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  • Thermodynamic behavior-rules for a bacterial individual-based model to study the denitrification process

     Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Vienna International Conference on Mathematical Modelling
    p. 233
    Presentation of work at congresses

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  • Individual-based observations and individual-based simulations to study Saccharomyces cerevisiae cultures  Open access

     Portell Canal, Xavier
    Universitat Politècnica de Catalunya
    Theses

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    El Saccharomyces cerevisiae és un dels llevats que gaudeix de més significació econòmica, social i per a la salut humana. Depenent de les condicions experimentades, el llevat S. erevisiae pot créixer mitjançant un metabolisme fermentatiu, respiratori o respirofermentatiu. La formació de cicatrius, una divisió desigual, una vida replicativa limitada i un increment de la mida de la cèl·lula amb l'edat replicativa són característiques individuals d'aquest llevat que afecten el comportament dels bioprocessos. Aquestes característiques incrementen la complexitat dels models predictius i dificulten, per tant, la seva inclusió en un model continu de manera realista. No obstant això, un model basat en l'individu sí que és capaç d'acomodar tota aquesta complexitat en un únic model computacional. Una vegada implementat, un model basat en l'individu ha de ser parametritzat, calibrat i la seva adequació ha de ser avaluada. Tots aquests processos requereixen idealment un gran nombre d'observacions experimentals, tant individuals com a nivell del sistema estudiat. L'objectiu general de la tesi present és avançar en el desenvolupament d'una metodologia basada en l'individu per estudiar sistemes microbians conduïts pel llevat S. cerevisiae. Primerament s'avalua l'adequació de INDISIM-YEAST, un model basat en l¿individu, ja existent, focalitzat en un llevat genèric. Es verifica i s'avalua la diversitat del S. cerevisiae en observacions experimentals orientades a l'individu en diferents condicions de creixement i en diversos estadis de la corba de creixement de la població. Això permet obtenir observacions basades en l'individu molt valuoses a l'hora de donar suport a la metodologia desitjada.Es desenvolupa i s'implementa en Fortran 90 INDISIM-Saccha, un model quantitatiu basat en l'individu i focalitzat en el creixement fermentatiu (anaerobi) del S. cerevisiae. El model desenvolupat és parametritzat, calibrat, la seva adequació és avaluada i és utilitzat per estudiar in silico la producció d¿etanol mitjançant experiments virtuals. El procés de calibratge, l'obtenció i l'anàlisi de les dades dels experiments virtuals s'han realitzat utilitzant el programari estadístic R. L'adequació del model s¿avalua testejant diferents prediccions del model a nivell de sistema (corbes de disminució de la glucosa i de creixement de la població) i a nivell de la cèl·lula individual (evolucions temporals de la fracció de cèl·lules gemades, de la distribució d'edats genealògiques i de la distribució dels diàmetres cel·lulars). Les observacions del diàmetre de les cèl·lules individuals obtingudes a la tesi present juguen un paper significatiu en aquesta avaluació. Els resultats dels experiments virtuals suggereixen que les diferències en la distribució de mides cel·lulars poden afectar dràsticament l'evolució i la productivitat de les fermentacions i suggereixen una caracterització rutinària de l'inòcul a la indústria biotecnològica.L'INDISIM-Saccha també és adaptat per tenir en compte el creixement aeròbic del S. cerevisiae i és contrastat mitjançant dos assajos experimentals amb dos nivells d'oxigen al medi. Els resultats preliminars de la simulació denoten que aquesta aproximació també té el potencial de reproduir cultius discontinus aerobis del S. cerevisiae. Això representa un pas endavant cap a l'obtenció d'un model basat en l'individu que tingui en compte tot el conjunt d'alternatives metabòliques experimentades pel S. cerevisiae. Finalment, aquesta tesi també dissenya i implementa INDISIM-YEAST-NL en l'ambient de programació lliure anomenat NetLogo per tal de comunicar de manera eficient, d¿incrementar l'accessibilitat i d¿afavorir l'ús de la metodologia INDISIM-Saccha. La implementació d'aquest model simplificat amb NetLogo posa les bases per a una comprensió més alta de la metodologia desenvolupada, i dels models microbians basats en l'individu en general, i facilitarà futures interaccions amb usuaris potencials de l'INDISIM-Saccha.

