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    Thermodynamic concepts in the study of microbial populations: age structure in plasmodium falciparum infected red blood cells  Open access

     Ferrer Savall, Jordi; Prats Soler, Clara; Lopez Codina, Daniel; Vidal-Mas, Jaume; Gargallo-Viola, Domingo; Guglietta, Antonio; Giro Roca, Antoni
    PLoS one
    Date of publication: 2011-10-31
    Journal article

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    Variability is a hallmark of microbial systems. On the one hand, microbes are subject to environmental heterogeneity and undergo changeable conditions in their immediate surroundings. On the other hand, microbial populations exhibit high cellular diversity. The relation between microbial diversity and variability of population dynamics is difficult to assess. This connection can be quantitatively studied from a perspective that combines in silico models and thermodynamic methods and interpretations. The infection process of Plasmodium falciparum parasitizing human red blood cells under laboratory cultivation conditions is used to illustrate the potential of Individual-based models in the context of predictive microbiology and parasitology. Experimental data from several in vitro cultures are compared to the outcome of an individual-based model and analysed from a thermodynamic perspective. This approach allows distinguishing between intrinsic and external constraints that give rise to the diversity in the infection forms, and it provides a criterion to quantitatively define transient and stationary regimes in the culture. Increasing the ability of models to discriminate between different states of microbial populations enhances their predictive capability which finally leads to a better the control over culture systems. The strategy here presented is of general application and it can substantially improve modelling of other types of microbial communities.

  • 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
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  • V Edició del Premi Gaudí-Gresol d'Ensenyament

     Giro Roca, Antoni
    Award or recognition

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    On the evolution of cell size distribution during bacterial growth cycle: experimental observations and individual-based model simulations  Open access

     Prats Soler, Clara; Ferrer Savall, Jordi; Lopez Codina, Daniel; Giro Roca, Antoni; Vives-Rego, Josep
    African journal of microbiology research
    Date of publication: 2010-03
    Journal article

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    Individual-based modelling and simulation: towards a better understanding of growth dynamics from small inocula  Open access

     Dalmau Andreu, Roger; Portell Canal, Xavier; Prats Soler, Clara; Ginovart Gisbert, Marta; Giro Roca, Antoni
    SAFE Consortium International Congress on Food Safety: Novel Technologies and Food Quality, Safety and Health
    Presentation's date: 2009
    Presentation of work at congresses

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  • Individual-based modelling of bacterial cultures in the study of the lag phase  Open access

     Prats Soler, Clara
    Defense's date: 2008-06-13
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    La microbiologia predictiva és una de les parts més importants de la microbiologia dels aliments. En el creixement d'un cultiu bacterià es poden observar quatre fases: latència, exponencial, estacionària i mort. La fase de latència té un interès específic en microbiologia predictiva; al llarg de dècades ha estat abordada des de dues perspectives diferents: a nivell cel·lular i intracel·lular (escala microscòpica), i a nivell de població (escala macroscòpica). La primera estudia els processos que tenen lloc a l'interior dels bacteris durant la seva adaptació a les noves condicions del medi, com els canvis en l'expressió gènica i en el metabolisme. La segona descriu l'evolució de la població bacteriana per mitjà de models matemàtics continus i d'experiments que avaluen variables relacionades amb la densitat cel·lular. L'objectiu d'aquest treball és millorar la comprensió de la fase de latència dels cultius bacterians i dels fenòmens intrínsecs a la mateixa. Aquest objectiu s'ha abordat amb la metodologia Individual-based Modelling (IbM) amb el simulador INDISIM (INDividual DIScrete SIMulation), que ha calgut optimitzar. La IbM introdueix una perspectiva mecanicista a través de la modelització de les cèl·lules com a unitats bàsiques. Les simulacions IbM permeten estudiar el creixement d'entre 1 i 106 bacteris, així com els fenòmens que emergeixen de la interacció entre ells. Aquests fenòmens pertanyen al que anomenem escala mesoscòpica. Aquesta perspectiva és imprescindible per entendre l'efecte en la població dels processos d'adaptació individuals. Per tant, la metodologia IbM és un pont entre els individus i la població o, el que és el mateix, entre els models a escala microscòpica i a escala macroscòpica.En primer lloc hem estudiat dos dels diversos mecanismes que poden causar la fase de latència: inòculs amb massa mitjana petita, i canvis de medi.S'ha verificat també la relació de la durada de la latència amb variables com la temperatura o la grandària de l'inòcul. En aquest treball s'ha identificat la distribució de biomassa del cultiu com una variable cabdal per analitzar l'evolució del cultiu durant el cicle de creixement. S'han definit les funcions matemàtiques que anomenem distàncies per avaluar quantitativament l'evolució d'aquesta distribució.Hem abordat, també, la fase de latència des d'un punt de vista teòric. L'evolució de la velocitat de creixement al llarg del cicle ha permès distingir dues etapes en la fase de latència que anomenem inicial i de transició. L'etapa de transició s'ha descrit per mitjà d'un model matemàtic continu validat amb simulacions INDISIM. S'ha constatat que la fase de latència ha de ser vista com un procés dinàmic, i no com un simple període de temps descrit per un paràmetre. Les funcions distància també s'han utilitzat per avaluar les propietats del creixement balancejat.Alguns dels resultats de les simulacions amb INDISIM s'han corroborat experimentalment per mitjà de citometria de flux. S'ha comprovat, al llarg de les diverses fases del creixement, el comportament de la distribució de biomassa previst per simulació, així com l'evolució de les funcions distància. La coincidència entre els resultats experimentals i els de simulació no és trivial, ja que el sistema estudiat és molt complex. Per tant, aquests resultats permeten comprovar la bondat de la metodologia INDISIM.Finalment, hem avançat en l'optimització d'eines per parametritzar IbMs, un pas essencial per poder utilitzar les simulacions INDISIM de manera quantitativa. S'han adaptat i assajat els mètodes grid search, NMTA i NEWUOA. Aquest darrer mètode ha donat els millors resultats en termes de temps, mantenint una bona precisió en els valors òptims dels paràmetres. Per concloure, podem afirmar que INDISIM ha estat validat com una bona eina per abordar l'estudi dels estats transitoris com la fase de latència.

