SC-SIMBIO - Sistemes complexos. Simulació discreta de materials i de sistemes biològics
http://hdl.handle.net/2117/3662
Thu, 20 Oct 2016 21:37:40 GMT2016-10-20T21:37:40ZComparison of the microbial dynamics and biochemistry of laboratory sourdoughs prepared with grape, apple and yogurt
http://hdl.handle.net/2117/27975
Comparison of the microbial dynamics and biochemistry of laboratory sourdoughs prepared with grape, apple and yogurt
Gordún Quiles, Elena; Valle Mendoza, Luis Javier del; Ginovart Gisbert, Marta; Carbó Moliner, Rosa
The microbiological culture-dependent characterization and physicochemical characteristics of laboratory sourdough prepared with grape (GS) were evaluated and compared with apple (AS) and yogurt (YS), which are the usual Spanish sourdough ingredients. Ripe GS took longer than AS and YS to reach the appropriate acidity and achieved lower values of lactic acid
Wed, 20 May 2015 10:22:58 GMThttp://hdl.handle.net/2117/279752015-05-20T10:22:58ZGordún Quiles, ElenaValle Mendoza, Luis Javier delGinovart Gisbert, MartaCarbó Moliner, RosaThe microbiological culture-dependent characterization and physicochemical characteristics of laboratory sourdough prepared with grape (GS) were evaluated and compared with apple (AS) and yogurt (YS), which are the usual Spanish sourdough ingredients. Ripe GS took longer than AS and YS to reach the appropriate acidity and achieved lower values of lactic acidThe bubble model: mathematically explaining how active TB is possible
http://hdl.handle.net/2117/27336
The bubble model: mathematically explaining how active TB is possible
Prats Soler, Clara; Valls Ribas, Joaquim; Sans, Neus; López Codina, Daniel; Vilaplana, Cristina; Marzo, Elena; Cardona Iglesias, Pere Joan
Tue, 14 Apr 2015 16:19:52 GMThttp://hdl.handle.net/2117/273362015-04-14T16:19:52ZPrats Soler, ClaraValls Ribas, JoaquimSans, NeusLópez Codina, DanielVilaplana, CristinaMarzo, ElenaCardona Iglesias, Pere JoanMaxent as an inevitable force in cell differentiation
http://hdl.handle.net/2117/27335
Maxent as an inevitable force in cell differentiation
Prats Soler, Clara
The maximum entropy principle applies to any thermodynamic system, including biological systems.
It has been widely explored in the framework of ecology, where Shannon entropy is used as a diversity
index, and it is maximized in order to find maximum entropy distributions between or within species. There
is wide agreement between theoretical deductions of such distributions and real data of ecosystems.
Microbial systems are also supposed to satisfy the maximum entropy principle. In particular, cell
differentiation can be studied in terms of diversity, and Shannon index may be used to quantify and
maximize such diversity. Cell differentiation is here considered in a wide sense, and three different examples
where theory, experiments and simulations converge on accomplishing Maxent are shown.
First, a simple bacterial batch culture, were biomass distribution between cells (gamma distribution)
fits the maximum diversity principle with two constraints related with energetic requirements and diversity
in cell division. Then, a more sophisticated system where malaria infected red blood cells in in vitro culture
are studied from their infection state; in this case, the maximization of entropy requires only one constraint
regarding energetic requirements, which results on an exponential distribution of infection states. Finally, and
at an upper scale, a cell differentiation case in terms of spatial distribution and aggregation; this is the case of
tuberculosis lesions in lungs, which also fit the exponential distribution. In all cases a transient phase is
initially seen, followed by a thermodynamically stationary phase where distributions remain approximately
constant and similar to those theoretically deduced with Maxent.
The importance of considering diversity and its evolution in dynamic microbial systems is shown.
Differentiation of cells according to individual properties or functionalities as well as their spatial
organization in upper structures seem to occur according to the maximum diversity principle. In addition,
microbial individual-based ecology (µIBE), that combines individual-based modelling and experimentation,
is shown as an appropriate strategy to study dynamic emergent behaviours related with diversity.
Tue, 14 Apr 2015 16:02:30 GMThttp://hdl.handle.net/2117/273352015-04-14T16:02:30ZPrats Soler, ClaraThe maximum entropy principle applies to any thermodynamic system, including biological systems.