    Tesi per compendi de publicacions. La consulta íntegra de la tesi, inclosos els articles no comunicats públicament per drets d'autor, es pot realitzar prèvia petició a l'Arxiu de la UPC

    Saccharomyces cerevisiae is one of the yeasts with major economic, social, and health significance in human culture. Depending on the growth conditions experienced by the cell, S. cerevisiae growth can proceed via fermentative, respirative, or respirofermentative metabolism. Scar formation, unequal division, a limited replicative lifespan, and increase in cell size commensurate with the cell's replicative age are individual characteristics of this yeast affecting the performance of bioprocesses. These characteristics increase the complexity of predictive models and introducing them with ease into a continuous model is not realistic. Nevertheless, an individual-based model is able to accommodate this complexity in a single computational model. Once an individual model is implemented, it has to be parameterized, calibrated, and its adequacy assessed. All these processes ideally require a high number of both individual and system-level experimental observations. The aim of the present thesis is to advance the development of an individual-based methodology to tackle the study of microbial systems driven by the relevant yeast S. cerevisiae. The adequacy of INDISIM-YEAST, an existing individual-based model of a generic budding yeast, is first assessed. In order to obtain valuable individual-based observations to support the desired individual-based methodology, the diversity of S. cerevisiae in experimental individually-oriented observations under different growth conditions and at different stages of the growth curve is verified and assessed. A quantitative individual-based model focusing on the fermentative (anaerobic) growth of the yeast S. cerevisiae has been designed, implemented in Fortran 90, and termed INDISIM-Saccha. The developed model is parameterized, calibrated, its adequacy evaluated, and used to assess in silico ethanol production by means of virtual experiments. The calibration procedure, and the performance and analysis of the data from the virtual experiments is undertaken using the statistical programming language R. The model adequacy is assessed by testing several model predictions both at a system level (glucose depletion, population growth curves) and single-cell level (fraction of budded cells, genealogical age distribution, and cell diameter distribution evolutions). Individual cell diameter observations obtained within the present thesis play a significant role in this assessment. Results of the virtual experiments suggest that differences in cell size distribution can drastically affect the performance and productivity of fermentations, and encourage routine characterization of the inocula in the biotechnological industry. INDISIM-Saccha is also adapted to take into account the aerobic growth of S. cerevisiae and contrasted with two experimental trials with different oxygen levels in the medium. The preliminary simulated results achieved with the model suggest that the approach also has the potential for reproducing aerobic batch cultures of S. cerevisiae. This represents a further step in obtaining a microbial individual-based model to account for the whole set of metabolic alternatives experienced by S. cerevisiae. In order to communicate efficiently, increase accessibility, and favour usability of the INDISIM-Saccha methodology developed, the present thesis also designs and implements INDISIM-YEAST-NL in the freely available programming environment NetLogo. The implementation of this streamlined model in NetLogo lays the foundations for a deeper understanding of the developed methodology and microbial individual-based models in general, and will facilitate future interactions with potential users of INDISIM-Saccha.

