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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 109 records · Page 6

The Role of Instability Waves in Predicting Jet Noise

Debate over whether linear instability waves play a role in the prediction of jet noise has been going on for many years. Parallel mean flow models, such as the one proposed by Lilley, usually neglect these waves because they cause the solution to become infinite. The present paper solves the true non-parallel acoustic equations for a two-dimensional shear layer by using a vector Greens function and assuming small mean flow spread rate. The results show that linear instability waves must be accounted for in order to construct a proper causal solution to the problem.

Goldstein, Marvin E.↗

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik↗

Resolving Wave-Particle Duality Could Accelerate the Mass Production of Quantum Computers

Quantum computers, hypothesized in 1980s, use concepts of superposition and entanglement phenomena. Although theoretical propositions and associated search algorithms for accurate measurements are being generated, the development of practical quantum computers themselves are advancing very slowly requiring enormous time and investments. The underlying concepts of a quantum computer are not new to the optical domain. However, the crucial enabling concepts of Entanglement and Superposition Principle are remaining clouded under the unresolved postulates, Wave-Particle Duality (WPD), and Wave Packet Reduction (WPR), implicating incompleteness in the interpretations of the mathematical formalism behind Quantum Mechanics. The WPD debate started during late1600 between Newton and Huygens. Young’s resolution of WPD through his double-slit experiment in 1802 was effectively overturned by Einstein’s interpretation of photoelectric effect as due to “indivisible light quanta”. However, Einstein disowned his “light quanta” postulate shortly before his death in1955, even though it had earned him the Nobel Prize. We resolve WPD by synthesizing Newton’s and Maxwell’s concepts and assume atoms do emit quanta but propagate as time-finite exponential pulses. This assumption also resolves WPR for light-matter interaction with the assumption that Schrodinger’s ψ represents atom’s internal dipolar amplitude stimulations. This over-turns Born’s interpretation that ψ only represents the abstract mathematical probability amplitude, rather than the physical “internal amplitude stimulation” of the quantum entity. However, our concept of atomic pulse emission forces us to re-derive the expression for the N-slit grating-spectrometer response since the classical derivation uses CW light, which does not exist. This pulsespectrometric response function strengthens our postulate since the grating response to the exponential pulse appears to be the convolution of a Lorentzian spectrum with the classical CW response function of the grating. The Fourier Transform of an exponential function is Lorentzian and QM predicts spontaneous emission line width to be Lorentzian. Then, conceptually one can extend the grating-expression (with N=2) to get the double-slit pattern. This approach preserves the classical causality that each of the two slits, like the N-signals out of a grating, are physically real and jointly stimulate the quantum detector array at the far field to generate the “Local” cosine fringes. The detector array executes the square modulus operation on its imposed dipolar amplitude stimulation and absorbs the necessary energy to fill up their quantum cups. Hence the double-slit pattern must also be “Local”, just as the N-slit grating spectrum is generated locally at the exit spectral-plane of the spectrometer. This removes the need to believe that “single photons” mysteriously generate the double slit pattern. Quantum computers, hypothesized in 1980s, use concepts of superposition and entanglement phenomena. Although theoretical propositions and associated search algorithms for accurate measurements are being generated, the development of practical quantum computers themselves are advancing very slowly requiring enormous time and investments. The underlying concepts of a quantum computer are not new to the optical domain. However, the crucial enabling concepts of Entanglement and Superposition Principle are remaining clouded under the unresolved postulates, Wave-Particle Duality (WPD), and Wave Packet Reduction (WPR), implicating incompleteness in the interpretations of the mathematical formalism behind Quantum Mechanics. The WPD debate started during late1600 between Newton and Huygens. Young’s resolution of WPD through his double-slit experiment in 1802 was effectively overturned by Einstein’s interpretation of photoelectric effect as due to “indivisible light quanta”. However, Einstein disowned his “light quanta” postulate shortly before his death in1955, even though it had earned him the Nobel Prize. We resolve WPD by synthesizing Newton’s and Maxwell’s concepts and assume atoms do emit quanta but propagate as time-finite exponential pulses. This assumption also resolves WPR for light-matter interaction with the assumption that Schrodinger’s ψ represents atom’s internal dipolar amplitude stimulations. This over-turns Born’s interpretation that ψ only represents the abstract mathematical probability amplitude, rather than the physical “internal amplitude stimulation” of the quantum entity. However, our concept of atomic pulse emission forces us to re-derive the expression for the N-slit grating-spectrometer response since the classical derivation uses CW light, which does not exist. This pulsespectrometric response function strengthens our postulate since the grating response to the exponential pulse appears to be the convolution of a Lorentzian spectrum with the classical CW response function of the grating. The Fourier Transform of an exponential function is Lorentzian and QM predicts spontaneous emission line width to be Lorentzian. Then, conceptually one can extend the grating-expression (with N=2) to get the double-slit pattern. This approach preserves the classical causality that each of the two slits, like the N-signals out of a grating, are physically real and jointly stimulate the quantum detector array at the far field to generate the “Local” cosine fringes. The detector array executes the square modulus operation on its imposed dipolar amplitude stimulation and absorbs the necessary energy to fill up their quantum cups. Hence the double-slit pattern must also be “Local”, just as the N-slit grating spectrum is generated locally at the exit spectral-plane of the spectrometer. This removes the need to believe that “single photons” mysteriously generate the double slit pattern.

