Data Intensive Modelling of the Rhizosphere Processes

Publications

Author(s): Ruiz, Siul Aljadi, Mckay Fletcher, Daniel, Williams, Katherine, Roose, Tiina
Published in: Annual Plant Reviews Online, Issue 6, 2018, Page(s) NA, ISBN 9781119312994
Publisher: Wiley
DOI: 10.1002/9781119312994.apr0755

Supplementary Information from Stabilizing gold nanoparticles for use in X-ray computed tomography imaging of soil systems

Author(s): Scotson, Callum P.; Munoz-Hernando, Maria; Duncan, Simon J.; Siul A. Ruiz; Keyes, Samuel D.; Veelen, Arjen Van; Dunlop, Iain E.; Roose, Tiina
Published in: Royal Society Open Science, 2019
Publisher: Royal Society
DOI: 10.6084/m9.figshare.9942854

Supplementary 01 from Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures

Author(s): K. R. Daly; S. D. Keyes; T. Roose
Published in: Proceedings of the Royal Society A, 2018
Publisher: Royal Society
DOI: 10.6084/m9.figshare.6668318.v1

Homogenisation of two fluid flow dependent on exudate concentration. from The effect of root exudates on rhizosphere water dynamics

Author(s): L. J. Cooper; K. R. Daly; P. D. Hallett; N. Koebernick; T. S. George; T. Roose
Published in: Proceedings of the Royal Society A, 2018
Publisher: Royal Society
DOI: 10.6084/m9.figshare.6982730

Supplementary 02 from Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures

Author(s): K. R. Daly; S. D. Keyes; T. Roose
Published in: Proceedings of the Royal Society A, 2018
Publisher: Royal Society
DOI: 10.6084/m9.figshare.6668315.v1

Supplementary Materials from Measurement of micro-scale soil deformation around roots using four-dimensional synchrotron tomography and image correlation

Author(s): S. D. Keyes; L. Cooper; S. Duncan; N. Koebernick; D. M. McKay Fletcher; C. P. Scotson; A. V. Van Veelen; I. Sinclair; T. Roose
Published in: Royal Society Interface, Issue 17425662, 2017, ISSN 1742-5662
Publisher: Royal Society
DOI: 10.6084/m9.figshare.5555092.v1

Projected Increases in Precipitation Are Expected To Reduce Nitrogen Use Efficiency and Alter Optimal Fertilization Timings in Agriculture in the South East of England

Author(s): Dan McKay Fletcher; Siul Ruiz; Katherine Williams; Chiara Petroselli; Nancy Walker; David Chadwick; Davey L. Jones; Tiina Roose
Published in: Crossref, Issue 26900645, 2021, ISSN 2690-0645
Publisher: American Chemical Society
DOI: 10.1021/acsestengg.1c00492

X‐ray computed tomography imaging of solute movement through ridged and flat plant systems

Author(s): Callum P. Scotson, Simon J. Duncan, Katherine A. Williams, Siul A. Ruiz, Tiina Roose
Published in: European Journal of Soil Science, Issue 72/1, 2021, Page(s) 198-214, ISSN 1351-0754
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ejss.12985

Impact of root hairs on microscale soil physical properties in the field

Author(s): M. Marin; P. D. Hallett; D. S. Feeney; L. K. Brown; M. Naveed; N. Koebernick; S. Ruiz; A. G. Bengough; T. Roose; T. S. George
Published in: Plant and Soil, Issue 0032079X, 2022, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-022-05530-1

Combining Seed Dressing and Foliar Applications of Phosphorus Fertilizer Can Give Similar Crop Growth and Yield Benefits to Soil Applications Together With Greater Recovery Rates

Author(s): Peter J. Talboys, John R. Healey, Paul J. A. Withers, Tiina Roose, Anthony C. Edwards, Paulo S. Pavinato, Davey L. Jones
Published in: Frontiers in Agronomy, Issue 2, 2020, ISSN 2673-3218
Publisher: Frontiers
DOI: 10.3389/fagro.2020.605655