    El Saccharomyces cerevisiae és un dels llevats que gaudeix de més significació econòmica, social i per a la salut humana. Depenent de les condicions experimentades, el llevat S. cerevisiae pot créixer mitjançant un metabolisme fermentatiu, respiratori o respirofermentatiu. La formació de cicatrius, una divisió desigual, una vida replicativa limitada i un increment de la mida de la cèl.lula amb l’edat replicativa són característiques individuals d’aquest llevat que afecten el comportament dels bioprocessos. Aquestes característiques incrementen la complexitat dels models predictius i dificulten, per tant, la seva inclusió en un model continu de manera realista. No obstant això, un model basat en l’individu sí que és capaç d’acomodar tota aquesta complexitat en un únic model computacional. Una vegada implementat, un model basat en l’individu ha de ser parametritzat, calibrat i la seva adequació ha de ser avaluada. Tots aquests processos requereixen idealment un gran nombre d’observacions experimentals, tant individuals com a nivell del sistema estudiat. L’objectiu general de la tesi present és avançar en el desenvolupament d’una metodologia basada en l’individu per estudiar sistemes microbians conduïts pel llevat S. cerevisiae. Primerament s’avalua l’adequació de INDISIM-YEAST, un model basat en l’individu, ja existent, focalitzat en un llevat genèric. Es verifica i s’avalua la diversitat del S. cerevisiae en observacions experimentals orientades a l’individu en diferents condicions de creixement i en diversos estadis de la corba de creixement de la població. Això permet obtenir observacions basades en l’individu molt valuoses a l’hora de donar suport a la metodologia desitjada. Es desenvolupa i s’implementa en Fortran 90 INDISIM-Saccha, un model quantitatiu basat en l’individu i focalitzat en el creixement fermentatiu (anaerobi) del S. cerevisiae. El model desenvolupat és parametritzat, calibrat, la seva adequació és avaluada i és utilitzat per estudiar in silico la producció d’etanol mitjançant experiments virtuals. El procés de calibratge, l’obtenció i l’anàlisi de les dades dels experiments virtuals s’han realitzat utilitzant el programari estadístic R. L’adequació del model s’avalua testejant diferents prediccions del model a nivell de sistema (corbes de disminució de la glucosa i de creixement de la població) i a nivell de la cèllula individual (evolucions temporals de la fracció de cèl.lules gemades, de la distribució d’edats genealògiques i de la distribució dels diàmetres cel.lulars). Les observacions del diàmetre de les cèl.lules individuals obtingudes a la tesi present juguen un paper significatiu en aquesta avaluació. Els resultats dels experiments virtuals suggereixen que les diferències en la distribució de mides cel.lulars poden afectar dràsticament l’evolució i la productivitat de les fermentacions i suggereixen una caracterització rutinària de l’inòcul a la indústria biotecnològica. L’INDISIM-Saccha també és adaptat per tenir en compte el creixement aeròbic del S. cerevisiae i és contrastat mitjançant dos assajos experimentals amb dos nivells d’oxigen al medi. Els resultats preliminars de la simulació denoten que aquesta aproximació també té el potencial de reproduir cultius discontinus aerobis del S. cerevisiae. Això representa un pas endavant cap a l’obtenció d’un model basat en l’individu que tingui en compte tot el conjunt d’alternatives metabòliques experimentades pel S. cerevisiae. Finalment, aquesta tesi també dissenya i implementa INDISIM-YEAST-NL en l’ambient de programació lliure anomenat NetLogo per tal de comunicar de manera eficient, d’incrementar l’accessibilitat i d’afavorir l’ús de la metodologia INDISIM-Saccha. La implementació d’aquest model simplificat amb NetLogo posa les bases per a una comprensió més alta de la metodologia desenvolupada, i dels models microbians basats en l’individu en general, i facilitarà futures interaccions amb usuaris potencials de l’INDISIM-Saccha.

  • INDISIM-Saccha, an individual-based model to tackle Saccharomyces cerevisiae fermentations

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Ecological modelling
    Vol. 279, p. 12-23
    DOI: 10.1016/j.ecolmodel.2014.02.007
    Date of publication: 2014-05-10
    Journal article

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    This contribution develops and implements INDISIM-Saccha, a spatially explicit IBM model to analyze the dynamics of Saccharomyces cerevisiae anaerobic cultures evolving in a liquid medium with glucose as a main carbon source and organic and inorganic nitrogen sources. The model has been parameterized, calibrated and its adequacy assessed using available experimental data. The growth of the yeast population and the glucose depletion were simulated, and changes in the ethanol production kinetics resulting from differences in the size distribution of the cells making up the inocula were examined in silico. Uncertainty on the initial estimated values of the model parameters was reduced by means of an iterative process involving a computational full factorial experiment, and the parameter values reproducing simultaneously glucose depletion and growth curves of batch cultures in two initial glucose concentrations were selected. The model adequacy was assessed with multiple both individual and population patterns not previously used in the calibration process carried out. Three virtual experiments were conducted from inocula with different cell size distributions. The maximum yeast cell number, the specific growth rate and the time to achieve the maximum ethanol produced were studied. Although the ethanol obtained was similar in the three studied situations, the time required to achieve it was significantly different, fermentations started by inocula made up of greater cells showed increased productivity. Due to the importance of S. cerevisiae in both fundamental research and industrial production contexts, having a calibrated computational model capable of studying the structures of this yeast population and the profiles of the fermentations carried out by it represents a noteworthy advancement in the field of microbial ecology. (C) 2014 Elsevier B.V. All rights reserved.