Quantum Computer↗

Linear Response Function Reveals the Most Effective Remote Forcing in Causing September Arctic Sea Ice Melting in CESM

We apply the linear response function method to investigate the most excitable mode of the September Arctic sea ice and its corresponding remote oceanic forcing in climate models. The method is useful in identifying the fundamental, dynamical and causal relationship between the remote forcing and sea ice response. We find that the most excitable mode of the September Arctic sea ice preferentially takes place over the Pacic side of the Arctic and its remote forcing corresponds to a dipole pattern of precipitation anomaly in the tropics with an increase of precipitation over the western and central tropical and subtropical Pacic ocean while a decrease over the Maritime Continent. The tropical precipitation anomaly likely drives a Rossby wave train propagating toward higher latitudes and leads to a ridge anomaly over the Pacic side of the Arctic, resulting in poleward atmospheric heat transport, enhanced downward longwave radiation and thus melting of the sea ice. In addition, a good agreement is found with the leading tropical Arctic teleconnection mode detected in a pre-industrial control simulation, which supports the usefulness and robustness of the linear response function method and the importance of tropical forcing in shaping the sea ice variability.

Wu, Yutian↗

Accident/Mishap Investigation System

InvestigationOrganizer (IO) is a Web-based collaborative information system that integrates the generic functionality of a database, a document repository, a semantic hypermedia browser, and a rule-based inference system with specialized modeling and visualization functionality to support accident/mishap investigation teams. This accessible, online structure is designed to support investigators by allowing them to make explicit, shared, and meaningful links among evidence, causal models, findings, and recommendations.

Keller, Richard↗

Exercise Effects on the Course of Gray Matter Changes Over 70 Days of Bed Rest

Long duration spaceflight affects posture control, locomotion, and manual control. The microgravity environment is an important causal factor for spaceflight induced sensorimotor changes through direct effects on peripheral changes that result from reduced vestibular stimulation and body unloading. Effects of microgravity on sensorimotor function have been investigated on earth using bed rest studies. Long duration bed rest serves as a space-flight analogue because it mimics microgravity in body unloading and bodily fluid shifts. It has been hypothesized that the cephalad fluid shift that has been observed in microgravity could potentially affect central nervous system function and structure, and thereby indirectly affect sensorimotor or cognitive functioning. Preliminary results of one of our ongoing studies indeed showed that 70 days of long duration head down-tilt bed rest results in focal changes in gray matter volume from pre-bed rest to various time points during bed rest. These gray matter changes that could reflect fluid shifts as well as neuroplasticity were related to decrements in motor skills such as maintenance of equilibrium. In consideration of the health and performance of crewmembers both inand post-flight we are currently conducting a study that investigates the potential preventive effects of exercise on gray matter and motor performance changes that we observed over the course of bed rest. Numerous studies have shown beneficial effects of aerobic exercise on brain structure and cognitive performance in healthy and demented subjects over a large age range. We therefore hypothesized that an exercise intervention in bed rest could potentially mitigate or prevent the effects of bed rest on the central nervous system. Here we present preliminary outcomes of our study.

Koppelmans, V.↗

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

Abstract Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic test input generation for multiple-fault isolation

Recent work is Causal Reasoning has provided practical techniques for multiple fault diagnosis. These techniques provide a hypothesis/measurement diagnosis cycle. Using probabilistic methods, they choose the best measurements to make, then update fault hypotheses in response. For many applications such as computers and spacecraft, few measurement points may be accessible, or values may change quickly as the system under diagnosis operates. In these cases, a hypothesis/measurement cycle is insufficient. A technique is presented for a hypothesis/test-input/measurement diagnosis cycle. In contrast to generating tests a priori for determining device functionality, it dynamically generates tests in response to current knowledge about fault probabilities. It is shown how the mathematics previously used for measurement specification can be applied to the test input generation process. An example from an efficient implementation called Multi-Purpose Causal (MPC) is presented.

