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See detailParameter identification for biological models
Fey, Dirk ULg

Doctoral thesis (2011)

This thesis concerns the identification of dynamic models in systems biology. and is structured into two parts. Both parts concern building dynamic models from observed data, but are quite different in ... [more ▼]

This thesis concerns the identification of dynamic models in systems biology. and is structured into two parts. Both parts concern building dynamic models from observed data, but are quite different in perspective, rationale and mathematics. The first part considers the development of novel identification techniques that are particularly tailored to (molecular) biology and considers two approaches. The first approach reformulates the parameter estimation problem as a feasibility problem. This reformulation allows the invalidation of models by analysing entire parameter regions. The second approach utilises nonlinear observers and a transformation of the model equations into parameter free coordinates. The parameter free coordinates allow the design of a globally convergent observer, which in turn estimates the parameter values, and further, allows to identify modelling errors or unknown inputs/influences. Both approaches are bottom up approaches that require a mechanistic understanding of the underlying processes (in terms of a biochemical reaction network) leading to complex nonlinear models. The second part is an example of what can be done with classical, well developed tools from systems identification when applied to hitherto unattended problems.In particular, part two of my thesis develops a modelling framework for rat movements in an experimental setup that it widely used to study learning and memory.The approach is a top down approach that is data driven resulting in simple linear models. [less ▲]

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See detailParameter identification for inverse problems in metal forming simulation
KLEINERMANN, J. P.; Ponthot, Jean-Philippe ULg; Hogge, Michel ULg

in Proceedings of FIELD ANALYSIS FOR DETERMINATION OF MATERIAL PARAMETERS. EXPERIMENTAL AND NUMERICAL ASPECTS (2003)

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See detailParameter Identification in a Model of the Cardiovascular System Including the Atria
Pironet, Antoine ULg; Revie, James A.; Paeme, Sabine ULg et al

in 10th Belgian Day on Biomedical Engineering (2011, December 02)

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See detailParameter Identification in a Model of the Cardiovascular System Including the Atria
Pironet, Antoine ULg; Revie, James A.; Paeme, Sabine ULg et al

Poster (2011, December 02)

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See detailParameter Identification of Material Models using the "GCMMA" method
KLEINERMANN, J. P.; Ponthot, Jean-Philippe ULg

in Proceedings of "NUMIFORM'98, Simulation of Materials Processing: Theory, Methods and Applications (1998, June)

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See detailParameter identification of nolinear mechanical systems using POD
Lenearts, Vincent; Kerschen, Gaëtan ULg; Golinval, Jean-Claude ULg

in 18th International Modal Analysis Conference, San Antonio, 2000 (2000)

Proper Orthogonal Decomposition (POD), also known as Karhunen-Loeve decomposition, or principal components analysis (PCA), is emerging as a useful experimental tool in dynamics and vibrations. The POD is ... [more ▼]

Proper Orthogonal Decomposition (POD), also known as Karhunen-Loeve decomposition, or principal components analysis (PCA), is emerging as a useful experimental tool in dynamics and vibrations. The POD is a statistical pattern analysis technique for finding the dominant structures in an ensemble of spatially distributed data. These structures can be used as an orthogonal basis for efficient representation of the ensemble. The Proper Orthogonal Modes (POM) have been interpreted mainly as empirical system modes. They have been shown to represent the optimal distributions of kinetic energy or power, and the proper orthogonal values indicate the power associated with these principal distributions. We investigate the use of the proper orthogonal modes of displacements for the identification of parameters of nonlinear dynamical structures with an optimization procedure based on the difference between the experimental and simulated POM. A numerical example of a beam with a local nonlinear component will illustrate the method. [less ▲]

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See detailParameter Identification Using Inverse Problems Methodology in Metal Forming Simulation
KLEINERMANN, J. P.; Stainier, Laurent ULg; Ponthot, Jean-Philippe ULg

in Proc. of the Second International Conference on Engineering Computational Technology “Finite Element Techniques and development (2000)

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See detailParameter identification of the STICS crop model, using an accelerated formal MCMC approach
Dumont, Benjamin ULg; Leemans, Vincent ULg; Mansouri, Majdi ULg et al

in Environmental Modelling & Software (2014), 52

This study presents a Bayesian approach for the parameters’ identification of the STICS crop model based on the recently developed Differential Evolution Adaptive Metropolis (DREAM) algorithm. The ... [more ▼]