It has been widely explored in the framework of ecology, where Shannon entropy is used as a diversity
index, and it is maximized in order to find maximum entropy distributions between or within species. There
is wide agreement between theoretical deductions of such distributions and real data of ecosystems.
Microbial systems are also supposed to satisfy the maximum entropy principle. In particular, cell
differentiation can be studied in terms of diversity, and Shannon index may be used to quantify and
maximize such diversity. Cell differentiation is here considered in a wide sense, and three different examples
where theory, experiments and simulations converge on accomplishing Maxent are shown.
First, a simple bacterial batch culture, were biomass distribution between cells (gamma distribution)
fits the maximum diversity principle with two constraints related with energetic requirements and diversity
in cell division. Then, a more sophisticated system where malaria infected red blood cells in in vitro culture
are studied from their infection state; in this case, the maximization of entropy requires only one constraint
regarding energetic requirements, which results on an exponential distribution of infection states. Finally, and
at an upper scale, a cell differentiation case in terms of spatial distribution and aggregation; this is the case of
tuberculosis lesions in lungs, which also fit the exponential distribution. In all cases a transient phase is
initially seen, followed by a thermodynamically stationary phase where distributions remain approximately
constant and similar to those theoretically deduced with Maxent.
The importance of considering diversity and its evolution in dynamic microbial systems is shown.
Differentiation of cells according to individual properties or functionalities as well as their spatial
organization in upper structures seem to occur according to the maximum diversity principle. In addition,
microbial individual-based ecology (µIBE), that combines individual-based modelling and experimentation,
is shown as an appropriate strategy to study dynamic emergent behaviours related with diversity.Ordinary differential equations and individual-based simulations to deal with the modelling of bacterial growth for use in diverse contexts
http://hdl.handle.net/2117/26652
Ordinary differential equations and individual-based simulations to deal with the modelling of bacterial growth for use in diverse contexts
Ginovart Gisbert, Marta
Investigation of bacterial growth provides excellent possibilities to combine laboratory exercises, mathematical modeling
and model-based data analysis. The aim of the tasks designed focused on the representation, identi cation and analyses of the di erent
phases (variations of the growth rate) in a bacterial growth (lag, acceleration, exponential, retardation, stationary and decline) by means
of two modeling methodologies, ordinary di erential equations and individual-based simulations. The students had the opportunity to
investigate the growth of a bacterial population from two di erent perspectives, a continuous and deterministic model versus a discrete
and stochastic model, which enriched the process of connecting mathematics with the study of life systems.
Tue, 10 Mar 2015 16:56:19 GMThttp://hdl.handle.net/2117/266522015-03-10T16:56:19ZGinovart Gisbert, MartaInvestigation of bacterial growth provides excellent possibilities to combine laboratory exercises, mathematical modeling
and model-based data analysis. The aim of the tasks designed focused on the representation, identi cation and analyses of the di erent
phases (variations of the growth rate) in a bacterial growth (lag, acceleration, exponential, retardation, stationary and decline) by means
of two modeling methodologies, ordinary di erential equations and individual-based simulations. The students had the opportunity to
investigate the growth of a bacterial population from two di erent perspectives, a continuous and deterministic model versus a discrete
and stochastic model, which enriched the process of connecting mathematics with the study of life systems.To achieve an earlier IFN-¿ response is not sufficient to control mycobacterium tuberculosis infection in mice
http://hdl.handle.net/2117/26327
To achieve an earlier IFN-¿ response is not sufficient to control mycobacterium tuberculosis infection in mice
Vilaplana, Cristina; Prats Soler, Clara; Marzo, Elena; Barril Basil, Carles; Vegué Llorente, Marina; Díaz, Jorge; Valls Ribas, Joaquim; López Codina, Daniel; Cardona Iglesias, Pere Joan
The temporo-spatial relationship between the three organs (lung, spleen and lymph node) involved during the initial stages
of Mycobacterium tuberculosis infection has been poorly studied. As such, we performed an experimental study to evaluate
the bacillary load in each organ after aerosol or intravenous infection and developed a mathematical approach using the
data obtained in order to extract conclusions. The results showed that higher bacillary doses result in an earlier IFN-c
response, that a certain bacillary load (BL) needs to be reached to trigger the IFN-c response, and that control of the BL is
not immediate after onset of the IFN-c response, which might be a consequence of the spatial dimension. This study may
have an important impact when it comes to designing new vaccine candidates as it suggests that triggering an earlier IFN-c
response might not guarantee good infection control, and therefore that additional properties should be considered for
these candidates.