  • Grup de recerca consolidat en Biologia Computacional i Sistemes Complexos

     Echebarria Dominguez, Blas; Auguet Sangra, Carlota Eugenia; Peñaranda Ayllon, Angelina; Ramirez de La Piscina Millan, Laureano; Alvarez Lacalle, Enrique; Alonso Muñoz, Sergio; Giro Roca, Antoni; Ginovart Gisbert, Marta; Lopez Codina, Daniel; Valls Ribas, Joaquim; Prats Soler, Clara; Carbo Moliner, Rosa; Gras Moreu, Anna Maria; Araujo Granda, Pablo Alejandro; Gonzalez Cinca, Ricardo; Arias Calderón, Santiago; Suñol Galofre, Francesc Xavier; Garcia Sabate, Anna; Odriozola Rodriguez Facio, Maria Noel
    Competitive project

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  • The microbial individual-based model INDISIM-YEAST ready to be used in the free access NetLogo modelling environment

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Prats Soler, Clara; Ginovart Gisbert, Marta
    Date of publication: 2014
    Book chapter

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  • An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium

     Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Date of publication: 2014
    Book chapter

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  • A free accessible individual-based simulator enabling virtual experiments on soil organic matter processes in classroom  Open access

     Gras Moreu, Anna Maria; Cañadas Lorenzo, Juan Carlos; Ginovart Gisbert, Marta
    Journal of technology and science education
    Vol. 3, num. 2, p. 73-88
    DOI: 10.3926/jotse.72
    Date of publication: 2013
    Journal article

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    This work addresses and aims to fulfil a very clear need in teaching biosystem engineering. When introducing students to the complexity of soil processes, one of the frustrations that teachers ofen experience is the impossibility to demonstrate practically, in the lab, some of the concepts and processes discussed in class. Either the experiments take far longer than a typical laboratory session or they require access to specific equipment. To deal with this situation, it would be ideal for students to be able to do virtual experiments. The purpose of this work is to display the individual-based simulation model INDISIM-SOM, available free from a website, and to show how it can be used in experiments or as a teaching-learning instrument in the classroom. The computational model has been designed specifically for the study of soil organic matter and is based mainly on the activity conducted by two diferent prototypes of microorganisms. One option of using INDISIMSOM is as a way to introduce the individual-based model as a methodology to improve understanding of the agents involved in soil microbial system and their processes. Another option is to develop the ability to work with simulators by connecting concepts and helping students in the development of modelling competence. Virtual experiments were carried out as an example of what may be expected from using the INDISIM-SOM web simulator. Temporal evolutions of five virtual soils with diferent organic C content and proportional content in organic N, easily hidrolyzable N, nitrate and ammonia were generated and discussed.

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    INDISIM-YEAST:Saccha, an individual-based model to tackle Saccharomyces cerevisiae batch cultures  Open access

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    Federation of European Microbiological Societies Congress
    Presentation's date: 2013
    Presentation of work at congresses

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  • The microbial individual-based model INDISIM-YEAST ready to be used in the free access NetLogo modelling environment

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Prats Soler, Clara; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 734
    Presentation's date: 2013
    Presentation of work at congresses

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  • The individual-based soil organic matter model INDISIM-SOM in NetLogo - open to new users and data

     Gras Moreu, Anna Maria; Banitz, Thomas; Ginovart Gisbert, Marta
    Federation of European Microbiological Societies Congress
    Presentation's date: 2013
    Presentation of work at congresses

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    An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium  Open access

     Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 1-5
    Presentation's date: 2013
    Presentation of work at congresses