Space and time‐resolved monitoring of phosphorus release from a fertilizer pellet and its mobility in soil using microdialysis and X‐ray computed tomography

Author(s): Chiara Petroselli, Katherine A. Williams, Arpan Ghosh, Daniel McKay Fletcher, Siul A. Ruiz, Tiago Gerheim Souza Dias, Callum P. Scotson, Tiina Roose
Published in: Soil Science Society of America Journal, Issue 85/1, 2021, Page(s) 172-183, ISSN 0361-5995
Publisher: Soil Science Society of America
DOI: 10.1002/saj2.20161

Mathematical and computational modelling of vegetated soil incorporating hydraulically-driven finite strain deformation

Author(s): N.D. Woodman, J.A. Smethurst, T. Roose, W. Powrie, G.J. Meijer, J.A. Knappett, T. Dias
Published in: Computers and Geotechnics, Issue 127, 2020, Page(s) 103754, ISSN 0266-352X
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compgeo.2020.103754

Linking root structure to functionality: the impact of root system architecture on citrate‐enhanced phosphate uptake

Author(s): Daniel M. McKay Fletcher, Siul Ruiz, Tiago Dias, Chiara Petroselli, Tiina Roose
Published in: New Phytologist, Issue 227/2, 2020, Page(s) 376-391, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.16554

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

Author(s): Nicolai Koebernick, Keith R. Daly, Samuel D. Keyes, Timothy S. George, Lawrie K. Brown, Annette Raffan, Laura J. Cooper, Muhammad Naveed, Anthony G. Bengough, Ian Sinclair, Paul D. Hallett, Tiina Roose
Published in: New Phytologist, Issue 216/1, 2017, Page(s) 124-135, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.14705

Quantification of root water uptake in soil using X-ray computed tomography and image-based modelling

Author(s): Keith R. Daly, Saoirse R. Tracy, Neil M.J. Crout, Stefan Mairhofer, Tony P. Pridmore, Sacha J. Mooney, Tiina Roose
Published in: Plant, Cell & Environment, 2017, ISSN 0140-7791
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pce.12983

The Application of Contrast Media for In Vivo Feature Enhancement in X-Ray Computed Tomography of Soil-Grown Plant Roots

Author(s): Samuel D. Keyes, Neil J. Gostling, Jessica H. Cheung, Tiina Roose, Ian Sinclair, Alan Marchant
Published in: Microscopy and Microanalysis, Issue 23/03, 2017, Page(s) 538-552, ISSN 1431-9276
Publisher: Cambridge University Press
DOI: 10.1017/S1431927617000319

An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography

Author(s): Samuel David Keyes, Konstantinos C. Zygalakis, Tiina Roose
Published in: Bulletin of Mathematical Biology, Issue 79/12, 2017, Page(s) 2785-2813, ISSN 0092-8240
Publisher: Academic Press
DOI: 10.1007/s11538-017-0350-x

Measurement of micro-scale soil deformation around roots using four-dimensional synchrotron tomography and image correlation

Author(s): S. D. Keyes, L. Cooper, S. Duncan, N. Koebernick, D. M. McKay Fletcher, C. P. Scotson, A. van Veelen, I. Sinclair, T. Roose
Published in: Journal of The Royal Society Interface, Issue 14/136, 2017, Page(s) 20170560, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2017.0560

Modeling Soil Processes: Review, Key Challenges, and New Perspectives

Author(s): H. Vereecken, A. Schnepf, J.W. Hopmans, M. Javaux, D. Or, T. Roose, J. Vanderborght, M.H. Young, W. Amelung, M. Aitkenhead, S.D. Allison, S. Assouline, P. Baveye, M. Berli, N. Brüggemann, P. Finke, M. Flury, T. Gaiser, G. Govers, T. Ghezzehei, P. Hallett, H.J. Hendricks Franssen, J. Heppell, R. Horn, J.A. Huisman, D. Jacques, F. Jonard, S. Kollet, F. Lafolie, K. Lamorski, D. Leitner, A. McBratney
Published in: Vadose Zone Journal, Issue 15/5, 2016, ISSN 1539-1663
Publisher: Soil Science Society of America
DOI: 10.2136/vzj2015.09.0131

