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At least 37 records · Page 2

Modeling of Biological Fluid Systems

This study presents a detailed methodology for modeling and validating three- dimensional fluid flow in realistic reconstructed vasculature geometry. Optical scanned data from a sectioned stenotic lumen having -65% area constriction within an arterial vessel of 9 mm diameter is processed and converted into a finite-element mesh. Mass and momentum transfer equations within the reconstructed stenotic vessel with a-flow rate of 200 ml/rnin is solved using the Galarkin Finite Element formulation. The calculated velocities at several axial locations along the length of the vessel are compared with the Particle Image Velocimetry (PIV) measurements. The computation results are in agreement with the initial steady state PIV measurements. In addition, initial results from pulsatile flow computations at different time points of a pulse cycle will be presented.

Banerjee, Rupak

Cellular track model of biological damage to mammalian cell cultures from galactic cosmic rays

The assessment of biological damage from the galactic cosmic rays (GCR) is a current interest for exploratory class space missions where the highly ionizing, high-energy, high-charge ions (HZE) particles are the major concern. The relative biological effectiveness (RBE) values determined by ground-based experiments with HZE particles are well described by a parametric track theory of cell inactivation. Using the track model and a deterministic GCR transport code, the biological damage to mammalian cell cultures is considered for 1 year in free space at solar minimum for typical spacecraft shielding. Included are the effects of projectile and target fragmentation. The RBE values for the GCR spectrum which are fluence-dependent in the track model are found to be more severe than the quality factors identified by the International Commission on Radiological Protection publication 26 and seem to obey a simple scaling law with the duration period in free space.

Cucinotta, Francis A.

Biological indicators for monitoring water quality of MTF canals system

Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

Sethi, S. L.

A numerical analysis of shipboard and coastal zone color scanner time series of new production within Gulf Stream cyclonic eddies in the South Atlantic Bight

Eddy-induced upwelling occurs along the western edge of the Gulf Stream between Cape Canaveral, Florida, and Cape Hatteras, North Carolina, in the South Atlantic Bight (SAB). Coastal zone color scanner images of 1-km resolution spanning the period April 13-21, 1979, were processed to examine these eddy features in relation to concurrent shipboard and current/temperature measurements at moored arrays. A quasi-one-dimensional (z), time dependent biological model, using only nitrate as a nutrient source, has been combined with a three-dimensional physical model in an attempt to replicate the observed phytoplankton field at the northward edge of an eddy. The model is applicable only to the SAB south of the Charleston Bump, at approximately 31.5 deg N, since no feature analogous to the bump exists in the model bathymetry. The modeled chlorophyll, nitrate, and primary production fields of the euphotic zone are very similar to those obtained from the satellite and shipboard data at the leading edges of the observed eddies south of the Charleston Bump. The horizontal and vertical simulated fluxes of nitrate and chlorophyll show that only approximately 10% of the upwelled nitrate is utilized by the phytoplankton of the modeled grid box on the northern edge of the cyclone, while approximately 75% is lost horizontally, with the remainder still in the euphotic zone after the 10-day period of the model. Loss of chlorophyll due to sinking is very small in this strong upwelling region of the cyclone. The model is relatively insensitive to variations in the sinking parameterization and the external nitrate and chlorophyll fields but is very sensitive to a reduction of the maximum potential growth rate to half that measured. Given the success of this model in simulating the new production of the selcted upwelling region, other upwelling regions for which measurements or successful models of physical and biological quantities and rates exist could be modeled similarly.

Pribble, J. Raymond

Cybernetics and space biology

Cybernetics applied to space biology and medicine through use of mathematical models, biological controls, and statistical dynamics

BIOLOGICAL MODEL

Biological production models as elements of coupled, atmosphere-ocean models for climate research

Process models of phytoplankton production are discussed with respect to their suitability for incorporation into global-scale numerical ocean circulation models. Exact solutions are given for integrals over the mixed layer and the day of analytic, wavelength-independent models of primary production. Within this class of model, the bias incurred by using a triangular approximation (rather than a sinusoidal one) to the variation of surface irradiance through the day is computed. Efficient computation algorithms are given for the nonspectral models. More exact calculations require a spectrally sensitive treatment. Such models exist but must be integrated numerically over depth and time. For these integrations, resolution in wavelength, depth, and time are considered and recommendations made for efficient computation. The extrapolation of the one-(spatial)-dimension treatment to large horizontal scale is discussed.

