My role as CPIB Research Adminstrator is to monitor the CPIB budget, prepare reports on expenditure, oversee CPIB purchases, manage the day to day administration of the centre for the Director, and coordinate recruitment administration.

Centre Research | Virtual Root

Mirela Axinte's homepage

Adib Becker is Professor of Mechanical Engineering, Head of Structural Integrity and Dynamics and Director of the Spencer Institute at the University of Nottingham.

Adib Becker’s homepage

Centre Research | Virtual Root

Adib Becker's homepage

Glyn was the bioinformatician associated with the Tomato project

Centre Research | A Systems Approach to Tomato Ripening

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Ruth is associated with the localisome project

Centre Research | Virtual Root

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Centre Research | Virtual Root

I have been working in CPIB since April 2009. I have been looking at mechanical properties of the root in a broad context and developing methodologies to characterise them. I have been working on the application of Atomic force microscopy to study mechanical properties, specifically of the epidermal cells. I am also looking at other tensile testing methodologies to implement in studying living root samples, including the DMA. I am investigating polarised light microscopy and resultant forms of birefringence which may help us map the inherent structural properties of roots. The goal is to obtain parameters which will fit into the CPIB models. Most of my work is collaborative and have been developing external biophysical experimental support for CPIB. The AFM work is in collaboration with Dept. Of Pharmacy, University of Nottingham. The Birefringence work has been initiated with the Department of Physics, University of Oxford.

Background and Research Interests:

I am biophysicist with a background in solid state physics, thin film physics and wood science. My research interests include biomechanics of all sorts, surface physics, gas sensing, cellulose structure and rheology.

I worked with Langmuir Blodgett films, including working on few unconventional materials like phthalocyanines, besides nanoparticles for my doctoral degree under Dr Tim Richardson, Dept of Physics & Astronomy, University of Sheffield. I chiefly worked with UV-Visible spectroscopy, conductometry, gas sensing and thermal polarised microscopy (Collaboration with the Dept. Of Chemistry, University of Hull).

I then switched fields and went to work in wood biophysics with Dr Mike Jarvis, Dept of Chemistry, University of Glasgow. I developed a technique to study tensile properties of wood (in co-ordination with IR microscopy) which could be extended to other materials like bacterial films and the like. Few of the techniques I worked with are IR microcopy, NMR and its variants, Raman microscopy in conjunction with tensile testing (Collaboration with Max Planck Institute, Golm, Germany) and X-ray Diffraction.

CPIB Talks:

“Application of Atomic Force Microscopy as a novel technique to investigate mechanical properties of root epidermal cells.” Plant Growth Biology and Modelling Workshop, 14-16 October 2009, Elche-Spain.

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Anwesha Fernandes's homepage

Jon Garibaldi is Associate Professor & Reader in the School of Computer Science at the University of Nottingham and Manager of Strand 3 of the CPIB virtual root project.

Dr Garibaldi’s main research interest is in the development of artificial intelligence techniques for biomedical decision support and in the modelling of human decision making, primarily in the context of biological and medical applications. His work to date has concentrated on utilising fuzzy logic to model the imprecision and uncertainty inherent in biomedical knowledge representation and decision making.

Jon Garibaldi’s homepage

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Jon Garibaldi's homepage

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My role in CPIB is finite element modelling of plant root growth at tissue (multi-cells) scale. The modelling should cover three aspects in plant root growth as follows:1) reversible deformation,2) irreversible growth,3) interplay between mechanics and chemistry.The modelling involves a mechanical constitutive law and its interplay with chemical regulatory. By using this model, Finite Element Analysis (FEA) is expected to present an effective platform to biologists for their deformation-related research in plant root growth.

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Ruoyu Huang's homepage

Arthur Jones is Associate Professor and Reader in Engineering Mechanics in the Department of Mechanical Materials and Manufacturing Engineering at the University of Nottingham.

Arthur Jones’s homepage

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Arthur Jones's homepage

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Natalio Krasnogor is an Associate Professor and Reader in Interdisciplinary Computer Science in the School of Computer Science at the University of Nottingham. He is a member of the Automated Scheduling, Optimisation and Planning Research Group (ASAP) and also leads the Interdisciplinary Optimisation Laboratory (IOL).

Dr Krasnogor’s research activities lie at the interface of Computer Science and the Natural Sciences, e.g. Biology, Physics, Chemistry. In particular, he develops innovative and competitive search methodologies and intelligent decision support systems for transdisciplinary optimisation, modelling of complex systems and very-large datasets processing.

He is associate editor of the Evolutionary Computation journal and founding technical editor-in-chief of the new journal Memetic Computing. He has acted as grant reviewer for the EPSRC (UK), BBSRC(UK), European Science Foundation, European Union, The Israel Science Foundation, DOE Computational Biology Programme (USA), CNRS (France), and co-chaired the First and Second European Conference on Synthetic Biology (ECSB I & II).

Natalio Krasnogor’s homepage

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Natalio Krasnogor's homepage

My role in CPIB was to address automated model synthesis where the structure of candidate models was reversed engineered from experimental data, using P-systems as the modelling framework. This wass essentially a complementary approach to more deterministic models developed by mathematicians at CPIB. To search for the appropriate model structure and parameters several state-of-the-art optimization algorithms were considered. I was also involved with parameter estimation for deterministic ODE-based models.

Claudio left CPIB in December 2010.

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My research interests are analysing biological datasets using computational methods and network biology as a way of determining relationships with plant biological networks. I am interested in different types of networks, and how these can be analysed with experimental biological data. I am working on using existing and developing new methods to analyse biological networks and obtain more information about the organism. I am very interested in finding new ways to analyse high-throughput datasets, and have experience in the fields of Bioinformatics, Systems Biology and Biology.

Centre Research | Secondary Cell Wall Thickening | A Systems Approach to Tomato Ripening

My role within CPIB is to produce specific antibodies to up to 500 key root proteins that will subsequently be used to study their spatial expression in root cells and tissues. This Root Atlas of key proteins will be a major step forward towards creating a virtual root and in addition will be a very important resource for the plant science community in the UK and abroad.

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My role in CPIB was to simulate cell elongation in the Arabidopsis root to understand the mechanics and properties of cell walls using Finite Element (FE) analysis. This involved modelling plant material using fibre-reinforced composite material models

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Ming left CPIB in July 2010.

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Colin Scotchford is Associate Professor in the Department of Mechanical Materials and Manufacturing Engineering at the University of Nottingham.

Colin Scotchford’s homepage

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Colin Scotchford's homepage

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Mike was CPIB’s Bioinformatics Engineer, researching standards and techniques for linking disparate modelling software systems and exploring ways to make CPIB models compatible with other Arabidopsis computer models.

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Mike Stout's homepage

My role is to address the requirements of CPIB for optimal parameter values involved in the ordinary differential equations (ODEs) developed by mathematicians to model the dynamic systems of biological pathways. Such models include the S-system which was developed to model gene regulatory networks and metabolic pathways. The kinetic parameters in the S-system reflect the interactions among the genes (or metabolites), which are estimated from the experimental data.

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Jianyong Sun's homepage

Geoff Tansley is Professor of Mechanical Engineering at Aston University and an Associate of the CPIB virtual root project.

Geoff Tansley’s homepage

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Greg Tucker is Professor of Plant Biochemistry in the School of Biosciences at the University of Nottingham.

Greg Tucker’s homepage

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Greg Tucker's homepage