Plant exudates may stabilize or weaken soil depending on species, origin and time

Author(s): M. Naveed, L. K. Brown, A. C. Raffan, T. S. George, A. G. Bengough, T. Roose, I. Sinclair, N. Koebernick, L. Cooper, C. A. Hackett, P. D. Hallett
Published in: European Journal of Soil Science, Issue 68/6, 2017, Page(s) 806-816, ISSN 1351-0754
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ejss.12487

Mathematical modelling of water and solute movement in ridge plant systems with dynamic ponding

Author(s): S. J. Duncan, K. R. Daly, P. Sweeney, T. Roose
Published in: European Journal of Soil Science, Issue 69/2, 2018, Page(s) 265-278, ISSN 1351-0754
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ejss.12503

Modelling water dynamics in the rhizosphere

Author(s): K.R. Daly, L.J. Cooper, N. Koebernick, J. Evaristo, S.D. Keyes, A. van Veelen, T. Roose
Published in: Rhizosphere, Issue 4, 2017, Page(s) 139-151, ISSN 2452-2198
Publisher: Elsevier
DOI: 10.1016/j.rhisph.2017.10.004

Fluid flow in porous media using image-based modelling to parametrize Richards' equation

Author(s): L. J. Cooper, K. R. Daly, P. D. Hallett, M. Naveed, N. Koebernick, A. G. Bengough, T. S. George, T. Roose
Published in: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science, Issue 473/2207, 2017, Page(s) 20170178, ISSN 1364-5021
Publisher: Royal Society of London
DOI: 10.1098/rspa.2017.0178

Rhizosphere-Scale Quantification of Hydraulic and Mechanical Properties of Soil Impacted by Root and Seed Exudates

Author(s): M. Naveed, L.K. Brown, A.C. Raffan, T.S. George, A.G. Bengough, T. Roose, I. Sinclair, N. Koebernick, L. Cooper, P.D. Hallett
Published in: Vadose Zone Journal, Issue 17/1, 2018, ISSN 1539-1663
Publisher: Soil Science Society of America
DOI: 10.2136/vzj2017.04.0083

Determination of macro-scale soil properties from pore-scale structures: model derivation

Author(s): K. R. Daly, T. Roose
Published in: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science, Issue 474/2209, 2018, Page(s) 20170141, ISSN 1364-5021
Publisher: Royal Society of London
DOI: 10.1098/rspa.2017.0141

Noninvasive Imaging of Processes in Natural Porous Media: From Pore to Field Scale

Author(s): Andreas Pohlmeier, Sarah Garré, Tiina Roose
Published in: Vadose Zone Journal, Issue 17/1, 2018, ISSN 1539-1663
Publisher: Soil Science Society of America
DOI: 10.2136/vzj2018.03.0044

Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures

Author(s): K. R. Daly, S. D. Keyes, T. Roose
Published in: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science, Issue 474/2215, 2018, Page(s) 20170745, ISSN 1364-5021
Publisher: Royal Society of London
DOI: 10.1098/rspa.2017.0745

Correlative Visualization of Root Mucilage Degradation Using X-ray CT and MRI

Author(s): Arjen van Veelen, Monique C. Tourell, Nicolai Koebernick, Giuseppe Pileio, Tiina Roose
Published in: Frontiers in Environmental Science, Issue 6, 2018, ISSN 2296-665X
Publisher: Frontiers
DOI: 10.3389/fenvs.2018.00032

Mathematical modelling of water and solute movement in ridged versus flat planting systems

Author(s): S. J. Duncan, K. R. Daly, P. Sweeney, T. Roose
Published in: European Journal of Soil Science, 2018, ISSN 1351-0754
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ejss.12711

A Model of Uranium Uptake by Plant Roots Allowing for Root-Induced Changes in the soil