    Predictive food microbiology has become an important specific field in microbiology. Bacterial growth of a batch culture may show up to four phases: lag, exponential, stationary and death. The bacterial lag phase, which is of specific interest in the framework of predictive food microbiology, has generally been tackled with two generic approaches: at a cellular and intracellular level, which we call the microscopic scale, and at a population level, which we call the macroscopic scale. Studies at the microscopic level tackle the processes that take place inside the bacterium during its adaptation to the new conditions such as the changes in genetic expression and in metabolism. Studies at the macroscopic scale deal with the description of a population growth cycle by means of mathematical continuous modelling and experimental measurements of the variables related to cell density evolution.In this work we aimed to improve the understanding of the lag phase in bacterial cultures and the intrinsic phenomena behind it. This has been carried out from the perspective of Individual-based Modelling (IbM) with the simulator INDISIM (INDividual DIScrete SIMulation), which has been specifically improved for this purpose. IbM introduces a mechanistic approach by modelling the cell as an individual unit. IbM simulations deal with 1 to 106 cells, and allow specific study of the phenomena that emerge from the interaction among cells. These phenomena belong to the mesoscopic level.Mesoscopic approaches are essential if we are to understand the effects of cellular adaptations at an individual level in the evolution of a population.Thus, they are a bridge between individuals and population, or, to put it another way, between models at a microscopic scale and models at a macroscopic scale.First, we studied separately two of the several mechanisms that may cause a lag phase: the lag caused by the initial low mean mass of the inoculum, and the lag caused by a change in the nutrient source. The relationship among lag duration and several variables such as temperature and inoculum size were also checked. This analysis allowed identification of the biomass distribution as a very important variable to follow the evolution of the culture during the growth cycle. A mathematical tool was defined in order to assess its evolution during the different phases of growth: the distance functions.A theoretical approach to the culture lag phase through the dynamics of the growth rate allowed us to split this phase into two stages: initial and transition. A continuous mathematical model was built in order to shape the transition stage, and it was checked with INDISIM simulations. It was seen that the lag phase must be defined as a dynamic process rather than as a simple period of time. The distance functions were also used to discuss the balanced growth conditions.Some of the reported INDISIM simulation results were subjected to experimental corroboration by means of flow cytometry, which allow the assessment of size distributions of a culture through time. The dynamics of biomass distribution given by INDISIM simulations were checked, as well as the distance function evolution during the different phases of growth. The coincidence between simulations and experiments is not trivial: the system under study is complex; therefore, the coincidence in the dynamics of the different modelled parameters is a validation of both the model and the simulation methodology.Finally, we have made progress in IbM parameter estimation methods, which is essential to improve quantitative processing of INDISIM simulations.Classic grid search, NMTA and NEWUOA methods were adapted and tested, the latter providing better results with regard to time spent, which maintains satisfactory precision in the parameter estimation results.Above all, the validity of INDISIM as a useful tool to tackle transient processes such as the bacterial lag phase has been amply demonstrated.

