Application of non-linear mathematics and stochastic modelling to complex biological systems
Lead Research Organisation:
Rothamsted Research
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
This project aims to develop novel mathematical approaches, based on non-linear mathematics and stochastic modelling, to analyse and predict the behaviour of complex agricultural and biological systems underpinning predictive systems biology. Key objectives of the project are:
1. Modelling impact of climate change
The probability and the magnitude of extreme events and impacts on crops are likely to increase under climate change. We will develop methodology and computational tools to analyse extreme impacts on crops and plant communities under climate change. Specifically:
a) to develop local-scale climate scenarios, based on the LARS-WG Weather Generator, a multi-model ensemble of global and regional climate models
b) to develop a dataset of LARS-WG baseline parameters for Europe with a 25 km grid.
2. Crop modelling
Crop models provide a consistent framework for integrating our understanding of plant processes as influenced by environments. Specifically:
a) to use crop simulation models to deconvolute complex traits, such as nitrogen use efficiency (NUE) or water use efficiency (WUE);
b) to develop computational tools for evaluating performance of new genotypes in diverse environments.
3. Individual-based modelling
The development of resistance in pest insects to insecticides is a significant barrier to sustainable farming. The evolution of resistance is affected by many factors limiting applications of classical modelling approaches. We will develop an individual-based model (IbM) that includes genetic status, individual behaviours, multitrophic interactions and environmental heterogeneity. Specifically:
a) to develop a predictive high-performance IbM;
b) to develop approaches for analysis of stochastic high-dimensional IbM output;
c) to predict of the evolution of resistance in model systems.
1. Modelling impact of climate change
The probability and the magnitude of extreme events and impacts on crops are likely to increase under climate change. We will develop methodology and computational tools to analyse extreme impacts on crops and plant communities under climate change. Specifically:
a) to develop local-scale climate scenarios, based on the LARS-WG Weather Generator, a multi-model ensemble of global and regional climate models
b) to develop a dataset of LARS-WG baseline parameters for Europe with a 25 km grid.
2. Crop modelling
Crop models provide a consistent framework for integrating our understanding of plant processes as influenced by environments. Specifically:
a) to use crop simulation models to deconvolute complex traits, such as nitrogen use efficiency (NUE) or water use efficiency (WUE);
b) to develop computational tools for evaluating performance of new genotypes in diverse environments.
3. Individual-based modelling
The development of resistance in pest insects to insecticides is a significant barrier to sustainable farming. The evolution of resistance is affected by many factors limiting applications of classical modelling approaches. We will develop an individual-based model (IbM) that includes genetic status, individual behaviours, multitrophic interactions and environmental heterogeneity. Specifically:
a) to develop a predictive high-performance IbM;
b) to develop approaches for analysis of stochastic high-dimensional IbM output;
c) to predict of the evolution of resistance in model systems.
Planned Impact
unavailable
Organisations
People |
ORCID iD |
Mikhail Semenov (Principal Investigator) |
Publications

BARNES A
(2010)
Adaptation to increasing severity of phoma stem canker on winter oilseed rape in the UK under climate change
in The Journal of Agricultural Science

Butterworth MH
(2010)
North-South divide: contrasting impacts of climate change on crop yields in Scotland and England.
in Journal of the Royal Society, Interface

Calanca P
(2012)
Local-scale climate scenarios for impact studies and risk assessments: integration of early 21st century ENSEMBLES projections into the ELPIS database
in Theoretical and Applied Climatology

Defoin-Platel M
(2011)
AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations.
in BMC bioinformatics

Evans N
(2011)
Erratum: The impact of climate change on disease constraints on production of oilseed rape
in Food Security

Evans N
(2010)
The impact of climate change on disease constraints on production of oilseed rape
in Food Security

He J
(2012)
Simulation of environmental and genotypic variations of final leaf number and anthesis date for wheat
in European Journal of Agronomy

