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At least 109 records · Page 6

Real time quantitative imaging for semiconductor crystal growth, control and characterization

A quantitative real time image processing system has been developed which can be software-reconfigured for semiconductor processing and characterization tasks. In thermal imager mode, 2D temperature distributions of semiconductor melt surfaces (900-1600 C) can be obtained with temperature and spatial resolutions better than 0.5 C and 0.5 mm, respectively, as demonstrated by analysis of melt surface thermal distributions. Temporal and spatial image processing techniques and multitasking computational capabilities convert such thermal imaging into a multimode sensor for crystal growth control. A second configuration of the image processing engine in conjunction with bright and dark field transmission optics is used to nonintrusively determine the microdistribution of free charge carriers and submicron sized crystalline defects in semiconductors. The IR absorption characteristics of wafers are determined with 10-micron spatial resolution and, after calibration, are converted into charge carrier density.

Wargo, Michael J.↗

The Impact of ARM on Climate Modeling

Climate models are among humanity's most ambitious and elaborate creations. They are designed to simulate the interactions of the atmosphere, ocean, land surface, and cryosphere on time scales far beyond the limits of deterministic predictability, and including the effects of time-dependent external forcings. The processes involved include radiative transfer, fluid dynamics, microphysics, and some aspects of geochemistry, biology, and ecology. The models explicitly simulate processes on spatial scales ranging from the circumference of the Earth down to one hundred kilometers or smaller, and implicitly include the effects of processes on even smaller scales down to a micron or so. The atmospheric component of a climate model can be called an atmospheric global circulation model (AGCM). In an AGCM, calculations are done on a three-dimensional grid, which in some of today's climate models consists of several million grid cells. For each grid cell, about a dozen variables are time-stepped as the model integrates forward from its initial conditions. These so-called prognostic variables have special importance because they are the only things that a model remembers from one time step to the next; everything else is recreated on each time step by starting from the prognostic variables and the boundary conditions. The prognostic variables typically include information about the mass of dry air, the temperature, the wind components, water vapor, various condensed-water species, and at least a few chemical species such as ozone. A good way to understand how climate models work is to consider the lengthy and complex process used to develop one. Lets imagine that a new AGCM is to be created, starting from a blank piece of paper. The model may be intended for a particular class of applications, e.g., high-resolution simulations on time scales of a few decades. Before a single line of code is written, the conceptual foundation of the model must be designed through a creative envisioning that starts from the intended application and is based on current understanding of how the atmosphere works and the inventory of mathematical methods available.

atmospheric circulation↗

Investigating Thaw and Plant Productivity Constraints on Old Soil Carbon Respiration From Permafrost

Isotopic radiocarbon (Δ 14 C) signatures of ecosystem respiration (Reco) can identify old soil carbon (C) loss and serve as an early indicator of permafrost destabilization in a warming climate. Warming also stimulates plant productivity causing plant respiration to dominate Reco Δ 14 C signatures and potentially obscuring old soil C loss. Here, we investigate how a wide spatio-temporal gradient of permafrost thaw and plant productivity affects Reco Δ 14 C patterns and isotopic partitioning. Spatial gradients came from a warming experiment with doubling thaw depth and variable biomass, and a vegetation removal manipulation to eliminate plant contributions. We sampled in August and September to capture transitions from high to low plant productivity, decreased surface soil temperature, and relatively small seasonal thaw extensions. We found that surface processes dominate spatial variation in old soil C loss and a process-based partitioning approach was crucial for constraining old soil C loss. Resampling the same plots in different times of the year revealed that old soil C losses tripled with cooling surface temperature, and the largest old soil C losses were detected when the organic-to-mineral soil horizons thawed (~50–60 cm). We suggest that the measured increase in old soil respiration over the season and when the organic-to-mineral horizon thawed, may be explained by mobilization of nitrogen that stimulates microbial decomposition at depth. Our results suggest that soil C in the organic to mineral horizon may be an important source of soil C loss as the entire Arctic region warms and could lead to nonlinearities in projected permafrost climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

