid and for direct integration of ISRU CO2, a synthetic Calvin-Benson-Bassam cycle was designed for use in Cyberlindnera jadinii and Escherichia coli. Genetic modifications in E. coli will be facilitated by a tailored CRISPR/Cas9 and λ red recombineering two-vector system. For expression of CA, a blue light regulated T7 promoter was employed for dynamic and small molecule free induction. Efficient bioproduction through a fed-batch exponential feeding strategy was determined via mass balance calculations from ISRU substrates to biomass and CA yield. Flux balance analysis was used to model ISRU substrate metabolism and metabolic pathway engineering in candidate organisms under cultivation strategy conditions for both metabolism reconstruction and pathway design optimization. Finally, a small-scale, disposable bag bioreactor concept for use in the NASA Bioculture System infrastructure was designed to enable CO2-based CA production in reduced-gravity environments.

Biomanufacturing, Pathway Engineering, Flux Balanc↗
NASA NTRS1978

Numerical analyses for treating diffusion in single-, two- and three-phase binary alloy systems

Numerical solutions were applicable for planar, cylindrical, or spherical geometries with any diffusion-zone size and any continuous variation of the diffusion coefficient with concentration. Special techniques were included in the analyses to account for differences in molal volumes, initiation and growth of an intermediate phase, disappearance of a phase, and the presence of an initial composition profile in the specimen. A major improvement in solution accuracy was achieved in the two phase analysis by employing a mass conservation criterion to establish the location of the interface rather than the conventional interface-flux-balance criterion. In the three phase analysis, computation time was minimized without sacrificing solution accuracy by treating the three phase problem as a two phase problem when the thickness of the intermediate phase was less than a preset small value. Three computer codes were developed to perform these analyses.

Tenney, D. R.↗
NASA NTRS1998

Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Methods and Applications

Thermal Infrared (TIR) remote sensing data can provide important measurements of surface energy fluxes and temperatures, which are integral to understanding landscape processes and responses. One example of this is the successful application of TIR remote sensing data to estimate evapotranspiration and soil moisture, where results from a number of studies suggest that satellite-based measurements from TIR remote sensing data can lead to more accurate regional-scale estimates of daily evapotranspiration. With further refinement in analytical techniques and models, the use of TIR data from airborne and satellite sensors could be very useful for parameterizing surface moisture conditions and developing better simulations of landscape energy exchange over a variety of conditions and space and time scales. Thus, TIR remote sensing data can significantly contribute to the observation, measurement, and analysis of energy balance characteristics (i.e., the fluxes and redistribution of thermal energy within and across the land surface) as an implicit and important aspect of landscape dynamics and landscape functioning. The application of TIR remote sensing data in landscape ecological studies has been limited, however, for several fundamental reasons that relate primarily to the perceived difficulty in use and availability of these data by the landscape ecology community, and from the fragmentation of references on TIR remote sensing throughout the scientific literature. It is our purpose here to provide evidence from work that has employed TIR remote sensing for analysis of landscape characteristics to illustrate how these data can provide important data for the improved measurement of landscape energy response and energy flux relationships. We examine the direct or indirect use of TIR remote sensing data to analyze landscape biophysical characteristics, thereby offering some insight on how these data can be used more robustly to further the understanding and modeling of landscape ecological processes.

Quattrochi, Dale A.↗
NASA NTRS1993

Research into the influence of spatial variability and scale on the parameterization of hydrological processes

The objectives of the research were as follows: (1) Extend the Representative Elementary Area (RE) concept, first proposed and developed in Wood et al, (1988), to the water balance fluxes of the interstorm period (redistribution, evapotranspiration and baseflow) necessary for the analysis of long-term water balance processes. (2) Derive spatially averaged water balance model equations for spatially variable soil, topography and vegetation, over A RANGE OF CLIMATES. This is a necessary step in our goal to derive consistent hydrologic results up to GCM grid scales necessary for global climate modeling. (3) Apply the above macroscale water balance equations with remotely sensed data and begin to explore the feasibility of parameterizing the water balance constitutive equations at GCM grid scale.