This study presents a Bayesian approach for the parameters’ identification of the STICS crop model based on the recently developed Differential Evolution Adaptive Metropolis (DREAM) algorithm. The posterior distributions of nine specific crop parameters of the STICS model were sampled with the aim to improve the growth simulations of a winter wheat (Triticum aestivum L.) culture. The results obtained with the DREAM algorithm were initially compared to those obtained with a Nelder-Mead Simplex algorithm embedded within the OptimiSTICS package. Then, three types of likelihood functions implemented within the DREAM algorithm were compared, namely the standard least square, the weighted least square, and a transformed likelihood function that makes explicit use of the coefficient of variation (CV). The results showed that the proposed CV likelihood function allowed taking into account both noise on measurements and heteroscedasticity which are regularly encountered in crop modelling [less ▲]

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See detailParameterization and initialization of a soil organic matter decomposition model in an agricultural soil.
Buysse, Pauline ULg; Le Dantec, Valérie; Mordelet, Patrick et al

Poster (2009, September)

Organic matter decomposition and associated heterotrophic respiration fluxes are widely studied, as these processes could be modified under global warming. Many models have been built at different ... [more ▼]

Organic matter decomposition and associated heterotrophic respiration fluxes are widely studied, as these processes could be modified under global warming. Many models have been built at different temporal and spatial scales to contribute to a better understanding of the mechanisms involved and to quantify soil carbon fluxes. Yet, agroecosystems have been less investigated so far, despite their considerable importance. In this study, a daily-time step ecosystem model derived from CENTURY is described, parameterized and initialized for the Carboeurope agricultural site of Lonzée in Belgium. At this stage, the model aims at describing soil heterotrophic respiration and carbon dynamics in the soil. Model parameterization was performed on the basis of a literature survey (biochemical parameters) and of data collected at the site itself (soil carbon content and soil texture). In order to set up the carbon repartition between the different pools of the model, an initialization phase was run until equilibrium was reached. For this phase, mean daily climatic data were used and the soil was cultivated with winter wheat, considering that all residues were brought to the soil at harvest. At the end, the repartition was found to be independent from the simulated soil carbon content. Simulations showed a very high sensitivity of the model to the amount of incorporated residues and allowed an estimation of the amount of residues that lead the soil to a stable state. It was compatible with field observations. The model was then run with 2007 climatic data and the above-mentioned carbon repartition to simulate heterotrophic respiration. A comparison between these simulated fluxes and automatic measurements of soil respiration, performed during a 3-month period in spring 2007 on a bare zone of the field, showed a reasonable good agreement. Most of the discrepancies between measured and simulated fluxes corresponded to dry events, attesting of a need to reconsider the relationship between soil heterotrophic respiration and soil moisture in the model. To go further with the assessment of the model reliability, a calibration on data from the French Carboeurope site of Lamasquère will be achieved. Other sites may also be used. This heterotrophic soil respiration model is intended to be part of a more complete soil respiration model focused on agroecosystems and developed at the annual and ecosystem scales. In the end, autotrophic respiration, nitrogen mineralization and crop management would also be included. [less ▲]

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See detailParameterization of a process-based tree growth model : comparison of optimization, MCMC and particle filtering algorithms
Gaucherel, C.; Campillo, F.; Misson, L. et al

in Environmental Modelling & Software (2008), 23(10-11), 1280-1288

Finely tuned process-based tree-growth models are of considerable help in understanding the variations of biomass increments measured in the dendrochronological series. Using site and species parameters ... [more ▼]

Finely tuned process-based tree-growth models are of considerable help in understanding the variations of biomass increments measured in the dendrochronological series. Using site and species parameters, as well as daily climate variables, the MAIDEN model computes the water balance at ecosystem level and the daily increment of carbon storage in the stem through photosynthesis processes to reproduce the structure of the tree-ring series. In this paper, we use three techniques to calibrate this model with Pinus halepensis data sampled in the Mediterranean part of France: a standard optimization (PEST), Monte Carlo Markov Chains (MCMC) and Particle Filtering (PF). Contrary to PEST, which tries to find an optimum fit (giving the lowest error between observations and simulations), the principle of MCMC and PF is to walk, from a priori distributions, in the parameter space according to particular statistical rules to compute each parameter distribution. The PEST and MCMC calibrations of our dendrochronological series lead to rather similar adjustments between simulations and observations. PF and MCMC calibrations give different parameter distributions, showing how complementary are these methods, with a better fit for MCMC. Yet, independent validations over 11 independent meteorological years show a higher efficiency of the recent PF method over the others. [less ▲]