Iizumi T
(2012)
ELPIS-JP: a dataset of local-scale daily climate change scenarios for Japan.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Iizumi T
(2012)
Future change of daily precipitation indices in Japan: A stochastic weather generator-based bootstrap approach to provide probabilistic climate information
in Journal of Geophysical Research: Atmospheres

Kauserud H
(2010)
Climate change and spring-fruiting fungi.
in Proceedings. Biological sciences
Description | A wheat simulation model, Sirius, has been developed and tested. This model was used in the impact assessment of climate change on wheat in the UK and Europe. Downscaling methodology for generation of local-scale climate scenarios has been developed. It was based on the LARS-WG weather generator and climate projections from the CMIP3 ensemble of global climate models. |
Exploitation Route | Local-scale climate scenarios has been already used in many impact studies in the UK, and worldwide. Sirius wheat model has been used in international model intercomparison and improvements such as AgMIP and MACSUR. |
Sectors | Agriculture Food and Drink Environment |
URL | http://www.rothamsted.ac.uk/mas-models/sirius |
Description | Results and publications were used in the IPCC Assessment Report 5 to advise governments on climate change adaptation and mitigation. |
First Year Of Impact | 2014 |
Sector | Agriculture, Food and Drink,Environment |
Impact Types | Policy & public services |
Description | Modelling resistance using IbM |
Amount | £150,000 (GBP) |
Organisation | Syngenta International AG |
Sector | Private |
Country | Switzerland |
Start | 05/2016 |
End | 05/2017 |
Title | ELPIS |
Description | ELPIS is a dataset of site parameters for the LARS-WG weather generator for Europe. |
Type Of Material | Database/Collection of data |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | ELPIS has been used to generate local-scale climate scenarios for Europe using LARS-WG and climate projections from the CMIP5 ensemble. These scenarios have been used in many projects including MACSUR. |
URL | http://www.rothamsted.ac.uk/mas-models/larswg |
Title | LARS-WG stochastic weather generator |
Description | LARS-WG is a model simulating time-series of daily weather at a single site. It can be used: 1. to generate long time-series suitable for the assessment of agricultural and hydrological risk; 2. to provide the means of extending the simulation of weather to unobserved locations; 3. to serve as a computationally inexpensive tool to produce daily site-specific climate scenarios for impact assessments of climate change. LARS-WG version 5.0 includes climate scenarios based on 15 Global Climate Models (GCMs) which have been used in the IPCC 4AR (2007). This large dataset of future climate projections was produced by leading modelling groups worldwide who performed a set of coordinated climate experiments in which GCMs have been run for a common set of experiments and emission scenarios. Multi-model ensembles allow to explore the uncertainty in climate predictions resulting from structural differences in the global climate model design as well as uncertainty in variations of initial conditions or model parameters. The new version also improves simulation of extreme weather events, such as extreme daily precipitation, long dry spells and heat waves. LARS-WG has been well validated in diverse climates around the world. |
Type Of Technology | Software |
Year Produced | 2015 |
Impact | LARS-WG has been used in more than 65 countries for research and in several Universities as an educational tool. Climate scenarios generated by LARS-WG have been used in the impact assessments of climate change for the IPCC Assessment Report 5. |
URL | http://www.rothamsted.ac.uk/mas-models/larswg |
Title | SIRIUS wheat simulation model |
Description | Sirius is a wheat simulation model that calculates biomass from intercepted photosynthetically active radiation and grain growth from simple partitioning rules. Leaf area index (LAI) is developed from a simple thermal time sub-model. Phenological development is calculated from the mainstem leaf appearance rate and final leaf number, with the latter determined by responses to daylength and vernalisation. Effects of water and N deficits are calculated through their influences on LAI development and radiation-use efficiency. Sirius has been calibrated for several modern wheat cultivars and was able to simulate crop growth accurately in a wide range of conditions, including Europe, NZ/Australia and USA and under climate change |
Type Of Technology | Software |
Year Produced | 2015 |
Impact | Sirius is used in research by many scientists to understand crop responses to environmental variations, and in practice by farmers to optimize water and N management. |
URL | http://www.rothamsted.ac.uk/mas-models/sirius |