{"type": "FeatureCollection", "features": [{"id": "10.1007/s11104-016-2872-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:13Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/10.1007/s11104-016-2872-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-016-2872-7", "name": "item", "description": "10.1007/s11104-016-2872-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-016-2872-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "10.1016/j.biortech.2018.12.064", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:59Z", "type": "Journal Article", "created": "2018-12-22", "title": "ADM1 based mathematical model of trace element complexation in anaerobic digestion processes", "description": "In this study, a new model based on anaerobic digestion model no.1 (ADM1) approach has been proposed to simulate trace elements (TEs) complexation, precipitation and their effect on the anaerobic batch methane production. TEs complexation reactions with VFAs and EDTA have been incorporated in an extended ADM1 model which considers TE precipitation/dissolution reactions as well as biodegradation processes. The kinetic model tracks the dynamics of 90 state variables which constitute the components of the proposed anaerobic digestion (AD) model. The incorporation of the complexation reactions required the definition of new inorganic components (EDTA species) and new complexation process rates in the ADM1 framework. The charge balance was modified accordingly to consider the effects of the additional components. The new model is able to predict: a) the effect of TE-EDTA/VFA complexation on methane production, and b) the effect of the initial calcium and magnesium concentrations on process performance.", "keywords": ["ADM1", "Trace elements", "0211 other engineering and technologies", "02 engineering and technology", "Models", " Theoretical", "Fatty Acids", " Volatile", "01 natural sciences", "7. Clean energy", "Trace Elements", "[SDU] Sciences of the Universe [physics]", "Kinetics", "Biodegradation", " Environmental", "Bioreactors", "13. Climate action", "Anaerobic digestion", "[SDU.STU] Sciences of the Universe [physics]/Earth Sciences", "Complexation", "Mathematical modeling", "Anaerobic digestion; Trace elements; Complexation; Mathematical modeling; ADM1;", "Anaerobiosis", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.biortech.2018.12.064"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2018.12.064", "name": "item", "description": "10.1016/j.biortech.2018.12.064", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2018.12.064"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2018.06.099", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:59Z", "type": "Journal Article", "created": "2018-07-03", "title": "ADM1 based mathematical model of trace element precipitation/dissolution in anaerobic digestion processes", "description": "Due to the complex biogeochemistry of trace elements (TEs, e.g. Fe, Ni and Co) in anaerobic digestion processes, their role and fate is poorly understood. Challenging, time consuming and low detection limits of analytical procedures necessitate recruitment of mathematical models. A dynamic mathematical model based on anaerobic digestion model no.1 (ADM1) has been proposed to simulate the effect of TEs. New chemical equilibrium association/dissociation and precipitation/dissolution reactions have been implemented to determine TE bioavailability and their effect on anaerobic digestion. The model considers interactions with inorganic carbonate (HCO3- and CO32-), phosphate (PO43-, HPO42-, H2PO4-) and sulfide (HS- and S2-). The effect of deficiency, activation, inhibition and toxicity of TEs on the biochemical processes has been modelled based on a dose-response type inhibition function. The new model can predict: the dynamics of TEs (among carbonate, sulfide and phosphate); the starvation of TEs; and the effect of initial sulfur-phosphorus ratio in an in-silico batch anaerobic system.", "keywords": ["ADM1", "Trace elements", "0211 other engineering and technologies", "Phosphorus", "Precipitation", "02 engineering and technology", "Models", " Theoretical", "01 natural sciences", "7. Clean energy", "Trace Elements", "Bioreactors", "Solubility", "Anaerobic digestion", "Anaerobic digestion; Trace elements; Mathematical modeling; Precipitation; ADM1", "Mathematical modeling", "Anaerobiosis", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.biortech.2018.06.099"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2018.06.099", "name": "item", "description": "10.1016/j.biortech.2018.06.099", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2018.06.099"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-01T00:00:00Z"}}, {"id": "10.1016/j.eti.2023.103229", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:23Z", "type": "Journal Article", "created": "2023-06-02", "title": "Modeling biochar-soil depth dependency on fecal coliform straining under subsurface drip irrigation", "description": "Funding Information: This work was supported by Shahrekord University, Iran. N. Sepehrnia