Dynamic energy budget approach to evaluate antibiotic effects on biofilms

Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix. Coupling a dynamic energy budget based description of cell metabolism to surrounding concentration fields, we are able to approximate survival curves measured for different antibiotics. We reproduce numerically stratified distributions of cell types within the biofilm and introduce ways to incorporate different resistance mechanisms. Qualitative predictions follow that are in agreement with experimental observations, such as higher survival rates of cells close to the substratum when employing antibiotics targeting active cells or enhanced polymer production when antibiotics are administered. The current computational model enables validation and hypothesis testing when developing therapies.Comment: to appear in Communications in Nonlinear Science and Numerical Simulatio

Biofilms as poroelastic materials

Biofilms are bacterial aggregates encased in a self-produced polymeric matrix which attach to moist surfaces and are extremely resistant to chemicals and antibiotics. Recent experiments show that their structure is defined by the interplay of elastic deformations and liquid transport within the biofilm, in response to the cellular activity and the interaction with the surrounding environment. We propose a poroelastic model for elastic deformation and liquid transport in three dimensional biofilms spreading on agar surfaces. The motion of the boundaries can be described by the combined use of Von Kármán type approximations for the agar/biofilm interface and thin film approximations for the biofilm/air interface. Bacterial activity informs the macroscopic continuous model through source terms and residual stresses, either phenomenological or derived from microscopic models. We present a procedure to estimate the structure of such residual stresses, based on a simple cellular automata description of bacterial activity. Inspired by image processing, we show that a filtering strategy effectively smooths out the rough tensors provided by the stochastic cellular automata rules, allowing us to insert them in the macroscopic model without numerical instability

La soberanía alimentaria: Cultivando nuevas alianzas entre campo, bosque y ciudad

In June, 2008, we convoked a forum and workshop in Chiapas, Mexico to strengthen alliances among farmers’ organizations, conservationists and academics. Speakers outlined the evolution of the relations among production systems, forests and biodiversity from the prehispanic era through the current crisis in the neoliberal economic model and industrial agriculture. They also framed a new conservation paradigm that prioritizes the role of farmers. We formed working groups that elaborated proposals for collaboration among the participating sectors. Cooperative networks emerged as appropriate structures for coordinating action and facilitating the exchange of information and support at various geographic scales. Solidarity-based markets are a venue where diverse interests converge, favoring the formation of such networks. We also identified some specific issues for collaboration, including: agrofuels and energy sovereignty, environmental services and rural education. Biodiversity and food sovereignty are the two axes of this agenda for cooperation that forms part of an international struggle to reconstruct our food systems.En junio de 2008 convocamos un foro-taller en Chiapas, México para potencializar alianzas entre organizaciones campesinas, conservacionistas y académicos. Los ponentes trazaron la evolución de las relaciones entre sistemas productivos, bosques y biodiversidad desde la época prehispánica hasta la actual crisis de la economía neoliberal y la agricultura industrial. También delinearon un nuevo paradigma para la conservación en donde los campesinos son protagonistas. En grupos de trabajo, elaboramos propuestas para cimentar una agenda común entre los distintos sectores representados. Las redes de cooperación emergieron como estructuras para coordinar acción y facilitar el intercambio de información y apoyo a distintas escalas geográficas. Los mercados solidarios son la confluencia de diversos intereses en dónde se pueden constituir dichas redes. También identificamos algunos temas específicos de trabajo, entre ellos: los agrocombustibles y la soberanía energética, los servicios ambientales y la educación para el campo. La biodiversidad y la soberanía alimentaria y territorial son los ejes de esta agenda de cooperación, que forma parte de una lucha internacional para reconstruir nuestros sistemas alimenticios

Método de detección de contornos: implementación dinámica del modelo de Chan-Vese y detección de contornos basado en multirresolución

Treball Final de Màster Universitari en Matemàtica Computacional. Codi: SIB027 Curs acadèmic: 2013/201

Food sovereignty: Cultivating new alliances among fields, forests and cities

En junio de 2008 convocamos un foro-taller en Chiapas, México para potencializar alianzas entre organizaciones campesinas, conservacionistas y académicos. Los ponentes trazaron la evolución de las relaciones entre sistemas productivos, bosques y biodiversidad desde la época prehispánica hasta la actual crisis de la economía neoliberal y la agricultura industrial. También delinearon un nuevo paradigma para la conservación en donde los campesinos son protagonistas. En grupos de trabajo, elaboramos propuestas para cimentar una agenda común entre los distintos sectores representados. Las redes de cooperación emergieron como estructuras para coordinar acción y facilitar el intercambio de información y apoyo a distintas escalas geográficas. Los mercados solidarios son la confluencia de diversos intereses en dónde se pueden constituir dichas redes. También identificamos algunos temas específicos de trabajo, entre ellos: los agrocombustibles y la soberanía energética, los servicios ambientales y la educación para el campo. La biodiversidad y la soberanía alimentaria y territorial son los ejes de esta agenda de cooperación, que forma parte de una lucha internacional para reconstruir nuestros sistemas alimenticios.Abstract: In June, 2008, we convoked a forum and workshop in Chiapas, Mexico to strengthen alliances among farmers’ organizations, conservationists and academics. Speakers outlined the evolution of the relations among production systems, forests and biodiversity from the prehispanic era through the current crisis in the neoliberal economic model and industrial agriculture. They also framed a new conservation paradigm that prioritizes the role of farmers. We formed working groups that elaborated proposals for collaboration among the participating sectors. Cooperative networks emerged as appropriate structures for coordinating action and facilitating the exchange of information and support at various geographic scales. Solidarity-based markets are a venue where diverse interests converge, favoring the formation of such networks. We also identified some specific issues for collaboration, including: agrofuels and energy sovereignty, environmental services and rural education. Biodiversity and food sovereignty are the two axes of this agenda for cooperation that forms part of an international struggle to reconstruct our food systems