  • Analysis and IbM simulation of the stages in bacterial lag phase: basis for an updated definition

     Prats Soler, Clara; Giro Roca, Antoni; Ferrer Savall, Jordi; Lopez Codina, Daniel; Vives-Rego, J
    Journal of theoretical biology
    Date of publication: 2008-05
    Journal article

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    The lag phase is the initial phase of a culture that precedes exponential growth and occurs when the conditions of the culture medium differ from the pre-inoculation conditions. It is usually defined by means of cell density because the number of individuals remains approximately constant or slowly increases, and it is quantified with the lag parameter l. The lag phase has been studied through mathematical modelling and by means of specific experiments. In recent years, Individual-based Modelling (IbM) has provided helpful insights into lag phase studies. In this paper, the definition of lag phase is thoroughly examined. Evolution of the total biomass and the total number of bacteria during lag phase is tackled separately. The lag phase lasts until the culture reaches a maximum growth rate both in biomass and cell density. Once in the exponential phase, both rates are constant over time and equal to each other. Both evolutions are split into an initial phase and a transition phase, according to their growth rates. A population-level mathematical model is presented to describe the transitional phase in cell density. INDividual DIScrete SIMulation (INDISIM) is used to check the outcomes of this analysis. Simulations allow the separate study of the evolution of cell density and total biomass in a batch culture, they provide a depiction of different observed cases in lag evolution at the individual-cell level, and are used to test the population-level model. The results show that the geometrical lag parameter l is not appropriate as a universal definition for the lag phase. Moreover, the lag phase cannot be characterized by a single parameter. For the studied cases, the lag phases of both the total biomass and the population are required to fully characterize the evolution of bacterial cultures. The results presented prove once more that the lag phase is a complex process that requires a more complete definition. This will be possible only after the phenomena governing the population dynamics at an individual level of description, and occurring during the lag and exponential growth phases, are well understood.

  • 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
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  • Evolution of biomass distribution during bacterial lag phase through flow cytometry, particle analysis and Individual-based Modelling

     Prats Soler, Clara; Ferrer Savall, Jordi; Flix, B; Giro Roca, Antoni; Lopez Codina, Daniel; Vives-Rego, J
    International Conference Predictive Modelling in Foods
    Presentation of work at congresses

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  • Individual-based model and simulation of Plasmodium falciparum infected erythrocyte in vitro cultures

     Ferrer Savall, Jordi; Vidal, J; Prats Soler, Clara; Valls Ribas, Joaquim; Herreros, E; Lopez Codina, Daniel; Giro Roca, Antoni; Gargallo, D
    Journal of theoretical biology
    Date of publication: 2007-10
    Journal article

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    Malaria is still one of the most fatal diseases in the world. Development of an effective treatment or vaccine requires the cultivation of the parasite that causes it: Plasmodium falciparum. Several methods for in vitro cultivation of P. falciparum infected erythrocytes have been successfully developed and described in the last 30 years. Some problems arising from the current harvests are the low parasitaemia and daily human supervision requirements. The lack of a suitable model for global culture behavior makes the assay of new methodologies a costly and tenuous task. In this paper we present a model and simulation tool for these systems. We use the INDividual DIScrete SIMulation protocol (INDISIM) to qualitatively reproduce the temporal evolution of the erythrocyte and merozoite populations. Whole system dynamics are inferred by setting the rules of behavior for each individual red blood cell, such as the nutrient uptake, metabolism and infection processes, as well as the properties and rules for the culture medium: composition, diffusion and external manipulation. We set the individual description parameters according to the values in published data, and allow population heterogeneity. Cells are arranged in a three-dimensional grid and the study is focused on the geometric constraints and physical design of experimental sets. Several published experimental cultures have been reproduced with computer simulations of this model, showing that the observed experimental behavior can be explained by means of individual interactions and statistical laws.

  • Flocculation in brewing yeast: a computer simulation study

     Ginovart Gisbert, Marta; Lopez Codina, Daniel; Giro Roca, Antoni; Silbert, Moises
    Biosystems
    Date of publication: 2006-01
    Journal article

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  • Spatial properties in Individual- based modelling of microbial systems. Study of the composting process.

