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Data Intensive Modelling of the Rhizosphere Processes

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Publications

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
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
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
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
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
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, 0ISSN 1539-1663
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
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
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
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
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, 0ISSN 1539-1663
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
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, 0ISSN 1539-1663
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
DOI: 10.1093/jxb/erv544