Thu, 12 Feb 2015 18:24:28 GMThttp://hdl.handle.net/2117/263272015-02-12T18:24:28ZVilaplana, CristinaPrats Soler, ClaraMarzo, ElenaBarril Basil, CarlesVegué Llorente, MarinaDíaz, JorgeValls Ribas, JoaquimLópez Codina, DanielCardona Iglesias, Pere JoanThe temporo-spatial relationship between the three organs (lung, spleen and lymph node) involved during the initial stages
of Mycobacterium tuberculosis infection has been poorly studied. As such, we performed an experimental study to evaluate
the bacillary load in each organ after aerosol or intravenous infection and developed a mathematical approach using the
data obtained in order to extract conclusions. The results showed that higher bacillary doses result in an earlier IFN-c
response, that a certain bacillary load (BL) needs to be reached to trigger the IFN-c response, and that control of the BL is
not immediate after onset of the IFN-c response, which might be a consequence of the spatial dimension. This study may
have an important impact when it comes to designing new vaccine candidates as it suggests that triggering an earlier IFN-c
response might not guarantee good infection control, and therefore that additional properties should be considered for
these candidates.Forward backward asymmetries of lepton pairs in events with a large transverse momentum jet at hadron colliders
http://hdl.handle.net/2117/24587
Forward backward asymmetries of lepton pairs in events with a large transverse momentum jet at hadron colliders
Águila López, Francisco del; Ametller Congost, Lluís; Talavera Sánchez, Pedro
We discuss forward-backward charge asymmetries for lepton-pair production in association with a large-transverse-momentum jet at hadron colliders. The lepton charge asymmetry relative to the jet direction AjFB gives a new determination of the effective weak mixing angle sin2lept
eff M2 Z with a statistical precision after cuts of 10 3 (8 10 3) at LHC (Tevatron). This is to be compared with the current uncertainty at LEP and SLD from the asymmetries alone, 2 10 4. The identification of b jets
also allows for the measurement of the bottom-quark–Z asymmetry AbFB at hadron colliders, the resulting statistical precision for sin2lept eff M2
Z being 9 10 4 (2 10 2 at Tevatron), also lower than the reported precision at e+ e- colliders, 3 10 -4.
Thu, 06 Nov 2014 19:13:03 GMThttp://hdl.handle.net/2117/245872014-11-06T19:13:03ZÁguila López, Francisco delAmetller Congost, LluísTalavera Sánchez, PedroWe discuss forward-backward charge asymmetries for lepton-pair production in association with a large-transverse-momentum jet at hadron colliders. The lepton charge asymmetry relative to the jet direction AjFB gives a new determination of the effective weak mixing angle sin2lept
eff M2 Z with a statistical precision after cuts of 10 3 (8 10 3) at LHC (Tevatron). This is to be compared with the current uncertainty at LEP and SLD from the asymmetries alone, 2 10 4. The identification of b jets
also allows for the measurement of the bottom-quark–Z asymmetry AbFB at hadron colliders, the resulting statistical precision for sin2lept eff M2
Z being 9 10 4 (2 10 2 at Tevatron), also lower than the reported precision at e+ e- colliders, 3 10 -4.A two years simulation using a real data cellular automaton: A predictive case study with the schistosomiasis expansion process along the coastline of Brazil
http://hdl.handle.net/2117/24219
A two years simulation using a real data cellular automaton: A predictive case study with the schistosomiasis expansion process along the coastline of Brazil
Albuquerque, Jones O.; Bocanegra, Silvana; Ferrer-Savall, Jordi; López Codina, Daniel; de Souza, Marco Antônio; Souza Santos, Reinaldo; Barbosa, Constança
This work presents a Cellular Automata model to characterize the social and environmental factors which contribute for the analysis of the expansion process of Schistosoma mansoni infection in Pernambuco - Brazil. The model has been experimented with a set of two years real data from a study area at North Coast of Pernambuco – Brazil. The main constraint equations, the modelling process and the results obtained until now with the simulating scenarios generated are presented here. The results identify, as in field works, endemic areas and human risk infection areas. Furthermore, predictive scenarios for a look ahead with a perspective into fifteen years are also presented.