is funded by a Marie Sk\u0142odowska-Curie Individual Fellowship, United Kingdom under the grant agreement No. 101026287. We acknowledge University of Aberdeen, UK for supporting this project. ; Peer reviewed", "keywords": ["GE", "Soil Science", "610", "Plant Science", "04 agricultural and veterinary sciences", "01 natural sciences", "6. Clean water", "510", "Biochar", "Maximum allowable depletion", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Irrigation strategy", "HYDRUS", "Soil bacteria contamination", "GE Environmental Sciences", "General Environmental Science", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.eti.2023.103229"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Technology%20%26amp%3B%20Innovation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.eti.2023.103229", "name": "item", "description": "10.1016/j.eti.2023.103229", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.eti.2023.103229"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-01T00:00:00Z"}}, {"id": "10.1016/j.jenvman.2018.01.064", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:51Z", "type": "Journal Article", "created": "2018-02-05", "title": "Elemental sulfur-based autotrophic denitrification and denitritation: microbially catalyzed sulfur hydrolysis and nitrogen conversions", "description": "The hydrolysis of elemental sulfur (S0) coupled to S0-based denitrification and denitritation was investigated in batch bioassays by microbiological and modeling approaches. In the denitrification experiments, the highest obtained NO3--N removal rate was 20.9\u202fmg/l\u00b7d. In the experiments with the biomass enriched on NO2-, a NO2--N removal rate of 10.7\u202fmg/l\u00b7d was achieved even at a NO2--N concentration as high as 240\u202fmg/l. The Helicobacteraceae family was only observed in the biofilm attached onto the chemically-synthesized S0 particles with a relative abundance up to 37.1%, suggesting it was the hydrolytic biomass capable of S0 solubilization in the novel surface-based model. S0-driven denitrification was modeled as a two-step process in order to explicitly account for the sequential reduction of NO3- to NO2- and then to N2 by denitrifying bacteria.", "keywords": ["Surface-based hydrolysis", "Autotrophic Processes", "Autotrophic denitrification; Autotrophic denitritation; Community structure; Elemental sulfur; Mathematical modeling; Surface-based hydrolysis", "Elemental sulfur", "Nitrates", "Nitrogen", "Hydrolysis", "0211 other engineering and technologies", "02 engineering and technology", "Autotrophic denitrification", "01 natural sciences", "6. Clean water", "Community structure", "Bioreactors", "Autotrophic denitritation", "Denitrification", "Autotrophic denitrification; Autotrophic denitritation; Elemental sulfur; Community structure; Surface-based hydrolysis; Mathematical modeling", "Mathematical modeling", "14. Life underwater", "Sulfur", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/698214/5/anastasiia%20JEMA.pdf"}, {"href": "https://doi.org/10.1016/j.jenvman.2018.01.064"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jenvman.2018.01.064", "name": "item", "description": "10.1016/j.jenvman.2018.01.064", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jenvman.2018.01.064"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-01T00:00:00Z"}}, {"id": "10.1016/j.soildyn.2018.12.017", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-04-13T16:17:26Z", "type": "Journal Article", "created": "2019-01-09", "title": "Modeling of high damping rubber bearings under bidirectional shear loading", "description": "Abstract   The behavior of high damping rubber bearings is highly complex. The models that are currently available are generally limited to unidirectional motion and, in most cases, difficult to extend to general bidirectional loading. One of the major limitations is their inability to characterize the behavior of the bearings at different levels of shear deformation. In the present work, a set of bidirectional models are presented, obtained by combining relatively simple bi-dimensional formulations. The models are calibrated over a set of unidirectional test data and are shown to accurately describe the response of the bearings at low, intermediate and high strain levels using a single set of parameters. Validation is carried out using bidirectional displacement-controlled tests available in the literature and numerical simulations are performed of a base-isolated building subjected to free vibration and bidirectional earthquake excitation.", "keywords": ["ta212", "high damping rubber bearings (HDRB)", "mathematical modeling", "02 engineering and technology", "Seismic Isolation", "01 natural sciences", "0201 civil engineering", "0104 chemical sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.soildyn.2018.12.017"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Dynamics%20and%20Earthquake%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soildyn.2018.12.017", "name": "item", "description": "10.1016/j.soildyn.2018.12.017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soildyn.2018.12.017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.tplants.2018.05.