Wood, Eric F.↗
NASA NTRS1991

Multispectral satellite data in the context of land surface heat balance

Multispectral satellite data are demonstrated to be an important potential contributor to the understanding and completeness of heat balance analysis. Satellite observations are presented, including visible, near-IR, IR, and microwave bands, which estimate surface characteristics and surface fluctuations. The relationship of the interannual variations of the satellite data and the land surface changes is discussed. It is shown that spatially representative values of global fluxes and parameters from multispectral data can consistently enhance the results of heat balance analysis. Daily net radiation can be estimated with a 10 percent error, while the error for albedo would be higher. Computations for all heat fluxes except the latent heat flux are shown. Soil moisture and surface temperature estimates can be derived from microwave and IR observations, respectively. Spectral reflectances in the visible and near-IR bands are suggested as important heat-balance indices for future consideration.

Choudhury, Bhaskar J.↗
NASA NTRS2023

Using Orbiting Carbon Observatory-2 (OCO-2) column CO2 retrievals to rapidly detect and estimate biospheric surface carbon flux anomalies

The global carbon cycle is experiencing continued perturbations via increases in atmospheric carbon concentrations, which are partly reduced by terrestrial biosphere and ocean carbon uptake. Greenhouse gas satellites have been shown to be useful in retrieving atmospheric carbon concentrations and observing surface and atmospheric CO2 seasonal-to-interannual variations. However, limited attention has been placed on using satellite column CO2 retrievals to evaluate surface CO2 fluxes from the terrestrial biosphere without advanced inversion models at low latency. Such applications could be useful to monitor, in near real time, biosphere carbon fluxes during climatic anomalies like drought, heatwaves, and floods, before more complex terrestrial biosphere model outputs and/or advanced inversion modelling estimates become available. Here, we explore the ability of Orbiting Carbon Observatory-2 (OCO-2) column-averaged dry air CO2 (XCO2) retrievals to directly detect and estimate terrestrial biosphere CO2 flux anomalies using a simple mass-balance approach. An initial global analysis of surface–atmospheric CO2 coupling and transport conditions reveals that the western US, among a handful of other regions, is a feasible candidate for using XCO2 for detecting terrestrial biosphere CO2 flux anomalies. Using the CarbonTracker model reanalysis as a test bed, we first demonstrate that a well-established mass-balance approach can estimate monthly surface CO2 flux anomalies from XCO2 enhancements in the western United States. The method is optimal when the study domain is spatially extensive enough to account for atmospheric mixing and has favorable advection conditions with contributions primarily from one background region. We find that errors in individual soundings reduce the ability of OCO-2 XCO2 to estimate more frequent, smaller surface CO2 flux anomalies. However, we find that OCO-2 XCO2 can often detect and estimate large surface flux anomalies that leave an imprint on the atmospheric CO2 concentration anomalies beyond the retrieval error/uncertainty associated with the observations. OCO-2 can thus be useful for low-latency monitoring of the monthly timing and magnitude of extreme regional terrestrial biosphere carbon anomalies.

Andrew F. Feldman↗
NASA NTRS1981

Analysis of the surface heat balance over the world ocean

The net surface heat fluxes over the global ocean for all calendar months were evaluated. To obtain a formula in the form Qs = Q2(T*A - Ts), where Qs is the net surface heat flux, Ts is the sea surface temperature, T*A is the apparent atmospheric equilibrium temperature, and Q2 is the proportionality constant. Here T*A and Q2, derived from the original heat flux formulas, are functions of the surface meteorological parameters (e.g., surface wind speed, air temperature, dew point, etc.) and the surface radiation parameters. This formulation of the net surface heat flux together with climatological atmospheric parameters provides a realistic and computationally efficient upper boundary condition for oceanic climate modeling.

Esbenson, S. K.↗
NASA NTRS1974

The structure and circulation of the deep Venus atmosphere

A simple model for the structure of a nonrotating Hadley regime in an atmosphere with large thermal inertia is developed. The radiative fluxes are estimated by using a linearization about the radiative equilibrium state, and the dynamical fluxes are estimated by using scaling analysis. The requirement that differential heating by these fluxes be in balance in both the meridional and vertical directions leads to two equations for the mean static stability and meridional temperature contrast. The solution depends on two parameters: the strength of the radiative heating, as measured by the static stability of the radiative equilibrium state; and the ratio of the time it takes an external gravity wave to traverse the atmosphere to the time it would take the atmosphere to cool off radiatively. It is shown that it is not necessary to invoke convection to explain the approximate adiabatic lapse rate in the Venus atmosphere, but a greenhouse effect is necessary to explain the high surface temperatures.