Modeling protected species distributions and habitats to inform siting and management of pioneering ocean industries: A case study for Gulf of Mexico aquaculture

Marine Spatial Planning (MSP) provides a process that uses spatial data and models to evaluate environmental, social, economic, cultural, and management trade-offs when siting (i.e., strategically locating) ocean industries. Aquaculture is the fastest-growing food sector in the world. The United States (U.S.) has substantial opportunity for offshore aquaculture development given the size of its exclusive economic zone, habitat diversity, and variety of candidate species for cultivation. However, promising aquaculture areas overlap many protected species habitats. Aquaculture siting surveys, construction, operations, and decommissioning can alter protected species habitat and behavior. Additionally, aquaculture-associated vessel activity, underwater noise, and physical interactions between protected species and farms can increase the risk of injury and mortality. In 2020, the U.S. Gulf of Mexico was identified as one of the first regions to be evaluated for offshore aquaculture opportunities as directed by a Presidential Executive Order. We developed a transparent and repeatable method to identify aquaculture opportunity areas (AOAs) with the least conflict with protected species. First, we developed a generalized scoring approach for protected species that captures their vulnerability to adverse effects from anthropogenic activities using conservation status and demographic information. Next, we applied this approach to data layers for eight species listed under the Endangered Species Act, including five species of sea turtles, Rice’s whale, smalltooth sawfish, and giant manta ray. Next, we evaluated four methods for mathematically combining scores (i.e., Arithmetic mean, Geometric mean, Product, Lowest Scoring layer) to generate a combined protected species data layer. The Product approach provided the most logical ordering of, and the greatest contrast in, site suitability scores. Finally, we integrated the combined protected species data layer into a multi-criteria decision-making modeling framework for MSP. This process identified AOAs with reduced potential for protected species conflict. These modeling methods are transferable to other regions, to other sensitive or protected species, and for spatial planning for other ocean-uses.

54 ENVIRONMENTAL SCIENCES↗

TRACER-VOC: Speciated Volatile Organic Compounds at the Tracking Aerosol Convection Interactions Experiment Field Campaign Report

Formation of secondary organic aerosol (SOA) is responsible for the growth of particles into cloud condensation nuclei (CCN)-relevant sizes and accounts for a substantial fraction of aerosol mass in the troposphere. Despite its wide abundance and importance, capturing SOA in regional and climate models is still challenging due to complex chemical transformations involved in production of SOA. Oxidation products of biogenic hydrocarbons, such as isoprene, monoterpenes, and sesquiterpenes account for the largest fraction of SOA mass over the continents. As such, biogenic SOA is an important source of continental CCN, and has been recently shown to nucleate ice in the deposition mode. To better account for the processes involved in SOA formation in global and regional climate models, we need better measurements of sources and transformations of volatile organic compounds (VOCs), the precursors to SOA formation in the atmosphere. Understanding aerosol-deep convection interactions is an important science driver of the Tracking Aerosol Convection Interactions Experiment (TRACER), requiring a characterization of the critical controls on aerosol properties and processes, and how those properties and processes vary spatially and temporally in the Houston area. In that environment, the atmospheric photo-oxidative chemistry that drives the evolution and transformation of aerosol properties and processes is strongly impacted by the emission of VOCs, which have both anthropogenic (e.g., industrial, urban, transportation, biomass burning) and biogenic (e.g., marine) sources in the region. Understanding (and disentangling) the complex role of VOCs in such a heterogenous region requires high-time-resolution, speciated VOC measurements that are spatially resolved. To meet these measurement requirements, the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s time-of-flight proton transfer reaction-mass spectrometer (ToF-PTR-MS) was deployed during the TRACER intensive operational period (IOP) from June to September, 2022 at the ancillary site (ANC), which was sited to provide a characterization of the rural atmospheric environment in contrast to the main site.

54 ENVIRONMENTAL SCIENCES↗

Do we have globally representative data to understand soil processes?