Author(s): Andrea Boghi, Tiina Roose, Guy J. D. Kirk
Published in: Environmental Science & Technology, Issue 52/6, 2018, Page(s) 3536-3545, ISSN 0013-936X
Publisher: American Chemical Society
DOI: 10.1021/acs.est.7b06136

The effect of root exudates on rhizosphere water dynamics

Author(s): L. J. Cooper, K. R. Daly, P. D. Hallett, N. Koebernick, T. S. George, T. Roose
Published in: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science, Issue 474/2217, 2018, Page(s) 20180149, ISSN 1364-5021
Publisher: Royal Society of London
DOI: 10.1098/rspa.2018.0149

Quantifying citrate-enhanced phosphate root uptake using microdialysis

Author(s): D. M. McKay Fletcher, R. Shaw, A. R. Sánchez-Rodríguez, K. R. Daly, A. van Veelen, D. L. Jones, T. Roose
Published in: Plant and Soil, 2019, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-019-04376-4

Root‐induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES

Author(s): Arjen Veelen, Nicolai Koebernick, Callum S. Scotson, Daniel McKay‐Fletcher, Thomas Huthwelker, Camelia N. Borca, J. Fred W. Mosselmans, Tiina Roose
Published in: New Phytologist, Issue 225/4, 2019, Page(s) 1476-1490, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.16242

Significance of root hairs at the field scale – modelling root water and phosphorus uptake under different field conditions

Author(s): S. Ruiz, N. Koebernick, S. Duncan, D. McKay Fletcher, C. Scotson, A. Boghi, M. Marin, A. G. Bengough, T. S. George, L. K. Brown, P. D. Hallett, T. Roose
Published in: Plant and Soil, Issue 447/1-2, 2020, Page(s) 281-304, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-019-04308-2

Stabilizing gold nanoparticles for use in X-ray computed tomography imaging of soil systems

Author(s): Callum P. Scotson, Maria Munoz-Hernando, Simon J. Duncan, Siul A. Ruiz, Samuel D. Keyes, Arjen van Veelen, Iain E. Dunlop, Tiina Roose
Published in: Royal Society Open Science, Issue 6/10, 2019, Page(s) 190769, ISSN 2054-5703
Publisher: Royal Society
DOI: 10.1098/rsos.190769

Multiple Scale Homogenisation of Nutrient Movement and Crop Growth in Partially Saturated Soil

Author(s): Simon J. Duncan, Keith R. Daly, Daniel M. McKay Fletcher, Siul Ruiz, Paul Sweeney, Tiina Roose
Published in: Bulletin of Mathematical Biology, Issue 81/10, 2019, Page(s) 3778-3802, ISSN 0092-8240
Publisher: Academic Press
DOI: 10.1007/s11538-019-00656-3

Soil carbon dioxide venting through rice roots

Author(s): Guy J.D. Kirk, Andrea Boghi, Marie‐Cecile Affholder, Samuel D. Keyes, James Heppell, Tiina Roose
Published in: Plant, Cell & Environment, Issue 42/12, 2019, Page(s) 3197-3207, ISSN 0140-7791
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pce.13638

A multi image-based approach for modelling plant-fertiliser interaction

Author(s): Daniel M. McKay Fletcher, Samuel D. Keyes, Keith R. Daly, Arjen van Veelen, Tiina Roose
Published in: Rhizosphere, Issue 10, 2019, Page(s) 100152, ISSN 2452-2198
Publisher: Elsevier
DOI: 10.1016/j.rhisph.2019.100152

Surface tension, rheology and hydrophobicity of rhizodeposits and seed mucilage influence soil water retention and hysteresis

Author(s): M. Naveed, M. A. Ahmed, P. Benard, L. K. Brown, T. S. George, A. G. Bengough, T. Roose, N. Koebernick, P. D. Hallett
Published in: Plant and Soil, Issue 437/1-2, 2019, Page(s) 65-81, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-019-03939-9

Imaging microstructure of the barley rhizosphere: particle packing and root hair influences