Thu, 02 Oct 2014 17:27:28 GMThttp://hdl.handle.net/2117/242192014-10-02T17:27:28ZAlbuquerque, Jones O.Bocanegra, SilvanaFerrer-Savall, JordiLópez Codina, Danielde Souza, Marco AntônioSouza Santos, ReinaldoBarbosa, ConstançaThis work presents a Cellular Automata model to characterize the social and environmental factors which contribute for the analysis of the expansion process of Schistosoma mansoni infection in Pernambuco - Brazil. The model has been experimented with a set of two years real data from a study area at North Coast of Pernambuco – Brazil. The main constraint equations, the modelling process and the results obtained until now with the simulating scenarios generated are presented here. The results identify, as in field works, endemic areas and human risk infection areas. Furthermore, predictive scenarios for a look ahead with a perspective into fifteen years are also presented.A connection between discrete individual-based and continuous population-based models: A forest modelling case study
http://hdl.handle.net/2117/24214
A connection between discrete individual-based and continuous population-based models: A forest modelling case study
Gómez Mourelo, Pablo; Ginovart Gisbert, Marta
Modelling is perceived as a way of dealing with real life activities. The aim of this work is to compare two approaches to
study forest dynamics, namely discrete individual-based and continuous population-based models, in order to contribute to
an improvement in their use among researchers. An analysis of the strengths, weaknesses, opportunities and threats of the
two different approaches, jointly with a mention of the state-of-the-art, allows us to illustrate this discussion. We will also
provide a bridge or connection between these two modelling methodologies. This link will be developed in detail in a
particular study case. Firstly, an individual-tree based model to deal with dynamics of forests is presented. Secondly, this
model is scaled up to a system of partial differential equations, which represents the limiting behaviour of the individualbased
model.
Thu, 02 Oct 2014 17:02:29 GMThttp://hdl.handle.net/2117/242142014-10-02T17:02:29ZGómez Mourelo, PabloGinovart Gisbert, MartaModelling is perceived as a way of dealing with real life activities. The aim of this work is to compare two approaches to
study forest dynamics, namely discrete individual-based and continuous population-based models, in order to contribute to
an improvement in their use among researchers. An analysis of the strengths, weaknesses, opportunities and threats of the
two different approaches, jointly with a mention of the state-of-the-art, allows us to illustrate this discussion. We will also
provide a bridge or connection between these two modelling methodologies. This link will be developed in detail in a
particular study case. Firstly, an individual-tree based model to deal with dynamics of forests is presented. Secondly, this
model is scaled up to a system of partial differential equations, which represents the limiting behaviour of the individualbased
model.An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium
http://hdl.handle.net/2117/24089
An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium
Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
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.
Wed, 17 Sep 2014 16:39:36 GMThttp://hdl.handle.net/2117/240892014-09-17T16:39:36ZAraujo Granda, Pablo AlejandroGras Moreu, Anna MariaGinovart Gisbert, MartaIn 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.Lowest resonance in QCD from low-energy data
http://hdl.handle.net/2117/23029
Lowest resonance in QCD from low-energy data
Ametller Congost, Lluís; Talavera Sánchez, Pedro
We worked out a generalization of su(2) chiral perturbation theory, including a perturbative singlet scalar field.
The approach suggests that the prediction for sensible low-energy observables converge faster towards their physical value. The physical mass and width of the scalar particle are obtained through a simultaneous analysis of the pion vector form factor and the ¿¿¿p
0
p
0 cross section. Both values are statistically consistent with the ones
obtained by using Roy equations in p-p scattering. In addition we find indications that the photon-photon-singlet
coupling is quite small.
Wed, 21 May 2014 12:02:41 GMThttp://hdl.handle.net/2117/230292014-05-21T12:02:41ZAmetller Congost, LluísTalavera Sánchez, PedroWe worked out a generalization of su(2) chiral perturbation theory, including a perturbative singlet scalar field.
The approach suggests that the prediction for sensible low-energy observables converge faster towards their physical value. The physical mass and width of the scalar particle are obtained through a simultaneous analysis of the pion vector form factor and the ¿¿¿p
0
p
0 cross section. Both values are statistically consistent with the ones
obtained by using Roy equations in p-p scattering. In addition we find indications that the photon-photon-singlet
coupling is quite small.