Understanding and modeling soils and soil organic matter (SOM) are central to a variety of human needs, from food production to ecosystem management. Soil data have been collected for over a century, but the global spatial and process representativeness of soil data remains unclear. We assessed the representativeness of currently available soil data that could be used to understand a variety of SOM processes. We used 16 open-source soil databases and data from over 281,000 unique locations globally, categorizing the databases into three main data types necessary to understand SOM processes: soil carbon stocks and fluxes, mechanistic drivers of these stocks and fluxes, and soil carbon gain or loss potential. We found that stock and driver data have extensive global coverage. However, data on soil carbon gain or loss potential, particularly data describing change in soils over time such as time series data, are severely limited in their global coverage. We conclude that while significant strides have been made in measuring soil carbon stocks and fluxes, and their drivers, we are limited in global data related to changes in soils over time. Our recommendations for soil data generators are to ensure precise metadata reporting and prioritizing sampling in underrepresented areas like tropical, arctic, mountainous, wetland and arid regions. We also encourage designing revisit schemes that explicitly support change detection and reporting multi-modal datasets that can aid in model development. Targeted measurement of low coverage soil data types and regions is necessary for a range of applications including current and future biogeochemical predictions, and their management and policy implications.

carbon fluxes↗

Real-time optical image processing techniques

Nonlinear real-time optical processing on spatial pulse frequency modulation has been pursued through the analysis, design, and fabrication of pulse frequency modulated halftone screens and the modification of micro-channel spatial light modulators (MSLMs). Micro-channel spatial light modulators are modified via the Fabry-Perot method to achieve the high gamma operation required for non-linear operation. Real-time nonlinear processing was performed using the halftone screen and MSLM. The experiments showed the effectiveness of the thresholding and also showed the needs of higher SBP for image processing. The Hughes LCLV has been characterized and found to yield high gamma (about 1.7) when operated in low frequency and low bias mode. Cascading of two LCLVs should also provide enough gamma for nonlinear processing. In this case, the SBP of the LCLV is sufficient but the uniformity of the LCLV needs improvement. These include image correlation, computer generation of holograms, pseudo-color image encoding for image enhancement, and associative-retrieval in neural processing. The discovery of the only known optical method for dynamic range compression of an input image in real-time by using GaAs photorefractive crystals is reported. Finally, a new architecture for non-linear multiple sensory, neural processing has been suggested.

Liu, Hua-Kuang↗

Fitting Matérn smoothness parameters using automatic differentiation

The Mat$\acute{e}$rn covariance function is ubiquitous in the application of Gaussian processes to spatial statistics and beyond. Perhaps the most important reason for this is that the smoothness parameter $\nu$ gives complete control over the mean-square differentiability of the process, which has significant implications for the behavior of estimated quantities such as interpolants and forecasts. Unfortunately, derivatives of the Mat$\acute{e}$rn covariance function with respect to $\nu$ require derivatives of the modified second-kind Bessel function $K$ $\nu$ with respect to $\nu$. While closed form expressions of these derivatives do exist, they are prohibitively difficult and expensive to compute. For this reason, many software packages require fixing $\nu$ as opposed to estimating it, and all existing software packages that attempt to offer the functionality of estimating $\nu$ use finite difference estimates for $\partial$ $\nu$ $K$ $\nu$ . In this work, we introduce a new implementation of $K$$\nu$ that has been designed to provide derivatives via automatic differentiation (AD), and whose resulting derivatives are significantly faster and more accurate than those computed using finite differences. Here, we provide comprehensive testing for both speed and accuracy and show that our AD solution can be used to build accurate Hessian matrices for second-order maximum likelihood estimation in settings where Hessians built with finite difference approximations completely fail.

97 MATHEMATICS AND COMPUTING↗

Lensless X-Ray Nanoimaging: Revolutions and opportunities

Lensless x-ray nanoimaging is providing 3D views of a wide range of materials with a spatial resolution better than 20 nanometers. These advances are enabled in part by dramatic gains in coherent x-ray flux, but they also rely on advances in signal processing to obtain images from coherent diffraction data. Here, we outline the various imaging approaches, the associated reconstruction methods, and highlight opportunities for future advances.