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    In order to understand some environmental factors that control N2O production by microbes in agricultural soils, a virtual bioreactor for Paracoccus denitrificans was designed using a culture medium containing succinate as a carbon source, ammonium as nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitrogen monoxide and dinitrogen oxide. INDISIM was the core individual-based model for the bacterial behavior and five metabolic pathways were selected and translated into balanced chemical equations using the Thermodynamic Electron Equivalents Model. This thermodynamic approach is the basis of the individual metabolism that this microbe carries out for its cellular maintenance and production of new biomass. The preliminary simulation results achieved with the implementation of this model in NetLogo showed that it is possible to investigate the behavior of this denitrifying bacterium and some of the outputs regarding the temporal evolutions of the diverse substrates are consistent with previous experimental data carried out with it.

  • An individual-based model for dealing with organic amendments and mineral nitrogen soil fertilizations

     Gras Moreu, Anna Maria; Comas Angelet, Jordi; Ginovart Gisbert, Marta
    Date of publication: 2012
    Book chapter

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  • Upgrading the uptake and metabolism sub-models of the Individual-based Model INDISIM-YEAST to tackle the behaviour of Saccharomyces cerevisiae in different culture conditions

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    International Conference on Predicitive Modeling in Foods
    p. 317-320
    Presentation's date: 2011-09-13
    Presentation of work at congresses

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    Individual-based modelling of carbon and nitrogen dynamics in soils: parameterization and sensitivity analysis of microbial components  Open access

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Valls Ribas, Joaquim; Baveye, Philippe C.
    Ecological modelling
    Vol. 222, num. 12, p. 1998-2010
    DOI: 10.1016/j.ecolmodel.2011.03.009
    Date of publication: 2011-06-24
    Journal article

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    The fate of soil carbon and nitrogen compounds in soils in response to climate change is currently the object of significant research. In particular, there is much interest in the development of a new generation of micro-scale models of soil ecosystems processes. Crucial to the elaboration of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms, distributed in a highly heterogeneous environment. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader experimental data set than previously considered. INDISIM-SOM models the dynamics and evolution of carbon and nitrogen associated with organic matter in soils. The model involves a number of state variables and parameters related to soil organic matter and microbial activity, including growth and decay of microbial biomass, temporal evolutions of easily hydrolysable N, mineral N in ammonium and nitrate, CO2 and O2. The present article concentrates on the biotic components of the model. Simulation results demonstrate that the model can be calibrated to provide good fit to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. In addition, analysis of the sensitivity toward its biotic parameters shows that the model is far more sensitive to some parameters, i.e., the microbial maintenance energy and the probability of random microbial death, than to others. These results suggest that, in the future, research should focus on securing better measurements of these parameters, on environmental determinants of the switch from active to dormant states, and on the causes of random cell death in soil ecosystems.

  • Modelización basada en el individuo (IBM) perspectiva multidisclipinar en microbiologia aplicada: alimentos, medioambiente y salud

     Prats Soler, Clara; Valls Ribas, Joaquim; Carbo Moliner, Rosa; Ginovart Gisbert, Marta; Giro Roca, Antoni; Gras Moreu, Anna Maria; Portell Canal, Xavier; Ferrer Savall, Jordi; Silbert, Moises; Lopez Codina, Daniel
    Competitive project

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  • Population analysis of a commercial Saccharomyces cerevisiae wine yeast in a batch culture by electric particle analysis, light difraction and flow cytometry

     Portell Canal, Xavier; Ginovart Gisbert, Marta; Carbo Moliner, Rosa; Gras Moreu, Anna Maria; Vives Rego, J.
    Fems yeast research
    Vol. 11, p. 18-28
    DOI: 10.1111/j.1567-1364.2010.00682.x
    Date of publication: 2011
    Journal article

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    Data from electric particle analysis, light diffraction and flow cytometry analysis provide information on changes in cell morphology. Here, we report analyses of Saccharomyces cerevisiae populations growing in a batch culture using these techniques. The size distributions were determined by electric particle analysis and by light diffraction in order to compare their outcomes. Flow cytometry parameters forward (related to cell size) and side (related to cell granularity) scatter were also determined to complement this information. These distributions of yeast properties were analysed statistically and by a complexity index. The cell size of Saccharomyces at the lag phase was smaller than that at the beginning of the exponential phase, whereas during the stationary phase, the cell size converged with the values observed during the lag phase. These experimental techniques, when used together, allow us to distinguish among and characterize the cell size, cell granularity and the structure of the yeast population through the three growth phases. Flow cytometry patterns are better than light diffraction and electric particle analysis in showing the existence of subpopulations during the different phases, especially during the stationary phase. The use of a complexity index in this context helped to differentiate these phases and confirmed the yeast cell heterogeneity.