Stone, P. H.↗
NASA NTRS1972

The electron heating rate and ion chemistry in the thermosphere above Wallops Island during the solar eclipse of 7 March 1970.

Measurement of the N2 concentration and temperature, the ion composition and concentrations, and the electron temperature up to 290 km about 30 and 5 min before totality during the Mar. 7, 1970, eclipse. The rockets traveled similar trajectories, thus permitting the purely temporal changes between flights to be resolved. The neutral temperature and N2 concentration changed little, but the electron temperature decreased by as much as 20% in the lower F region. The ion concentration decreased by about 30% in the F region and about 50% in the E region, with little change in relative ion composition. The electron cooling rates decreased by a factor of 6 in the lower F region, approximately in proportion to the change in the visible solar disk. A smaller than expected decrease in the cooling rate below 150 km between the two flights indicates a hardening of the solar spectrum and suggests a significant heat contribution from the solar corona near totality. The ion composition measurements were consistent with solutions of the ion continuity equations. A proper fit required a factor-of-three enhancement of the flux below 200 A, an amount also consistent with the electron heat balance analysis. Reactions involving the minor ions N(+) and N2(+) were found to be important for the ion chemistry of the major ions O2(+) and NO(+), especially at the time of eclipse.-

Brace, L. H.↗
NASA NTRS1993

Moist wind relationships

Equations describing the temporal and spatial behavior of the kinematic moisture and heat flux are introduced. In these nonlinear equations, the contribution by diabatic processes to the large-scale flux is composed of two parts. One part is associated with a Rayleigh damping term, while the other arises from temporal and spatial changes in the pressure gradient term. The influence of diabatic processes on the large-scale moisture fluxes depends greatly on the degree of balance between forcing and damping terms in the governing equations. The existence of a near balance requires a reduction in the large-scale horizontal geostrophic wind speed. From a scale analysis of the moisture flux equations it is argued that reductions in the large-scale horizontal wind speed, observed within major cumulus cloud systems, help conserve large-scale moisture fluxes. The deviation of the wind from geostrophic conditions is easily estimated. This wind modification induces secondary vertical circulations that contribute to the convergence, creating or supporting long-lived mesoscale flows. In the tropics the wind modification has an antitriptic relationship. These diagnostic findings suggest possible modifications to the wind field in the application of cumulus parameterization, and may be important in diabatic initialization of numerical weather prediction models.

Raymond, William H.↗
NASA NTRS1994

A season of heat, water vapor, total hydrocarbon, and ozone fluxes at a subarctic fen

High-latitude environments are thought to play several critical roles in the global balance of radiatively active trace gases. Adequate documentation of the source and sink strengths for trace gases requires long time series of detailed measurements, including heat and moisture budgets. A fen near Schefferville, Quebec, was instrumented during the summer of 1990 for the measurement of the surface energy, radiation, and moisture balances as well as for eddy correlation estimates of ozone and methane flux. Despite the limited fetch at this site, analysis of the tower flux 'footprint' indicates that at least 80% of the flux observed originates from sources within the fen. Sensible heat fluxes averaged 25% of the daytime net radiation at the site, while the latent heat flux, determined from the energy balance, was 63%; the Bowen ratio varied from 0.2 to 0.8 from day to day, without a seasonal trend to the variation. The competing effects of rooted macrophyte development (with concomitant effects on roughness and transpiration) and the normal shift in synoptic pattern around day 200 to warm, dry conditions results in a lack of net seasonal effect on the energy partitioning. Over the period from days 170 to 230, the evaporation (167 mm) was double the rainfall, while the decline in water level was 107 mm, leaving a net runoff of 0.44 mm/d. The total hydrocarbon flux was 75-120 mg m(exp -2)/d, following a diurnal pattern similar to heat or moisture flux, while the daytime ozone flux was about -1.11 x 10(exp 11) molecules cm(exp -2)/s. A period near the end of the experiment, during week 30, produced the strongest total hydrocarbon flux, associated with warmer deep (1 m) soil temperatures, lower fen water levels, and the late summer shift in wind direction at that time. An early summer 'flush' of total hydrocarbon was not observed.