42 ENGINEERING↗

Mars Global Climate Modeling.

Scientists use Global Climate Models (GCMs) to better under the current and past climate states of terrestrial (solid surface) bodies in our solar system and beyond, and the physical processes that control them. GCMs are complex, multi-dimensional computer codes that can generally be divided into two parts: the geophysical fluid dynamics (GFD) framework, which represents accelerations and spatially resolved processes, and the physics routines, which provide the forcing functions for the circulation. Producing a GCM that is appropriate for a particular body—Mars, for example—requires implementing the appropriate physics routines (e.g., radiative transfer, planetary boundary layer physics, dust lifting physics to generate dust storms, etc.) for that body. In this talk, I will give an overview of the components of the NASA Ames Mars GCM and discuss some of the scientific questions we address with this state-of-the-art numerical model.

Melinda A. Kahre↗

Novel Image Processing Interface to Relate DSB Spatial Distribution from Immunofluorescence Foci Experiments to the State-of-the-Art Models of DNA Breakage

A recently developed software (NASARadiationTrackImage) allows a quick and automatic segmentation of foci that indicate spatial localization of specific proteins that are visualized by immunofluorescence. Of interest are the spatial and temporal distribution of foci such as gammaH2AX, a signal of the phosphorylation of a variant of the histone H2A that has been shown to correspond to DSBs, or proteins involved in DSB processing, such as ATM, Rad51, and p53, following exposures of human cells to high charge and energy (HZE) ion irradiation. Experimental data are recorded as sets of two-dimensional images in color with cells and foci of gammaH2AX, ATM, Rad51 or others shown. Different cells, levels of radiation and timing after radiation were recorded. The software allows us to calculate the number of foci per cell, overall intensity of light in foci and their spatial organization. A simple statistical model allows for testing of foci overlap (eclipse). A more complex statistical model previously known as DNAbreak simulates track structure and random chromosome geometry. It has one adjustable parameter corresponding to an average intensity of DSB creation in cubic micrometers of DNA volume per particle track or unit dose. Its limitation is the low-resolution limit both in physical space and DSB's along DNA. It works adequately on the scale of a cell and provides further insights on how the geometry of tracks and DNA affects genomic damage of the cell and subsequent repair. Future developments of the model for the description of the time evolution of DNA damage response proteins, and more robust track structure models will be discussed.

Ponomarev, A. L.↗

Modes of Visual Recognition and Perceptually Relevant Sketch-based Coding for Images

A review of visual recognition studies is used to define two levels of information requirements. These two levels are related to two primary subdivisions of the spatial frequency domain of images and reflect two distinct different physical properties of arbitrary scenes. In particular, pathologies in recognition due to cerebral dysfunction point to a more complete split into two major types of processing: high spatial frequency edge based recognition vs. low spatial frequency lightness (and color) based recognition. The former is more central and general while the latter is more specific and is necessary for certain special tasks. The two modes of recognition can also be distinguished on the basis of physical scene properties: the highly localized edges associated with reflectance and sharp topographic transitions vs. smooth topographic undulation. The extreme case of heavily abstracted images is pursued to gain an understanding of the minimal information required to support both modes of recognition. Here the intention is to define the semantic core of transmission. This central core of processing can then be fleshed out with additional image information and coding and rendering techniques.

Jobson, Daniel J.↗

Understanding Processes Controlling the Temporal and Spatial Variations of PBL Structures Over the ARM SGP Site

The surface heat, moisture, and momentum fluxes are transferred to the atmosphere above through the planetary boundary layer (PBL), where vertical mixing due to turbulent eddies of different sizes plays critical roles. Therefore, reliably representing PBL processes in numerical models is critical for weather, climate, and air quality prediction. Currently, there are over ten PBL schemes that are selectable within the advanced research version of the Weather Research and Forecasting (WRF) model, indicative of the challenges in capturing the impacts of turbulence within the PBL in models. Further improvements in PBL parameterizations are needed for both weather and climate models, as emphasized in many recent national reports, but require an advanced understanding of the underlying boundary layer processes from observations. This project takes advantage of Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) investments in the atmospheric boundary layer observations and Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) simulations to characterize PBL structures, understand key physical processes controlling the mixed layer development, and to evaluate PBL parameterization.