Schaefer, Phil↗

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

59 BASIC BIOLOGICAL SCIENCES↗

Possible Martian brines - Radar observations and models

The 1971 and 1973 Goldstone 12.6-cm radar observations of Mars are separate data sets which include reflectivity as a function of latitude, longitude, and season. It has been argued that secular reflectivity variations of Mars' surface are indicated by the data and that shallow subsurface melting is the causal mechanism most compatible with the observations; however, the melting hypothesis conflicts with accepted notions of the state and distribution of water on Mars. The data are examined to identify temporal and spatial domains within which statistically significant changes in measured reflectivity are clustered. Brines which might satisfy the best supported reflectivity variations are out of equilibrium with the chemical megaenvironment. It is unclear whether such a brine, if emplaced in the Martian regolith at a depth shallow enough to affect the radar reflectivity, could survive even a single freeze-thaw cycle. Some combination of unique scattering properties or some as yet unidentified process other than melting is responsible for any genuine reflectivity variations.

Zent, Aaron P.↗

Soybean ( Glycine max ) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics

Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.

54 ENVIRONMENTAL SCIENCES↗

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Proteinaceous aggregates containing ?-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson’s disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

Petyuk, Vladislav A.↗

Revealing Relationships among Relevant Climate Variables with Information Theory

The primary objective of the NASA Earth-Sun Exploration Technology Office is to understand the observed Earth climate variability, thus enabling the determination and prediction of the climate's response to both natural and human-induced forcing. We are currently developing a suite of computational tools that will allow researchers to calculate, from data, a variety of information-theoretic quantities such as mutual information, which can be used to identify relationships among climate variables, and transfer entropy, which indicates the possibility of causal interactions. Our tools estimate these quantities along with their associated error bars, the latter of which is critical for describing the degree of uncertainty in the estimates. This work is based upon optimal binning techniques that we have developed for piecewise-constant, histogram-style models of the underlying density functions. Two useful side benefits have already been discovered. The first allows a researcher to determine whether there exist sufficient data to estimate the underlying probability density. The second permits one to determine an acceptable degree of round-off when compressing data for efficient transfer and storage. We also demonstrate how mutual information and transfer entropy can be applied so as to allow researchers not only to identify relations among climate variables, but also to characterize and quantify their possible causal interactions.

Knuth, Kevin H.↗

Adaptive laboratory evolution and genetic engineering improved terephthalate utilization in Pseudomonas putida KT2440

Poly(ethylene terephthalate) (PET) is one of the most ubiquitous plastics and can be depolymerized through biological and chemo-catalytic routes to its constituent monomers, terephthalic acid (TPA) and ethylene glycol (EG). TPA and EG can be re-synthesized into PET for closed-loop recycling or microbially converted into higher-value products for open-loop recycling. Here, in this study, we expand on our previous efforts engineering and applying Pseudomonas putida KT2440 for PET conversion by employing adaptive laboratory evolution (ALE) to improve TPA catabolism. Three P. putida strains with varying degrees of metabolic engineering for EG catabolism underwent an automation-enabled ALE campaign on TPA, a TPA and EG mixture, and glucose as a control. ALE increased the growth rate on TPA and TPA-EG mixtures by 4.1- and 3.5-fold, respectively, in approximately 350 generations. Evolved isolates were collected at the midpoints and endpoints of 39 independent ALE experiments, and growth rates were increased by 0.15 and 0.20 h -1 on TPA and a TPA-EG, respectively, in the best performing isolates. Whole-genome re-sequencing identified multiple converged mutations, including loss-of-function mutations to global regulators gacS, gacA, and turA along with large duplication and intergenic deletion events that impacted the heterologously-expressed tphAB II catabolic genes. Reverse engineering of these targets confirmed causality, and a strain with all three regulators deleted and second copies of tphAB II and tpaK displayed improved TPA utilization compared to the base strain. Taken together, an iterative strain engineering process involving heterologous pathway engineering, ALE, whole genome sequencing, and genome editing identified five genetic interventions that improve P. putida growth on TPA, aimed at developing enhanced whole-cell biocatalysts for PET upcycling.

36 MATERIALS SCIENCE↗

The vecro hypothesis

We consider three fundamental issues in quantum gravity: (a) the black hole information paradox (b) the unboundedness of entropy that can be stored inside a black hole horizon (c) the relation between the black hole horizon and the cosmological horizon. With help from the small corrections theorem, we convert each of these issues into a sharp conflict. We then argue that all three conflicts can be resolved by the following hypothesis: the vacuum wave functional of quantum gravity contains a “vecro” component made of virtual fluctuations of configurations of the same type that arise in the fuzzball structure of black hole microstates. Further, if we assume that causality holds to leading order in gently curved spacetime, then we must have such a vecro component in order to resolve the above conflicts. The term vecro stands for “Virtual Extended Compression-Resistant Object”, and characterizes the nature of the vacuum fluctuations that resolve the puzzles. It is interesting that puzzle (c) may relate the role of quantum gravity in black holes to observations in the sky.