  • An individual-based model for dealing with organic amendments and mineral nitrogen soil fertilizations

     Gras Moreu, Anna Maria; Comas Angelet, Jordi; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 13-17
    Presentation's date: 2011
    Presentation of work at congresses

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  • Individual-based modelling and simulation of microbial processes: yeast fermentation and multi-species composting

     Prats Soler, Clara; Ferrer Savall, Jordi; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Mathematical and Computer Modelling of Dynamical Systems (online)
    Vol. 16, num. 3, p. 489-510
    DOI: 10.1080/13873954.2010.481809
    Date of publication: 2010-12-06
    Journal article

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    Combined use of local and global sensitivity analyses for the investigation of an individual-based model of yeast populations  Open access

     Prats Soler, Clara; Portell Canal, Xavier; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    International ICFMH Symposium (Food Micro)
    p. 173
    Presentation's date: 2010-09-01
    Presentation of work at congresses

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  • INDISIM-YEAST, a simulator for individual-based modelling of yeast metabolism and process dynamics in asynchronous batch fermentations

     Ginovart Gisbert, Marta; Gras Moreu, Anna Maria; Carbo Moliner, Rosa
    International Conference Predictive Modelling in Food
    p. 333-336
    Presentation of work at congresses

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  • Individual-based modeling of carbon and nitrogen dynamics in soils: parameterization and sensitivity analysis of abiotic components

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Portell Canal, Xavier; Baveye, Philippe C.
    Soil science
    Vol. 175, num. 8, p. 363-374
    DOI: 10.1097/SS.0b013e3181eda507
    Date of publication: 2010
    Journal article

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  • Modeling of Pachysolen tannophilus batch cultures by individual-based simulations

     Castro, Eulogio; Ginovart Gisbert, Marta; Gras Moreu, Anna Maria
    International Biotechnology Symposium
    p. 136
    DOI: 10.1016/j.jbiotec.2010.08.357
    Presentation's date: 2010
    Presentation of work at congresses

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  • INDISIM-SOM: an individual-based simulator on a website for experimenting and investigating diverse dynamics of Carbon and Nitrogen in mineral soils

     Gras Moreu, Anna Maria; Cañadas Lorenzo, Juan Carlos; Ginovart Gisbert, Marta
    BioMicroWorld2009 - III International Conference on Environmental, Industrial and Applied Microbiology
    p. 70
    Presentation's date: 2009-12
    Presentation of work at congresses

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  • Individual-based modelling and simulation of microbial processes: yeast fermentation and multispecies composting

     Prats Soler, Clara; Ferrer Savall, Jordi; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Vienna International Conference on Mathematical Modelling (MATHMOD 2009)
    Presentation's date: 2009-02-12
    Presentation of work at congresses

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    Explaining low farm-gate prices in the Catalan wine sector  Open access

     Costa-Font, Montserrat; Serra Devesa, Teresa; Gil Roig, Jose Maria; Gras Moreu, Anna Maria
    International journal of wine business research
    Vol. 21, num. 2, p. 169-184
    DOI: 10.1108/17511060910968006
    Date of publication: 2009
    Journal article

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  • Individual-based Modelling and simulation of microbial processes: yeast fermentation and multi-species composting

     Prats Soler, Clara; Ferrer Savall, Jordi; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Vienna Conference on Mathematical Modelling
    p. 1495-1506
    Presentation's date: 2009
    Presentation of work at congresses

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  • INDISIM-SOM, an individual-based simulator on a website for experimenting and investigating diverse dynamics of Carbon and Nitrogen in mineral soils