Platt, Trevor

Ecosystem Modeling of Biological Processes to Global Budgets

From an ecological perspective, the search for life on distant planets begins from several key assumptions. The first of these is that, viewed from a remote location in space, the signature of life on a distant planet will be the result of net gas exchange of organisms with their environment. On the basis of extensive biogeochemical measurements and biogenic trace gas fluxes in modem Earth environments, it is probable that certain groups of organisms both produce and consume the same trace gas(es) within a single bioprofile of Solid (porous) substrate or surface water. The net gas exchange rate with the atmosphere measured at the living surface is frequently the result of competing metabolic reactions, which may carried out by different functional groups of organisms located at dissimilar 'climatic' or chemical microsites within the same bioprofile. Biogenic gases produced at one (deep) level of a bioprofile may be consumed by another functional group of organisms located closer to the level of surface exchange with the atmosphere. A second key assumption is that the net biogenic fluxes of atmospheric gases on Earth can be used to infer relative abundance and functional composition of the major organisms on a distant planet. Examples of this principle include the presence of methanogenic microorganisms abundant today in freshwater ecosystems worldwide, which are major source of atmospheric methane and its seasonal variability in Earth's atmosphere. A third assumption is that scaling up biogenic gas fluxes from a single biological community to the planetary level requires flux measurements at the whole ecosystem level. This implies that measurements of biogenic gas exchange with the global atmosphere cannot be easily inferred from measurements of gas production rates of single organisms, which may have been isolated in some manner from the setting of their native ecosystem. Hence, the unit of biological organization used in modern Earth Science for scaling up to biosphere effects on atmospheric composition is the ecosystem level. These assumptions are the foundation for developing modern emission budgets for biogenic gases such as carbon dioxide, methane, carbon monoxide, isoprene, nitrous and nitric oxide, and ammonia. Such emission budgets commonly include information on seasonal flux patterns, typical diurnal profiles, and spatial resolution of at least one degree latitude/longitude for the globe. On the basis of these budgets, it is possible to compute 'base emission rates' for the major biogenic trace gases from both terrestrial and ocean sources, which may be useful benchmarks for defining the gas production rates of organisms, especially those from early Earth history, which are required to generate a detectable signal on a global atmosphere. This type of analysis is also the starting point for evaluation of the 'biological processes to global gas budget' extrapolation procedure described above for early Earth ecosystems.

Christopher, Potter S.

A mixture parameterized biologically based dosimetry model to predict body burdens of polycyclic aromatic hydrocarbons in developmental zebrafish toxicity assays

Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental toxicants found ubiquitously as complex mixtures in human-impacted environments. Developmental zebrafish exposures have been used widely to study PAH toxicity, but most studies report nominal exposure concentrations. Nominal exposure concentrations can be unreliable dose metrics due to differences in toxicant bioavailability resulting from disparate exposure methodologies and chemical properties. Toxicokinetic modeling can predict toxicant tissue doses to facilitate comparison between exposures of different chemicals, methodologies, and biological models. We parameterize a biologically based dosimetry model for developmental zebrafish toxicity assays for 9 PAHs. The model was optimized with measurements from media, tissue, and plastic plate walls throughout a static developmental exposure to a mixture of 10 PAHs of high abundance within the Portland Harbor Superfund Site. Plate binding, volatilization, zebrafish permeability, and tissue—media partitioning coefficients vary widely between PAHs. Model predictions accounted for 83% and 54% of 48 hpf body burdens within a factor of 2 resulting from exposures to mixtures and individual PAHs, respectively. Accounting for solubility significantly improves model performance. Competition for active sites in metabolizing enzymes may change biotransformation kinetics between individual PAH and mixture exposures. Area under the curve estimations of concentrations in zebrafish resulted in altered hazard rankings from nominal exposure concentrations. Future work will be oriented to generalizing the model to other PAHs. This PAH dosimetry model improves the interpretability of developmental zebrafish toxicity assays by providing time-resolved body burdens from nominal exposure concentrations.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN

Development of a GCR Event-based Risk Model

A goal at NASA is to develop event-based systems biology models of space radiation risks that will replace the current dose-based empirical models. Complex and varied biochemical signaling processes transmit the initial DNA and oxidative damage from space radiation into cellular and tissue responses. Mis-repaired damage or aberrant signals can lead to genomic instability, persistent oxidative stress or inflammation, which are causative of cancer and CNS risks. Protective signaling through adaptive responses or cell repopulation is also possible. We are developing a computational simulation approach to galactic cosmic ray (GCR) effects that is based on biological events rather than average quantities such as dose, fluence, or dose equivalent. The goal of the GCR Event-based Risk Model (GERMcode) is to provide a simulation tool to describe and integrate physical and biological events into stochastic models of space radiation risks. We used the quantum multiple scattering model of heavy ion fragmentation (QMSFRG) and well known energy loss processes to develop a stochastic Monte-Carlo based model of GCR transport in spacecraft shielding and tissue. We validated the accuracy of the model by comparing to physical data from the NASA Space Radiation Laboratory (NSRL). Our simulation approach allows us to time-tag each GCR proton or heavy ion interaction in tissue including correlated secondary ions often of high multiplicity. Conventional space radiation risk assessment employs average quantities, and assumes linearity and additivity of responses over the complete range of GCR charge and energies. To investigate possible deviations from these assumptions, we studied several biological response pathway models of varying induction and relaxation times including the ATM, TGF -Smad, and WNT signaling pathways. We then considered small volumes of interacting cells and the time-dependent biophysical events that the GCR would produce within these tissue volumes to estimate how GCR event rates mapped to biological signaling induction and relaxation times. We considered several hypotheses related to signaling and cancer risk, and then performed simulations for conditions where aberrant or adaptive signaling would occur on long-duration space mission. Our results do not support the conventional assumptions of dose, linearity and additivity. A discussion on how event-based systems biology models, which focus on biological signaling as the mechanism to propagate damage or adaptation, can be further developed for cancer and CNS space radiation risk projections is given.

