Discrete Solution of Differential Equations by P Metabolic Algorithm

The relationships existing between MP graphs, metabolic P systems, and ODE systems are investigated. Formal results show that every MP system, once derived by its MP graph, results in an ODE system whose solution equals, in the limit, the solution obtained by a non-cooperative MP system that is ODE equivalent to the original one. The freedom of choice of the ODE equivalent from the original MP system resembles the same freedom which is left in the choice and optimization of a numerical scheme while computing the solution of an ODE system

Evolutionary games on graphs

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first three sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fourth section surveys the topological complications implied by non-mean-field-type social network structures in general. The last three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.Comment: Review, final version, 133 pages, 65 figure

Theoretical aspects and modelling of cellular decision making, cell killing and information-processing in photodynamic therapy of cancer

BACKGROUND: The aim of this report is to provide a mathematical model of the mechanism for making binary fate decisions about cell death or survival, during and after Photodynamic Therapy (PDT) treatment, and to supply the logical design for this decision mechanism as an application of rate distortion theory to the biochemical processing of information by the physical system of a cell. METHODS: Based on system biology models of the molecular interactions involved in the PDT processes previously established, and regarding a cellular decision-making system as a noisy communication channel, we use rate distortion theory to design a time dependent Blahut-Arimoto algorithm where the input is a stimulus vector composed of the time dependent concentrations of three PDT related cell death signaling molecules and the output is a cell fate decision. The molecular concentrations are determined by a group of rate equations. The basic steps are: initialize the probability of the cell fate decision, compute the conditional probability distribution that minimizes the mutual information between input and output, compute the cell probability of cell fate decision that minimizes the mutual information and repeat the last two steps until the probabilities converge. Advance to the next discrete time point and repeat the process. RESULTS: Based on the model from communication theory described in this work, and assuming that the activation of the death signal processing occurs when any of the molecular stimulants increases higher than a predefined threshold (50% of the maximum concentrations), for 1800s of treatment, the cell undergoes necrosis within the first 30 minutes with probability range 90.0%-99.99% and in the case of repair/survival, it goes through apoptosis within 3-4 hours with probability range 90.00%-99.00%. Although, there is no experimental validation of the model at this moment, it reproduces some patterns of survival ratios of predicted experimental data. CONCLUSIONS: Analytical modeling based on cell death signaling molecules has been shown to be an independent and useful tool for prediction of cell surviving response to PDT. The model can be adjusted to provide important insights for cellular response to other treatments such as hyperthermia, and diseases such as neurodegeneration

Biology and potential biogeochemical impacts of novel predatory flavobacteria

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2010Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches.Support by the National Science Foundation (NSF) Division of Molecular and Cellular Biosciences Grant (MCB- 0348425), the MIT Student Assistance Fund, the Woods Hole Oceanographic Institution (WHOI) Academic Programs Office, WHOI Coastal Ocean Institute (COI) and WHOI Ocean Venture Fund grant, COI and the WHOI Ocean Life Institute

A computational modeling for real ecosystems based on P systems

In this paper, a P systems based general framework for modeling ecosystems dynamics is presented. Particularly, ecosystems are specified by means of multienvironment P systems composed of a finite number of environments, each of them having an extended P system with active membranes. The semantics is of a probabilistic type and it is implemented by assigning each rule of the system a probabilistic constant which depends on the environment and the run time. As a case study, two real ecosystems are described: scavenger birds in the Catalan Pyrenees and the zebra mussel (Dreissena Polymorpha) in Ribarroja reservoir (Spain).Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-0420

Biology and potential biogeochemical impacts of novel predatory flavobacteria

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2010Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches.Support by the National Science Foundation (NSF) Division of Molecular and Cellular Biosciences Grant (MCB- 0348425), the MIT Student Assistance Fund, the Woods Hole Oceanographic Institution (WHOI) Academic Programs Office, WHOI Coastal Ocean Institute (COI) and WHOI Ocean Venture Fund grant, COI and the WHOI Ocean Life Institute

Mechanisms of plant diversity-productivity relationships in complex ecological networks

The importance of biodiversity for providing ecosystem functions and services crucial to human well-being is well documented. However, the mechanisms underlying biodiversity-ecosystem functioning (BEF) relationships are insufficiently understood. I address this issue by zooming in on plant diversity-productivity relationships and their potential drivers. Specifically, I combine theoretical and empirical approaches focusing on resource- and animal-based processes, as well as their joint effect on plant community composition and productivity. Additionally, I consider spatial aspects of resource-based, animal-based, and generalized empirical interactions. My findings show that plant diversity only affects productivity positively when plants have complementarity resource requirements and spatially overlap in their resource access, thereby risking negative effects from competition. This includes the competitive exclusion of inferior competitors. However, in complex food webs, competitive exclusion of plant species is largely mitigated. This aligns with my empirical findings that suggest coexistence mechanisms playing a central role in driving plant diversity-productivity relationships. Despite positive effects on plant coexistence, animal-based processes induce strong variation on plant diversity-productivity relationships. Specifically, unconstrained animal movement can lead to negative relationships, whereas movement scaled with animal body masses turns them positive. My findings further suggest considerable interactive effects between resource- and animal-based mechanisms. However, clear differences in how either mechanism assembles plant communities could serve as a tool to disentangle them. This opens a way to focus conservation and restoration efforts that counteract the global biodiversity crisis, ensuring the provisioning of ecosystem service that are crucial to human society

Ecosystem limits to food web fluxes and fisheries yields in the North Sea simulated with an end-to-end food web model

Equilibrium yields from an exploited fish stock represent the surplus production remaining after accounting for losses due to predation. However, most estimates of maximum sustainable yield, upon which fisheries management targets are partly based, assume that productivity and predation rates are constant in time or at least stationary. This means that there is no recognition of the potential for interaction between different fishing sectors. Here, an end-to-end ecosystem model is developed to explore the possible scale and mechanisms of interactions between pelagic and demersal fishing in the North Sea. The model simulates fluxes of nitrogen between detritus, inorganic nutrient and guilds of taxa spanning phytoplankton to mammals. The structure strikes a balance between graininess in space, taxonomy and demography, and the need to constrain the parameter-count sufficiently to enable automatic parameter optimization. Simulated annealing is used to locate the maximum likelihood parameter set, given the model structure and a suite of observations of annual rates of production and fluxes between guilds. Simulations of the impact of fishery harvesting rates showed that equilibrium yields of pelagic and demersal fish were strongly interrelated due to a variety of top-down and bottom-up food web interactions. The results clearly show that management goals based on simultaneously achieving maximum sustainable biomass yields from all commercial fish stocks is simply unattainable. Trade-offs between, for example, pelagic and demersal fishery sectors and other properties of the ecosystem have to be considered in devising an overall harvesting strategy