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:41Z", "type": "Journal Article", "created": "2018-06-15", "title": "Out of Shape During Stress: A Key Role for Auxin", "description": "In most abiotic stress conditions, including salinity and water deficit, the developmental plasticity of the plant root is regulated by the phytohormone auxin. Changes in auxin concentration are often attributed to changes in shoot-derived long-distance auxin flow. However, recent evidence suggests important contributions by short-distance auxin transport from local storage and local auxin biosynthesis, conjugation, and oxidation during abiotic stress. We discuss here current knowledge on long-distance auxin transport in stress responses, and subsequently debate how short-distance auxin transport and indole-3-acetic acid (IAA) metabolism play a role in influencing eventual auxin accumulation and signaling patterns. Our analysis stresses the importance of considering all these components together and highlights the use of mathematical modeling for predictions of plant physiological responses.", "keywords": ["0301 basic medicine", "0303 health sciences", "abiotic stress", "Indoleacetic Acids", "auxin transport", "mathematical modeling", "Biological Transport", "IAA homeostasis", "Models", " Theoretical", "Plants", "Plant Roots", "Article", "03 medical and health sciences", "Plant Growth Regulators", "root phenotypic plasticity", "Stress", " Physiological", "auxin", "Plant Physiological Phenomena", "Signal Transduction"]}, "links": [{"href": "https://doi.org/10.1016/j.tplants.2018.05.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tplants.2018.05.011", "name": "item", "description": "10.1016/j.tplants.2018.05.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tplants.2018.05.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-01T00:00:00Z"}}, {"id": "10.15488/17031", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-13T16:20:31Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/10.15488/17031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.15488/17031", "name": "item", "description": "10.15488/17031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15488/17031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "10.2166/wst.2018.398", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-13T16:21:21Z", "type": "Journal Article", "created": "2018-10-04", "title": "Sensitivity analysis for an elemental sulfur-based two-step denitrification model", "description": "Abstract                <p>A local sensitivity analysis was performed for a chemically synthesized elemental sulfur (S0)-based two-step denitrification model, accounting for nitrite (NO2\uffe2\uff88\uff92) accumulation, biomass growth and S0 hydrolysis. The sensitivity analysis was aimed at verifying the model stability, understanding the model structure and individuating the model parameters to be further optimized. The mass specific area of the sulfur particles (a*) and hydrolysis kinetic constant (k1) were identified as the dominant parameters on the model outputs, i.e. nitrate (NO3\uffe2\uff88\uff92), NO2\uffe2\uff88\uff92 and sulfate (SO42\uffe2\uff88\uff92) concentrations, confirming that the microbially catalyzed S0 hydrolysis is the rate-limiting step during S0-driven denitrification. Additionally, the maximum growth rates of the denitrifying biomass on NO3\uffe2\uff88\uff92 and NO2\uffe2\uff88\uff92 were detected as the most sensitive kinetic parameters.</p>", "keywords": ["Elemental sulfur", "Environmental Engineering", "0207 environmental engineering", "Biological surface-based hydrolysis; Elemental sulfur; Mathematical modeling; Sensitivity analysis; Two-step autotrophic denitrification; Environmental Engineering; Water Science and Technology", "02 engineering and technology", "01 natural sciences", "Two-step autotrophic denitrification", "Bioreactors", "European Joint Doctorates", "European Commission", "Knowmad Institut", "Biological surface-based hydrolysis", "Nitrites", "Netherlands", "Water Science and Technology", "0105 earth and related environmental sciences", "Aurora Universities Network", "EC", "Nitrates", "H2020", "Energy Research", "13. Climate action", "Denitrification", "Mathematical modeling", "Sensitivity analysis", "Sulfur"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/724909/2/2018%20-%20Kostrytsia%20et%20al.%20-%20Water%20Science%20%26%20Technology%20-%20Sensitivity%20analysis%20for%20S0-based%20denitrification%20model.pdf"}, {"href": "http://iwaponline.com/wst/article-pdf/78/6/1296/504647/wst078061296.pdf"}, {"href": "https://doi.org/10.2166/wst.2018.398"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Science%20and%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2166/wst.2018.398", "name": "item", "description": "10.2166/wst.2018.398", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2166/wst.2018.398"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-20T00:00:00Z"}}, {"id": "10.31219/osf.io/jfdb9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:36Z", "type": "Journal Article", "created": "2021-03-15", "title": "Overcoming the challenges to enhancing experimental plant biology with computational modeling", "description": "<p>The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.