     Gras Moreu, Anna Maria; Cañadas Lorenzo, Juan Carlos; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 167-171
    Presentation's date: 2009
    Presentation of work at congresses

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    INDISIM-SOM models the dynamics and evolution of C and N related to organic matter in soils by using individual-based simulations. It is an Individual-based Model that controls a group of microbial cells at each time step, using a set of time-dependent variables for each microorganism. The space is divided into square cells. In each spatial cell, the amounts of different types of organic compounds are controlled. These are identified as polymerized organic C and N, labile organic C and N, and mineral compounds such us NNH4, NNO3, CO2 and O2. The model takes into account the activity of two types of microorganisms: decomposers (heterotrophic) and nitrifiers. Metabolic pathways and sources of C and N that they can use are identified. Some state variables and parameters related to soil organic matter and microbial activity are studied. This study presents a website at which the simulator INDISIM-SOM is accessible, and explains how to carry out some virtual experiments, in order to further advance the skills associated with this individual simulation model.

  • Influencia de Brettanomyces/Dekkera en la evolución de la fermentación alcohólica

     Gras Moreu, Anna Maria
    Congreso Español de Ingeniería de Alimentos y Congreso Iberoamericano sobre Seguridad Alimentaria (CESIA-CIBSA)
    Presentation's date: 2008-11-01
    Presentation of work at congresses

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  • Detección del estado hídrico en vid (Vitis vinifera cv. Chardonnay) y su relación con el rendimiento y calidad de la uva

     Serrano Porta, Lydia; Gras Moreu, Anna Maria; Gorchs Altarriba, Gil
    IX Simposium Hispano Portugués de Relaciones Hídricas en las Plantas
    Presentation of work at congresses

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  • A comparative study of the use of an electronic particle analyser and a flow cytometer to assess the changes of cell size distributions of Saccharomyces cerevisiae var. bayanus during aerobic and anaerobic growth in batch cultures  Open access

     Ginovart Gisbert, Marta; Carbo Moliner, Rosa; Gras Moreu, Anna Maria; Portell Canal, Xavier; Vives-Rego, Josep
    The 21st International ICFMH Symposium - FOOD MICRO 2008
    Presentation's date: 2008
    Presentation of work at congresses

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  • Individual based Modelling (IbM) de sistemas microbiológicos para el desarrollo sostenible: medio ambiente, seguridad alimentaria y salud

     Giro Roca, Antoni; Prats Soler, Clara; Lopez Codina, Daniel; Silbert, Moises; Valls Ribas, Joaquim; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Portell Canal, Xavier; Ferrer Savall, Jordi
    Competitive project

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  • Explaining low farm-gate prices in the catalan wine sector: a Delphi study  Open access

     Costa Font, Montserrat; Serra Devesa, Teresa; Gil Roig, Jose Maria; Gras Moreu, Anna Maria
    Congreso de Economía Agraria de la Asociación Española de Economía Agraria
    Presentation's date: 2007-09-19
    Presentation of work at congresses

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  • The use of flow cytrometry and particle size analysis in the individual-based model INDISIM-YEAST, a simulater of yeast populations

     Ginovart Gisbert, Marta; Carbo Moliner, Rosa; Gras Moreu, Anna Maria; Vives-Rego, J
    5th. International Conference Predictive Modelling in Food. Fundamental, State of the Art and New Horizons
    p. 341-344
    Presentation's date: 2007
    Presentation of work at congresses

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  • Selecció d'indicadors basats en la reflectància espectral per a la seva aplicació en viticultura de precisió

     Serrano Porta, Lydia; Menchén, Lidia; Gras Moreu, Anna Maria
    II Congrés d'Agricultura, Alimentació i Medi Ambient
    Presentation of work at congresses

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  • An individual based model to study the main groups of microbes active in composting process

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Prats, C
    Date of publication: 2006-10
    Book chapter

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  • Nitrifier bacterial activity linked to mineralization of soil organic matter: individual based simulations

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Valls, J
    Date of publication: 2006-10
    Book chapter

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  • INDISIM-SOM, and individual-besed model to study short-term evolutions of carbon and nitrogen pools related to microbial activity in soil organic matter