Astronomy & Astrophysics↗

Necessary conditions for optimization in multiparameter discrete systems

A general first-order dynamic representation for discrete systems with several independent variables is proposed, based on the Dieudonne-Rashevsky form for partial differential equations. This representation does not restrict consideration to causal systems. A minimum principle for such systems is proved, thus extending results known for discrete-time systems to the case of several independent variables. The proof requires only the classical implicit function theorem.

Hegg, D. R.↗

Data for Soil Oxygen Dynamics: A Key Mediator of Tile Drainage Impacts on Coupled Hydrological, Biogeochemical, and Crop Systems

Tile drainage removes excess water and is an essential, widely adopted management practice to enhance crop productivity in the US Midwest and throughout the world. Tile drainage has been shown to significantly change hydrological and biogeochemical cycles by lowering the water table and reducing the residence time of soil water, although examining the complex interactions and feedbacks in an integrated hydrology–biogeochemistry–crop system remains elusive. Oxygen dynamics are critical to unraveling these interactions and have been ignored or oversimplified in existing models. Understanding these impacts is essential, particularly so because tile drainage has been highlighted as an adaptation under projected wetter springs and drier summers in the changing climate in the US Midwest. We used the ecosys model that uniquely incorporates first-principle soil oxygen dynamics and crop oxygen uptake mechanisms to quantify the impacts of tile drainage on hydrological and biogeochemical cycles and crop growth in corn–soybean rotation fields. The model was validated with data from a multi-treatment, multi-year experiment in Washington, IA. The relative root mean square error (rRMSE) for the corn and soybean yield in validation is 5.66 % and 12.57 %, respectively. The Pearson coefficient (r) of the monthly tile flow during the growing season is 0.78. Plant oxygen stress turns out as an emergent property of the equilibrium between the soil oxygen supply and biological demand. The impact of tile drainage on the system is achieved through a series of coupled feedback mechanisms. The model results show that tile drainage reduces the soil water content and enhances soil oxygenation. It additionally increases the subsurface discharge and elevates inorganic nitrogen leaching, with seasonal variations influenced by climate and crop phenology. The improved aerobic condition alleviates crop oxygen stress during wet springs, thereby promoting crop root growth during the early growth stage. The development of greater root density, in turn, mitigates water stress during dry summers, leading to an overall increase in the crop yield by ∼6 %. These functions indicate the potential of tile drainage in bolstering crop resilience to climate change and the use of this modeling tool for large-scale assessments of tile drainage. The model reveals the underlying causal mechanisms that drive the agroecosystem response to drainage on the coupled hydrology, biogeochemistry, and crop system dynamics.

Modeling↗

Soil oxygen dynamics: a key mediator of tile drainage impacts on coupled hydrological, biogeochemical, and crop systems

Tile drainage removes excess water and is an essential, widely adopted management practice to enhance crop productivity in the US Midwest and throughout the world. Tile drainage has been shown to significantly change hydrological and biogeochemical cycles by lowering the water table and reducing the residence time of soil water, although examining the complex interactions and feedbacks in an integrated hydrology–biogeochemistry–crop system remains elusive. Oxygen dynamics are critical to unraveling these interactions and have been ignored or oversimplified in existing models. Understanding these impacts is essential, particularly so because tile drainage has been highlighted as an adaptation under projected wetter springs and drier summers in the changing climate in the US Midwest. We used the ecosys model that uniquely incorporates first-principle soil oxygen dynamics and crop oxygen uptake mechanisms to quantify the impacts of tile drainage on hydrological and biogeochemical cycles and crop growth in corn–soybean rotation fields. The model was validated with data from a multi-treatment, multi-year experiment in Washington, IA. The relative root mean square error (rRMSE) for the corn and soybean yield in validation is 5.66 % and 12.57 %, respectively. The Pearson coefficient (r) of the monthly tile flow during the growing season is 0.78. Plant oxygen stress turns out as an emergent property of the equilibrium between the soil oxygen supply and biological demand. The impact of tile drainage on the system is achieved through a series of coupled feedback mechanisms. The model results show that tile drainage reduces the soil water content and enhances soil oxygenation. It additionally increases the subsurface discharge and elevates inorganic nitrogen leaching, with seasonal variations influenced by climate and crop phenology. The improved aerobic condition alleviates crop oxygen stress during wet springs, thereby promoting crop root growth during the early growth stage. The development of greater root density, in turn, mitigates water stress during dry summers, leading to an overall increase in the crop yield by ∼6 %. These functions indicate the potential of tile drainage in bolstering crop resilience to climate change and the use of this modeling tool for large-scale assessments of tile drainage. The model reveals the underlying causal mechanisms that drive the agroecosystem response to drainage on the coupled hydrology, biogeochemistry, and crop system dynamics.

60 APPLIED LIFE SCIENCES↗