Cucinotta, Francis A.

Applications of amorphous track models in radiation biology

The average or amorphous track model uses the response of a system to gamma-rays and the radial distribution of dose about an ion's path to describe survival and other cellular endpoints from proton, heavy ion, and neutron irradiation. This model has been used for over 30 years to successfully fit many radiobiology data sets. We review several extensions of this approach that address objections to the original model, and consider applications of interest in radiobiology and space radiation risk assessment. In the light of present views of important cellular targets, the role of target size as manifested through the relative contributions from ion-kill (intra-track) and gamma-kill (inter-track) remains a critical question in understanding the success of the amorphous track model. Several variations of the amorphous model are discussed, including ones that consider the radial distribution of event-sizes rather than average electron dose, damage clusters rather than multiple targets, and a role for repair or damage processing.

NASA Discipline Radiation Health

Biological life-support systems

The establishment of human living environments by biologic methods, utilizing the appropriate functions of autotrophic and heterotrophic organisms is examined. Natural biologic systems discussed in terms of modeling biologic life support systems (BLSS), the structure of biologic life support systems, and the development of individual functional links in biologic life support systems are among the factors considered. Experimental modeling of BLSS in order to determine functional characteristics, mechanisms by which stability is maintained, and principles underlying control and regulation is also discussed.

Shepelev, Y. Y.

Reanalysis of Rodent Data from Spacelab Life Science-1

The space bioscience field has long been plagued by the challenge of spaceflight with effects of radiation and microgravity. Having multiple and repeated spaceflight experiments for model organisms to solve these space stressors is costly and time consuming. Therefore, reusing and reanalyzing legacy experiments is one way that scientists can draw new conclusions in a timely manner and without using too many resources. Moreover, advances in general biological knowledge allows legacy experiments to be placed into more complete context.Here we aim to analyze all data and metadata taken from rats flown on the SLS-1 mission to create a comprehensive biological model that can be supplemented with current data to allow new discoveries in how space flown organisms adapt to the space environment. Our approach begins with the identification of all the data and metadata, including graphs and tables, for SLS-1 in NASA archives and other sources. Then, each piece of data and metadata will be digitized, reformatted and analyzed. Lastly, a previously developed astronaut model will be used to create the data framework and a comprehensive biological rodent model. The datasets we are using is from the 1991 SpaceLab Life Science 1 (SLS-1) NASA Mission. This was the first designated spacelab mission flown. All 29 rodents were tested for nine days in two different habitats: Research Animal Holding Facility (RAHF) and Animal Enclosure Module (AEM). The rodents were prepared for a live return and compared to a ground control. A total of 30 rodent experiments were accepted as flight studies on the mission. By digitization and reorganizing SLS-1 rat data we will both directly generate new insights and indirectly enable other scientists to by providing the data and metadata in a digitized form.

Space Biology

Reanalysis of Rodent Data from Spacelab Life Sciences-1

The space bioscience field has long been plagued by the challenge of spaceflight with effects of radiation and microgravity. Having multiple and repeated spaceflight experiments for model organisms to solve these space stressors is costly and time consuming. Therefore, reusing and reanalyzing legacy experiments is one way that scientists can draw new conclusions in a timely manner and without using too many resources. Moreover, advances in general biological knowledge allows legacy experiments to be placed into more complete context.Here we aim to analyze all data and metadata taken from rats flown on the SLS-1 mission to create a comprehensive biological model that can be supplemented with current data to allow new discoveries in how space flown organisms adapt to the space environment. Our approach begins with the identification of all the data and metadata, including graphs and tables, for SLS-1 in NASA archives and other sources. Then, each piece of data and metadata will be digitized, reformatted and analyzed. Lastly, a previously developed astronaut model will be used to create the data framework and a comprehensive biological rodent model. The datasets we are using is from the 1991 SpaceLab Life Science 1 (SLS-1) NASA Mission. This was the first designated spacelab mission flown. All 29 rodents were tested for nine days in two different habitats: Research Animal Holding Facility (RAHF) and Animal Enclosure Module (AEM). The rodents were prepared for a live return and compared to a ground control. A total of 30 rodent experiments were accepted as flight studies on the mission. By digitization and reorganizing SLS-1 rat data we will both directly generate new insights and indirectly enable other scientists to by providing the data and metadata in a digitized form.

Space Biology

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

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

Cell mechanics