54 ENVIRONMENTAL SCIENCES↗

Spatial quantification of maps or images - Cell size or pixel size implications

The paper discusses spatial quantification of maps or images. Spatial accuracies evaluated by mapping and inventory measures were observed with a range of cell sizes for a 10.36 sq km soil survey segment. The distribution of interboundary distances in a map was evaluated as unique, characterizing information; experimentally observed relationships between accuracy and cell size and interboundary distance distribution parameters and cell size led to a model of the process of spatial quantization. Grid positioning effects were evaluated and were significant only at the level of individual mapping units; two generations of 'universal' process models were derived, implemented, and evaluated.

Wehde, M. E.↗

Feeding Ten Billion People Is Possible Within Four Terrestrial Planetary Boundaries

Global agriculture puts heavy pressure on planetary boundaries, posing the challenge to achieve future food security without compromising Earth system resilience. On the basis of process-detailed, spatially explicit representation of four interlinked planetary boundaries (biosphere integrity, land-system change, freshwater use, nitrogen flows) and agricultural systems in an internally consistent model framework, we here show that almost half of current global food production depends on planetary boundary transgressions. Hotspot regions, mainly in Asia, even face simultaneous transgression of multiple underlying local boundaries. If these boundaries were strictly respected, the present food system could provide a balanced diet (2,355 kcal per capita per day) for 3.4 billion people only. However, as we also demonstrate, transformation towards more sustainable production and consumption patterns could support 10.2 billion people within the planetary boundaries analysed. Key prerequisites are spatially redistributed cropland, improved water–nutrient management, food waste reduction and dietary changes. Adoption of the Sustainable Development Goals by all nations in 2015 is the first ever commitment to a world development path that safeguards the stability of the Earth system as a prerequisite for meeting universal human standards1. The longstanding challenge of achieving food security through sustainable agriculture is particularly acute in this context as world agriculture is a leading cause for the current transgressions of multiple planetary boundaries (PBs) globally and regionally2–5. The PB framework is a comprehensive scientific attempt to synoptically define our planet’s biogeophysical limits to anthropogenic interference. It suggests bounds to nine interacting processes that together delineate a Holocene-like Earth system state. The Holocene is chosen as the reference state as it is the only period known to provide a safe operating space for a world population of several billion people, and according to a precautionary principle, the PBs are set in sufficient distance from processes that may critically undermine Earth system resilience and global sustainability. A challenging question, thus, is whether human development goals such as food security can be met while maintaining multiple PBs along with their subglobal manifestations. Further PB transgressions could jeopardize the chances of providing sufficient food for a world population projected to be wealthier and reach >9 billion by 2050. This conundrum portrays a tradeoff between Earth’s biophysical carrying capacity and humankind’s rising food demand, calling in response for radical rethinking of food production and consumption patterns6–9. Yield gap closures, avoidance of excessive input use, shifts towards less resource-demanding diets, food waste reductions and efficient international trade are crucial options for sustainably increasing the food supply10–15. For example, enhancing water-use efficiency on irrigated and rain-fed farms can triple or quadruple crop yields in low-performing systems, suggesting possible global gains of >20% (ref. 16). Even higher gains appear feasible through globally optimized configurations of the land-use pattern17, and cutting food losses by half could generate food for another billion people18. Thus, collective large-scale implementation of such options could sustain food for a further growing world population19. Yet achieving this within a safe operating space as defined by PBs requires not only a halt to but actually a reversal of existing PB transgressions. Previous studies suggest that such a reconciliation might be possible, but these were based on aggregate representations of PBs (not accounting for the spatial patterns of limits, transgressions and interactions) or considered only one boundary in isolation17,20–23. Here, we systematically quantify to what extent current food production depends on local to global transgressions of the PBs for biosphere integrity, land-system change, freshwater use and nitrogen (N) flows, along with the potential of a range of solutions to avoid these transgressions and still increase food supply (Table 1). To this end, we configured an internally consistent process-based model of the terrestrial biosphere including agriculture (LPJmL) with multiple spatially distributed PBs and their interactions. LPJmL is among the longest-established and best-evaluated biosphere models, showing robust performance regarding simulation of, for example, carbon, water and crop yield dynamics (Supplementary Figs. 1 and 2 and Supplementary Table 1; see ref. 24 for a comprehensive benchmarking and Supplementary Methods for more detail on model evaluations). In principle following established definitions4, we refine the computation of some PBs with respect to their regional patterns and interactions (Methods), providing globally gridded precautionary limits to human interference with the Earth system at a level of great detail. In particular, we account for the evidence that many PBs need to be represented spatially explicitly4 to cover their