Author(s): Nicolai Koebernick, Keith R. Daly, Samuel D. Keyes, Anthony G. Bengough, Lawrie K. Brown, Laura J. Cooper, Timothy S. George, Paul D. Hallett, Muhammad Naveed, Annette Raffan, Tiina Roose
Published in: New Phytologist, Issue 221/4, 2018, Page(s) 1878-1889, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.15516

Mapping soil deformation around plant roots using in vivo 4D X-ray computed tomography and digital volume correlation

Author(s): S.D. Keyes, F. Gillard, N. Soper, M.N. Mavrogordato, I Sinclair, T. Roose
Published in: Journal of Biomechanics, 2016, ISSN 0021-9290
Publisher: Elsevier BV
DOI: 10.1016/j.jbiomech.2016.04.023

Challenges in imaging and predictive modeling of rhizosphere processes

Author(s): T. Roose, S. D. Keyes, K. R. Daly, A. Carminati, W. Otten, D. Vetterlein, S. Peth
Published in: Plant and Soil, 2016, Page(s) Processing charge is the list price that was not paid since we got it Gold Open access via Springer hybrid offsetting scheme, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-016-2872-7

Image-based modelling of nutrient movement in and around the rhizosphere

Author(s): Keith R. Daly, Samuel D. Keyes, Shakil Masum, Tiina Roose
Published in: Journal of Experimental Botany, Issue 67/4, 2016, Page(s) 1059-1070, ISSN 0022-0957
Publisher: Oxford University Press
DOI: 10.1093/jxb/erv544

Precipitation-optimised targeting of nitrogen fertilisers in a model maize cropping system

Author(s): D.M. McKay Fletcher, S.A. Ruiz, T. Dias, D.R. Chadwick, D.L. Jones, T. Roose
Published in: Science of The Total Environment, Issue 756, 2021, Page(s) 144051, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2020.144051

Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi

Author(s): Sam Keyes; Arjen Veelen; Dan McKay Fletcher; Callum Scotson; Nico Koebernick; Chiara Petroselli; Katherine Williams; Siul Ruiz; Laura Cooper; Robbie Mayon; Simon Duncan; Marc Dumont; Iver Jakobsen; Giles Oldroyd; Andrzej Tkacz; Philip Poole; Fred Mosselmans; Camelia Borca; Thomas Huthwelker; David L. Jones; Tiina Roose
Published in: Keyes , S , van Veelen , A , McKay Fletcher , D , Scotson , C , Koebernick , N , Petroselli , C , Williams , K , Ruiz , S , Cooper , L , Mayon , R , Duncan , S , Dumont , M , Jakobsen , I , Oldroyd , G , Tkacz , A , Poole , P , Mosselmans , F , Borca , C , Huthwelker , T , Jones , D L & Roose , T 2022 , ' Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of myco, Issue 1, 2022, ISSN 1469-8137
Publisher: Wiley
DOI: 10.17863/cam.81466

Image-based quantification of soil microbial dead zones induced by nitrogen fertilization

Author(s): S.A. Ruiz, D.M. McKay Fletcher, A. Boghi, K.A. Williams, S.J. Duncan, C.P. Scotson, C. Petroselli, T.G.S. Dias, D.R. Chadwick, D.L. Jones, T. Roose
Published in: Science of The Total Environment, Issue 727, 2020, Page(s) 138197, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2020.138197

A 3D image-based modelling approach for understanding spatiotemporal processes in phosphorus fertiliser

Author(s): K. A. Williams, D. McKay Fletcher, C. Petroselli, S. A. Ruiz, T. Roose
Published in: Nature Scientific Reports, Issue 20452322, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-19047-1

Developing a system for in vivo imaging of maize roots containing iodinated contrast media in soil using synchrotron XCT and XRF

Author(s): Callum P. Scotson, Arjen van Veelen, Katherine A. Williams, Nicolai Koebernick, Dan McKay Fletcher, Tiina Roose
Published in: Plant and Soil, Issue 460/1-2, 2021, Page(s) 647-665, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-020-04784-x

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