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    European Conference on Modelling and Simulation
    p. 554-559
    Presentation's date: 2006
    Presentation of work at congresses

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  • Individual-based Modelling of microbial activity to study mineralization of C and N and nitrification process in soil

     Ginovart Gisbert, Marta; Lopez Codina, Daniel; Gras Moreu, Anna Maria
    Nonlinear analysis: real world applications
    Vol. 6, p. 773-795
    Date of publication: 2005
    Journal article

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    This work models the dynamics and evolution of carbon (C) and nitrogen (N) related to organic matter in soils by using individual-based simulations. The simulator INDISIM-SOM controls a group of microbial cells at each time step, using a set of time-dependent variables for each microorganism. The space is divided into square cells. In each spatial cell, the amounts of different types of organic compounds are controlled. These are identified as polymerized organic C and N, labile organic C and N, mineral compounds likeNNH4,NNO3,CO2 andO2. The model takes into account the activity of two prototypes of microbial cells: ammonifier microorganisms and nitrifier bacteria. Different metabolic pathways and sources of C and N they can use are identified. Some state variables and parameters related to soil organic matter and microbial activity: growth and decay of microbial biomass, and temporal evolutions of mineralized intermediate N, mineral N in ammonium and nitrate, CO2 and O2 are studied. The calibration of the simulation model has made use of data from laboratory incubation experiments performed on two different types of Mediterranean soils. Both, conceptual validation during the development of the model and agreement of the simulation results with experimental.

  • Nitrifier bacterial activity linked to mineralization of soil organic matter: individual based simulations

     Gras Moreu, Anna Maria; Valls Ribas, Joaquim; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 625
    Presentation's date: 2005
    Presentation of work at congresses

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  • A discrete model to study bacterial activity of activated sludge systems in wastewater treatment

     Ginovart Gisbert, Marta; Gras Moreu, Anna Maria
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 6
    Presentation's date: 2005
    Presentation of work at congresses

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  • An individual based model to study the main groups of microbes active in composting process

     Gras Moreu, Anna Maria; Prats Soler, Clara; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    p. 14-18
    Presentation's date: 2005
    Presentation of work at congresses

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  • CGL2004-01144 Modelización y Simulación (IbM) de Sistemas Microbiológicos. Aplicaciones: Industrias agroalimentarias y medio ambiente.

     Giro Roca, Antoni; Prats Soler, Clara; Silbert, Moises; Lopez Codina, Daniel; Valls Ribas, Joaquim; Ginovart Gisbert, Marta; Gras Moreu, Anna Maria; Ferrer Savall, Jordi
    Competitive project

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  • Discrete simulation model to study heterotrophic microbial activity in soil

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Applied Simulation and Modelling - ASM 204
    p. 125-130
    Presentation's date: 2004
    Presentation of work at congresses

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  • Individual Based Modelling of Microbial Activity to Study Mineralization and Nitrification Procedd in Soil

     Ginovart Gisbert, Marta; Gras Moreu, Anna Maria
    Alcala 2th International Conference on Mathematical Ecology
    Presentation's date: 2003
    Presentation of work at congresses

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  • IMPLEMENTACIÓN DE UN SISTEMA DE DECISIÓN DE LA DOSIS DE PRODUCTO FITOSANITARIO EN TRATAMIENTOS EN VIÑEDO

     Gil Moya, Emilio; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Competitive project

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  • Discrete simulation of bacterial activity in soils: amonification and nitrification precess

     Ginovart Gisbert, Marta; Gras Moreu, Anna Maria; López Ribas, David
    15th European Simulation Multiconference
    p. 1031-1035
    Presentation's date: 2001
    Presentation of work at congresses

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  • OPTIMIZACIÓN DEL PROCESO DE COMPOSTAJE DE RESIDUOS ORGÁNICOS UTILIZANDO UNA PLANTA PILOTO MÓVIL

     Flotats Ripoll, Xavier; Ginovart Gisbert, Marta; Prats Soler, Clara; Lopez Codina, Daniel; Gras Moreu, Anna Maria
    Competitive project

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