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See detailParameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations.
Bessonov, Kyrylo ULg; Vassall, Kenrick A.; Harauz, George

in Journal of Molecular Graphics and Modelling (2013), 39

We have parameterized and evaluated the proline homologue Aze (azetidine-2-carboxylic acid) for the gromos56a3 force-field for use in molecular dynamics simulations using GROMACS. Using bi-phasic ... [more ▼]

We have parameterized and evaluated the proline homologue Aze (azetidine-2-carboxylic acid) for the gromos56a3 force-field for use in molecular dynamics simulations using GROMACS. Using bi-phasic cyclohexane/water simulation systems and homo-pentapeptides, we measured the Aze solute interaction potential energies, ability to hydrogen bond with water, and overall compaction, for comparison to Pro, Gly, and Lys. Compared to Pro, Aze has a slightly higher H-bonding potential, and stronger electrostatic but weaker non-electrostatic interactions with water. The 20-ns simulations revealed the preferential positioning of Aze and Pro at the interface of the water and cyclohexane layers, with Aze spending more time in the aqueous layer. We also demonstrated through simulations of the homo-pentapeptides that Aze has a greater propensity than Pro to undergo trans-->cis peptide bond isomerization, which results in a severe 180 degrees bend in the polypeptide chain. The results provide evidence for the hypothesis that the misincorporation of Aze within proline-rich regions of proteins could disrupt the formation of poly-proline type II structures and compromise events such as recognition and binding by SH3-domains. [less ▲]

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See detailParameterizing a Dynamic Architectural Model of the Root System of Spring Barley from Minirhizotron Data
Garré, Sarah ULg; Pagès, Loïc; Laloy, Eric et al

in Vadose Zone Journal (2012)

The development of models describing water and nutrient fluxes to and through 3-D spatially resolved root structures in soils brings along the need to predict or describe the root architecture and root ... [more ▼]

The development of models describing water and nutrient fluxes to and through 3-D spatially resolved root structures in soils brings along the need to predict or describe the root architecture and root growth in detail. However, detailed data to calibrate and validate such architecture and growth models is typically not available. Here, we investigate the sensitivity of the root architecture model RootTyp (Pagès et al., 2004) to changes in its model parameters and reconstructed the root system architecture of barley growing in an undisturbed lysimeter using minirhizotron images at four different depths. Root arrival curves from a series of minirhizotron images were used to parameterize RootTyp using a range of realistic architectures. We adjusted a simple architecture to the data, which contained only long primary roots starting from the seed. This simple model unfortunately could not reproduce the observed increase of root density with depth. The model was subsequently improved by allowing root branching and elongation to be horizon-dependent and by making reiteration of root tips possible. Reiteration is an alternative form of branching, where secondary roots can become as long and thick as primary roots. Our results show that minirhizotron data do not contain enough information to warrant identification of the parameters governing these processes, as the additional parameters act similarly on data characteristics as the initial ones. Therefore, different experimental techniques should be combined to constrain the model parameters better in the future. [less ▲]

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See detailParameterizing the root system development of summer barley using minirhizotron data
Garré, Sarah ULg; Pagès, Loïc; Javaux, Mathieu et al

Poster (2011, April)

Detailed reference viewed: 13 (1 ULg)
See detailParamètres de dégradation et de fermentation dans le rumen des rations d'engraissement à base d'ensilage de maïs et de pulpes séchées complémentées ou non avec du lait
Mayombo, Asangule Pierre; Dufrasne, Isabelle ULg; Clinquart, Antoine ULg et al

in 8èmes Journées des Recherches sur l'Alimentation et la Nutrition des Herbivores. (1993)

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See detailParamètres de variation lexicale en Langue Belge des Signes
Rondal, Jean-Adolphe ULg; Bachelet, Jean-François ULg; Carter, M. et al

in Psychologica Belgica (1988), 28

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See detailParamètres hydrologiques et physico-chimiques de sources du Crétacé du Pays de Herve et de la Hesbaye sèche
Mols, J.; Petit, François ULg

in Bulletin de la Société Géographique de Liège (2005)

Detailed reference viewed: 26 (6 ULg)