Gerten, Dieter↗

Behavioral Assessment of Spaceflight Effects on Neurocognitive Performance: Extent and Longevity

Exposure to the microgravity environment during spaceflight missions impacts crewmembers' sensorimotor function. Bock et al. [1] studied the cognitive demands of human sensorimotor performance and dual tasking during long duration missions and concluded that both stress and scarcity of cognitive resources required for sensorimotor adaptation may be responsible for these deficits during spaceflight. Therefore, in consideration of the health and performance of crewmembers in- and post-flight, we are conducting this study to investigate the effects of spaceflight on the extent, longevity and neural bases of sensorimotor, cognitive, and neural changes. The data presented will focus on the behavioral measures that were collected pre-, in- and post-flight including spatial cognition, processing speed, bimanual coordination, functional mobility, computerized dynamic posturography (CDP), and vibrotactile induced vestibular evoked myogenic potential (VEMP). To date, data were collected over the course of two pre-flight sessions and four post-flight sessions on five crewmembers (n=13) using the protocol described in Koppelmans et al. [2]. Balance control was assessed using CDP, with eyes closed and a sway-referenced base of support (Sensory Organization Test 5), with and without head movements in the pitch plane. Spatial working memory was assessed using Thurston's Card Rotation Test and a Mental Rotation Test. The Rod and Frame Test was performed to test visual dependence. The Digit Symbol Substitution Test was performed to evaluate processing speed, and the Purdue Pegboard Task was performed to test bimanual coordination. Vestibular function was assessed by eliciting ocular VEMP via a hand held striker on the side of the head as subjects lay supine on a gurney. Subjects also performed the Functional Mobility Test of walking through an obstacle course to assess rate of early motor learning. Data were also collected on the same crewmembers during three in-flight sessions on the International Space Station (ISS). In-flight, spatial working memory was assessed using the Mental Rotation Test, adaptation to visuo-motor transformation in manual control was assessed using the Sensorimotor Adaptation Test, and multi-tasking ability was assessed using the Dual Task Test. These three tests were performed in a strapped-in configuration mimicking a seated position - waist bungees pulled the crewmember toward the "floor" with feet secured in foot loops. The Mental Rotation Test was also performed in a free-floating configuration while the crewmember floated while holding on to the gamepad controller used to provide input that was secured to the equipment rack on the ISS. Preliminary findings from data collected to date, will be included in the presentation. Eventual comparison to results from supporting bed rest and longitudinal studies will enable the parsing out of the multiple mechanisms contributing to any observed spaceflight-induced sensorimotor and cognitive behavioral changes.

De Dios, Y. E.↗

Agent-based modeling of microbes in space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal microgravity; however, much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER results agree with experimental data indicating that indirect effects of radiation (reactive oxygen species generation, metabolic impairment) have a greater impact on microorganisms than direct effects (DNA damage).

Jessica A Lee↗

Agent-Based Modeling of Microbes in Space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal gravity, and much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER growth curves recapitulate experimental results, and allow comparison between direct effects (DNA damage) and indirect effects (reactive oxygen species generation, metabolic impairment) of radiation.

microbiology↗