</p>", "keywords": ["Other Physical Sciences and Mathematics", "computational modeling", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "experimental design", "Systems Biology", "Plant Sciences", "Research Methods in Life Sciences", "mathematical modeling", "Life Sciences", "Plant culture", "bioinformatics", "Plant Science", "collaboration", "SB1-1110", "03 medical and health sciences", "Other Life Sciences", "Physical Sciences and Mathematics"]}, "links": [{"href": "https://doi.org/10.31219/osf.io/jfdb9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.31219/osf.io/jfdb9", "name": "item", "description": "10.31219/osf.io/jfdb9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.31219/osf.io/jfdb9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-15T00:00:00Z"}}, {"id": "2164/22487", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-13T16:27:03Z", "type": "Journal Article", "created": "2023-06-02", "title": "Modeling biochar-soil depth dependency on fecal coliform straining under subsurface drip irrigation", "description": "Funding Information: This work was supported by Shahrekord University, Iran. N. Sepehrnia is funded by a Marie Sk\u0142odowska-Curie Individual Fellowship, United Kingdom under the grant agreement No. 101026287. We acknowledge University of Aberdeen, UK for supporting this project. ; Peer reviewed", "keywords": ["GE", "Soil Science", "610", "Plant Science", "04 agricultural and veterinary sciences", "01 natural sciences", "6. Clean water", "510", "Biochar", "Maximum allowable depletion", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Irrigation strategy", "HYDRUS", "Soil bacteria contamination", "GE Environmental Sciences", "General Environmental Science", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/2164/22487"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Technology%20%26amp%3B%20Innovation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2164/22487", "name": "item", "description": "2164/22487", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2164/22487"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-01T00:00:00Z"}}, {"id": "2319912902", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-13T16:27:07Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/2319912902"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2319912902", "name": "item", "description": "2319912902", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2319912902"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "2808068377", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:17Z", "type": "Journal Article", "created": "2018-06-15", "title": "Out of Shape During Stress: A Key Role for Auxin", "description": "In most abiotic stress conditions, including salinity and water deficit, the developmental plasticity of the plant root is regulated by the phytohormone auxin. Changes in auxin concentration are often attributed to changes in shoot-derived long-distance auxin flow. However, recent evidence suggests important contributions by short-distance auxin transport from local storage and local auxin biosynthesis, conjugation, and oxidation during abiotic stress. We discuss here current knowledge on long-distance auxin transport in stress responses, and subsequently debate how short-distance auxin transport and indole-3-acetic acid (IAA) metabolism play a role in influencing eventual auxin accumulation and signaling patterns. Our analysis stresses the importance of considering all these components together and highlights the use of mathematical modeling for predictions of plant physiological responses.", "keywords": ["0301 basic medicine", "0303 health sciences", "abiotic stress", "Indoleacetic Acids", "auxin transport", "mathematical modeling", "Biological Transport", "IAA homeostasis", "Models", " Theoretical", "Plants", "Plant Roots", "Article", "03 medical and health sciences", "Plant Growth Regulators", "root phenotypic plasticity", "Stress", " Physiological", "auxin", "Plant Physiological Phenomena", "Signal Transduction"]}, "links": [{"href": "https://doi.org/2808068377"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2808068377", "name": "item", "description": "2808068377", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2808068377"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-01T00:00:00Z"}}, {"id": "3186494073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:46Z", "type": "Journal Article", "created": "2021-03-15", "title": "Overcoming the challenges to enhancing experimental plant biology with computational modeling", "description": "<p>The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.</p>", "keywords": ["Other Physical Sciences and Mathematics", "computational modeling", "2. 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