     Prats Soler, Clara; Ferrer Savall, Jordi; Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim
    Date of publication: 2006-10
    Book chapter

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  • A mathematical analysis of the stages in bacterial lag phase

     Prats Soler, Clara; Giro Roca, Antoni; Lopez Codina, Daniel; Ferrer Savall, Jordi; Valls Ribas, Joaquim; Vives-Rego, Josep
    International ICFMH Symposium
    Presentation's date: 2006-08-30
    Presentation of work at congresses

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  • A physical interpretation of the microbial growth rate temperature dependence

     Prats Soler, Clara; Ferrer Savall, Jordi; Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim
    Sitges Conference on Statistical Mechanics
    Presentation of work at congresses

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  • Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase

     Prats Soler, Clara; Lopez Codina, Daniel; Giro Roca, Antoni; Ferrer Savall, Jordi; Valls Ribas, Joaquim
    Journal of theoretical biology
    Date of publication: 2006-08
    Journal article

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    The lag phase has been widely studied for years in an effort to contribute to the improvement of food safety. Many analytical models have been built and tested by several authors. The use of Individual-based Modelling (IbM) allows us to probe deeper into the behaviour of individual cells; it is a bridge between theories and experiments when needed. INDividual DIScrete SIMulation (INDISIM) has been developed and coded by our group as an IbM simulator and used to study bacterial growth, including the microscopic causes of the lag phase. First of all, the evolution of cellular masses, specifically the mean mass and biomass distribution, is shown to be a determining factor in the beginning of the exponential phase. Secondly, whenever there is a need for an enzyme synthesis, its rate has a direct effect on the lag duration. The variability of the lag phase with different factors is also studied. The known decrease of the lag phase with an increase in the temperature is also observed in the simulations. An initial study of the relationship between individual and collective lag phases is presented, as a complement to the studies already published. One important result is the variability of the individual lag times and generation times. It has also been found that the mean of the individual lags is greater than the population lag. This is the first in a series of studies of the lag phase that we are carrying out. Therefore, the present work addresses a generic system by making a simple set of assumptions.

  • A mathematical analysis of the stages in bacterial lag phase

     Prats Soler, Clara; Giro Roca, Antoni; Lopez Codina, Daniel; Ferrer Savall, Jordi; Valls Ribas, Joaquim; Vives-Rego, Josep
    International ICFMH Symposium
    Presentation's date: 2006
    Presentation of work at congresses

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  • La Física está en la base de todo

     Giro Roca, Antoni
    Quark: ciencia, medicina, comunicación y cultura
    Date of publication: 2005-05
    Journal article

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  • Física i supercomputació

     Giro Roca, Antoni
    TERAFLOP: Revista del Centre de Supercomputació de Catalunya
    Date of publication: 2005-02
    Journal article

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  • SUMARI I CONCLUSIONS

     Giro Roca, Antoni
    Date of publication: 2005-10-31
    Book chapter

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  • SUMARI I CONCLUSIONS (Col.loqui)

     Giro Roca, Antoni
    Date of publication: 2005-10-31
    Book chapter

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  • Física per a estudiants d'informàtica

     Giro Roca, Antoni; Canales Gabriel, Manel; Rey Oriol, Rosendo; Sese Castel, Gemma; Trullàs Simó, Joaquim
    Date of publication: 2005-12
    Book

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  • Spatial properties in individual based simulations of microbiological systems, study of the composting process

     Prats Soler, Clara; Ferrer Savall, Jordi; Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation of work at congresses

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  • Taula rodona Conclusions

     Giro Roca, Antoni
    La Física a Catalunya
    Presentation's date: 2005-04-27
    Presentation of work at congresses

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  • Spatial properties in individual based modelling of microbiological systems. Study of the composting process

     Prats Soler, Clara; Lopez Codina, Daniel; Giro Roca, Antoni; Ferrer Savall, Jordi
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2005-03-15
    Presentation of work at congresses

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  • Els estudis de fisica en l'espai europeu d'educació superior

     Giro Roca, Antoni
    Revista de física (Barcelona)
    Date of publication: 2004-10
    Journal article

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  • Simulació amb ordinador en matèria condensada

     Giro Roca, Antoni
    Date of publication: 2004-09-30
    Book chapter

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  • Individual based modelling of bacterial cultures. A lag phase study

     Prats Soler, Clara; Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim
    International Conference on Biological Physics
    Presentation's date: 2004-08-24
    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
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  • moderador Evolució de la Recerca de la Física en els XX anys de trobades científiques a la mediterrània

     Giro Roca, Antoni
    XX Trobades Científiques de la Mediterrània. Fotònica: ciència i tecnologia de la llum.
    Presentation's date: 2004-09-25
    Presentation of work at congresses

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  • Individual based modelling of bacterial cultures. A lag phase study

     Prats Soler, Clara; Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim
    International Conference on Biological Physics
    Presentation's date: 2004
    Presentation of work at congresses