Moore, Kathleen E.↗
NASA NTRS2010

Enhanced Surface Warming and Accelerated Snow Melt in the Himalayas and Tibetan Plateau Induced by Absorbing Aerosols

Numerical experiments with the NASA finite-volume general circulation model show that heating of the atmosphere by dust and black carbon can lead to widespread enhanced warming over the Tibetan Plateau (TP) and accelerated snow melt in the western TP and Himalayas. During the boreal spring, a thick aerosol layer, composed mainly of dust transported from adjacent deserts and black carbon from local emissions, builds up over the Indo-Gangetic Plain, against the foothills of the Himalaya and the TP. The aerosol layer, which extends from the surface to high elevation (approx.5 km), heats the mid-troposphere by absorbing solar radiation. The heating produces an atmospheric dynamical feedback the so-called elevated-heat-pump (EHP) effect, which increases moisture, cloudiness, and deep convection over northern India, as well as enhancing the rate of snow melt in the Himalayas and TP. The accelerated melting of snow is mostly confined to the western TP, first slowly in early April and then rapidly from early to mid-May. The snow cover remains reduced from mid-May through early June. The accelerated snow melt is accompanied by similar phases of enhanced warming of the atmosphere-land system of the TP, with the atmospheric warming leading the surface warming by several days. Surface energy balance analysis shows that the short-wave and long-wave surface radiative fluxes strongly offset each other, and are largely regulated by the changes in cloudiness and moisture over the TP. The slow melting phase in April is initiated by an effective transfer of sensible heat from a warmer atmosphere to land. The rapid melting phase in May is due to an evaporation-snow-land feedback coupled to an increase in atmospheric moisture over the TP induced by the EHP effect.

Lau, William K.↗
NASA NTRS1981

Analysis of the surface heat balance over the world ocean

It is possible to estimate long term monthly mean latent and sensible heat fluxes over the ocean to within or approximately 20% relative accuracy of the bulk aerodynamic formulas, by using observations of the monthly mean surface wind speed and the monthly mean sea air temperature and humidity differences. It is possible to make an estimate of the fluxes on a month to month basis from monthly averaged surface data.

Esbensen, S. K.↗
NASA NTRS1992

Viscously driven plasma flows in the deep geomagnetic tail

An analysis, based on the principles of stress balance in a 1-dimensional current sheet is presented, which considers the problem of closed magnetic flux transport into the deep tail by a 'viscous'-like interaction between the solar wind and the magnetosphere. The analysis is illustrated with an example of ISEE-3 data showing strong tailward plasma sheet flows on apparently closed field lines in the deep tail. Apart from narrow regions adjacent to the magnetopause, these flows are not driven by the scattering of magnetosheath plasma into the magnetosphere. The fraction of the magnetosheath momentum flux needed to be anomalously transferred into the plasma sheet to drive the flows is estimated. In the example this is 6 percent. No previously suggested mechanism (e.g., the Kelvin-Helmholtz instability) has been shown capable of providing anomalous momentum transport of this magnitude. The current understanding of the 'viscous' interaction between the solar wind and magnetosphere is thus insufficient to explain these observations.

Owen, C. J.↗
NASA NTRS2018

TPSAS-NF1676L-29978-DND

Energy within an atmospheric column changes due to absorption of shortwave irradiance, emission of longwave irradiance, enthalpy released by precipitation, convergence of dry static and kinetic energy flux, and surface sensible heat flux. When satellite derived irradiance, precipitation, and surface sensible heat flux data products, as well as tendency and horizontal advection of dry static and kinetic energy fluxes from reanalysis are used to compute the atmospheric energy balance, energy fluxes does not balance exactly, resulting in an energy balance residual. A study by Kato et al. (2016) shows that large residuals exist over tropical oceans. In this study, we examine how the energy balance residual changes with time. If the energy balance residual for a given region is constant every year, this implies that annual anomalies of energy flux components balance over the region. If, however, the energy balance residual changes with time, an analysis of the dependence on atmospheric or cloud properties may provide information to understand the reason for the residual. A preliminary result indicates that significant interannual variabilities in energy balance residual exist when annual energy balance residuals over the entire ocean is examined. Temporal variability of regional energy budget residual and covariability of the energy budget residual with the multivariate ENSO index and the occurrence of specific cloud types will further be investigated.

Seiji Kato↗