Contact Dr Xavier Portell
Areas of expertise
- Computing, Simulation & Modelling
- Soil Resources
I am a computational biologist whose research focuses on mathematical modelling of biological systems, especially focusing on microbiological relevant scales. Specifically I have experience in modelling growth dynamics of yeast and the dynamics of the activity of soil bacteria at pore scale. My current research focuses on modelling of soil processes at the pore scale with special attention to fungal activity. I am familiar with a range of modelling techniques including population-based microbial growth models, the lattice-Boltzmann approach, and linear programming but my main background is in Individual-based (aka, agent-based) modelling.
My current research is framed into the NERC funded project named "Resilience of below-ground fungal communities: a mechanistic and trait-based approach". We aim mainly to identify which are the key soil properties and fungal traits make soil more or less resilient to changes, and which management options can be beneficial to make soil more resilient to physical changes. To tackle the stated aims I am using and continuing the development of a 3D trait-based agent-based model of the fungal activity in the soil pore matrix. In our approach, 3D computed tomography images are used to understand and to take into account the influence of the soil structure on the fungal and soil resilience to perturbations.
Articles In Journals
- Ginovart M, Carbó R, Blanco M & Portell X (2018) Digital image analysis of yeast single cells growing in two different oxygen concentrations to analyze the population growth and to assist individual-based modeling, Frontiers in Microbiology, 8 Article No. 2628.
- Wilmoth J, Doak P, Timm A, Halsted M, Anderson JD, Prats C, Ginovart M, Portell X, Retterer S & Fuentes-Cabrera M (2018) A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: the case of Pseudomonas aeruginosa and H1-Type VI Secretion Interactions, Frontiers in Microbiology, 9 Article No. 33.
- Portell X, Pot V, Garnier P, Otten W & Baveye P (2018) Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations, Frontiers in Microbiology, 9 Article No. 1583. Dataset/s: 10.17862/cranfield.rd.6744158
- Carbó R, Ginovart M, Carta A, Portell X & del Valle L (2015) Effect of aerobic and microaerophilic culture in the growth dynamics of Saccharomyces cerevisiae and in training of quiescent and non-quiescent subpopulations, Archives of Microbiology, 197 (8) 991-999.
- Portell X, Gras A & Ginovart M (2014) INDISIM-Saccha, an individual-based model to tackle Saccharomyces cerevisiae fermentations, Ecological Modelling, 279 12-23.
- Ginovart M, Blanco M, Portell X & Ferrer-Closas P (2012) Individual-based modeling: An attractive methodology to study bio systems, Ensenanza de Las Ciencias, 30 (2) 93-108.
- Ginovart M, Prats C, Portell X & Silbert M (2011) Analysis of the effect of inoculum characteristics on the first stages of a growing yeast population in beer fermentations by means of an individual-based model, Journal of Industrial Microbiology and Biotechnology, 38 (1) 153-165.
- Portell X, Ginovart M, Carbó R & Vives-Rego J (2011) Differences in stationary-phase cells of a commercial Saccharomyces cerevisiae wine yeast grown in aerobic and microaerophilic batch cultures assessed by electric particle analysis, light diffraction and flow cytometry, Journal of Industrial Microbiology and Biotechnology, 38 (1) 141-151.
- Ginovart M, Prats C, Portell X & Silbert M (2011) Exploring the lag phase and growth initiation of a yeast culture by means of an individual-based model, Food Microbiology, 28 (4) 810-817.
- Gras A, Ginovart M, Portell X & Baveye P (2010) Individual-based modeling of carbon and nitrogen dynamics in soils: Parameterization and sensitivity analysis of abiotic components, Soil Science, 175 (8) 363-374.
- Portell X, Ginovart M, Carbo R, Gras A & Vives-Rego J (211) Population analysis of a commercial Saccharomyces cerevisiae wine yeast in a batch culture by electric particle analysis, light diffraction and flow cytometry, FEMS Yeast Research, 11 (1) 18-28.
- Falconer RE, Houston AN, Portell X & Otten O (2019) Hardware acceleration of reaction-diffusion systems: A guide to optimisation of pattern formation algorithms using OpenACC. In: 2019 Spring Simulation Conference (SpringSim 19), Tucson, 29 April - 2 May 2019.
- Portell X & Ginovart M (2016) Towards an individual-based simulator of the yeast Saccharomyces cerevisiae for the food science with predictive capabilities. In: Ninth International Conference on Simulation and Modelling in the Food and Bio-Industry 2016 (FOODSIM 2016), Ghent, 3-7 April 2016.
- Ginovart M, Prats C & Portell X (2011) Sensitivity analysis and individual-based models in the study of yeast populations. In: 25th European Conference on Modelling and Simulation (ECMS 2011), Krakow, 7-10 June 2011.