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  • An Individual-based Model to study Growth Inhibitors of yeast cells In batch Cultures

     Giro Roca, Antoni; Ginovart Gisbert, Marta; Lopez Codina, Daniel; Silbert, Moises
    International Conference on Biological Physics
    Presentation's date: 2004
    Presentation of work at congresses

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  • Física

     Giro Roca, Antoni; Canales Gabriel, Manel; Rey Oriol, Rosendo; Sese Castel, Gemma; Trullàs Simó, Joaquim
    Date of publication: 2003-09
    Book

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  • Models de seguretat alimentària

     Giro Roca, Antoni
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  • Flocculation in brewing yeasts: a computer simulation study

     Ginovart Gisbert, Marta; Lopez Codina, Daniel; Giro Roca, Antoni; Silbert, Moises
    4th International Conference on Predictive Modelling in foods
    Presentation of work at congresses

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  • Computer simulation of the Lag Phase

     Giro Roca, Antoni; Lopez Codina, Daniel; Valls Ribas, Joaquim; Ginovart Gisbert, Marta
    4th International Conference on Predictive Modelling in foods
    Presentation of work at congresses

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  • La Qualitat docent a l'entorn europeu

     Giro Roca, Antoni
    Butlletí d'informació sobre la qualitat universitària
    Date of publication: 2002-03
    Journal article

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  • 25è Aniversari de la Facultat d'Informàtica

     Giro Roca, Antoni
    Date of publication: 2002-05-31
    Book chapter

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  • Grup de recerca consolidat. Grup de simulació per ordinador en matèria condensada

     Guardia Manuel, Elvira; Sese Castel, Gemma; Giro Roca, Antoni; Rey Oriol, Rosendo; Trullàs Simó, Joaquim
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  • Tercera ponència

     Giro Roca, Antoni
    Date of publication: 2001-01-31
    Book chapter

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  • Grup de simulació per ordinador en materia condensada

     Guardia Manuel, Elvira; Sese Castel, Gemma; Giro Roca, Antoni; Rey Oriol, Rosendo; Marti Rabassa, Jordi; Trullàs Simó, Joaquim
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  • Simulación por ordenador de sistemas condensados: líquidos iónicos y moleculares.

     Sese Castel, Gemma; Guardia Manuel, Elvira; Giro Roca, Antoni; Marti Rabassa, Jordi; Trullàs Simó, Joaquim
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  • Txernòbil, deu anys desprès

     Giro Roca, Antoni
    Butlletí de les societats catalanes de física, química, matemàtiques i tecnologia
    Date of publication: 1998-01
    Journal article

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  • Presentació

     Giro Roca, Antoni
    Date of publication: 1998-02-28
    Book chapter

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  • Física per a estudiants d'Informàtica

     Giro Roca, Antoni; Canales Gabriel, Manel; Rey Oriol, Rosendo; Sese Castel, Gemma; Trullàs Simó, Joaquim
    Date of publication: 1998-10
    Book

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  • Grup de recerca consolidat. Grup de Simulació per Ordinador en Matèria Condensada.

     Giro Roca, Antoni; Serra Tort, Ana Maria; Marti Rabassa, Jordi
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  • Static structure and ionic transport in molten AgBr and AgCl

     Tasseven, Çetin; Trullàs Simó, Joaquim; Alcaraz Sendra, Olga; Silbert, Moises; Giro Roca, Antoni
    Journal of chemical physics
    Date of publication: 1997
    Journal article

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    The static structure of molten AgBr and AgCl have been calculated using the hypernetted chain theory of liquids ~HNC! and molecular dynamics simulations ~MD! with effective potentials based on the functional form originally proposed by Vashishta and Rahman @Phys. Rev. Lett. 40, 1337 ~1978!# to study a-AgI. The HNC and MD are in good agreement among themselves as well as in good qualitative agreement with experiment. MD simulations have been also used to calculate the time correlation functions and ionic transport properties of these melts. The results for the velocity autocorrelation functions suggest, in both cases, a mechanism for diffusion akin to that we suggested for molten AgI and CuX (X5Cl, Br, I) @J. Phys. Condens. Matter 2, 6643 ~1990!# even though the cations velocity autocorrelation function is no longer purely diffusive. The results for the diffusion coefficients resemble the type of behavior found in superionic melts, as if the transition to a superionic state is finally realized in AgCl and AgBr on melting. The results for the specific ionic conductivities are in good agreement with experiment if it is assumed that the ions, in their transport, carry with them their full complement of electrons.