Communication and Stochastic Processes in Some Bacterial Populations: Significance for Membrane Computing

Intercellular communication between bacterial cells belonging to the same population is well documented in Microbiology, sporulation and cannibalism in B. Subtilis and genetic competence and fratricide in S. pneumoniae being deeply studied in the last years. The investigation of individual cell behavior has revealed that populations of these bacteria sometimes bifurcate into phenotypically distinct, but genetically identical, subpopulations by random switching mechanisms. The probabilistic nature of the random switching mechanisms, the occurrence of some biochemical processes related to it at plasma membrane and the need to study the processes at the level of each individual cell make intercellular communication and stochastic processes very suitable to be modeled by P systems

Some Notes on the Interplay Between P Systems and Chemotaxis in Bacteria

We describe some chemotactic behaviors of bacteria, that is, their movement response to changes in the environment, and the underlying molecular mechanisms. We outline how such processes could be linked to membrane computing, by taking inspiration from them for new type of rules or new features to be introduced in P systems, as well as by considering how the application of recent P system-based models can produce relevant results for the description and the analysis of chemotaxis processes

On Modelling Ion Fluxes Across Biological Membranes with P Systems

In this report we address the challenge of using P systems to integrate at the whole cell level both active and passive transport of different ions, done by different types of membrane transport proteins which work simultaneously and concurrently

New Proposals for the Formalization of Membrane Proteins

This paper presents three new proposals to take advantage, in the framework of P systems, from proteins acting in bacteria. One attempt aims to focus on the transport protein that act as a logic AND gate at the cell membrane. The multiplicity of type of transporters involved in maintaining osmotic pressure within physiological values, both at short and long term level are also presented, as an example of parallelism occurring in living cell. Finally, the change of enzyme activity by reversible aggregation could be important for P systems as a new rule to follow, and process to model

Membrane Proteins as Maxwell’s Demons and Their Significance for P Systems

The aim of these notes is to contribute to the dialog between P systems and Biological Sciences focussing on membrane proteins involved either in iron transport inside the bacterial cells or in elimination outside the bacterial cells of substances which are dangerous for the cell. The ability of these membrane proteins to behave as Maxwell’s demon, gate keeper, or as “a being who can see the individual molecules” could be important for P systems as examples of discrete processes which could be modeled by discrete mathematics and as real molecular objects for in vitro implementation of P systems

A Biological Perspective on Sorting with P Systems

The aim of this contribution is to argue that the processes occurring in biological membranes in bacteria are also important as natural examples of communication between membranes, which, in the formal framework of P systems, leads (among other things) to simulations of sorting operations

Controlled biomineralization of magnetite (Fe₃O₄) by <i>Magnetospirillum gryphiswaldense</i>

Results from a study of the chemical composition and micro-structural characteristics of bacterial magnetosomes extracted from the magnetotactic bacterial strain Magnetospirillum gryphiswaldense are presented here. Using high-resolution transmission electron microscopy combined with selected-area electron diffraction and energy dispersive X-ray microanalysis, biogenic magnetite particles isolated from mature cultures were analysed for variations in crystallinity and particle size, as well as chain character and length. The analysed crystals showed a narrow size range (∼14-67 nm) with an average diameter of 46±6.8 nm, cuboctahedral morphologies and typical Gamma type crystal size distributions. The magnetite particles exhibited a high chemical purity (exclusively Fe3O4) and the majority fall within the single-magnetic-domain range

Computing Using Signals: From Cells to P Systems

In cell biology one of the fundamental topic is the study of how biological signals are managed by cells. Signals can arise from inside the cell or from the external environment and the correct answer to certain signals is essential for bacteria to survive in a certain environment. Starting from these biological motivations we consider a model of P systems where the computa- tion is controlled by signals which move across the regions. In particular, we consider Signals-Based P systems where the symbol-objects cannot be moved and the rules can be activated/inactivated using a ¯nite number of signals (signal-promoters) moved across the membranes; di®erently from standard P systems using promoters, in our case promoters cannot be created during the computation. After discussing the biological motivations we show how this model becomes universal when it uses one catalyst, and a bounded number of signal-promoters

Studying the Chlorophyll Fluorescence in Cyanobacteria with Membrane Computing Techniques

In this paper, we report a pioneer study of the decrease in chlorophyll uorescence produced by the reduction of MTT (a dimethyl thiazolyl diphenyl tetrazolium salt) monitored using an epi uorescence microscope coupled to automate image analysis in the framework of P systems. Such analysis has been performed by a family of tissue P systems working on the images as data inpuJunta de Andalucía P08-TIC-04200Ministerio de Economía y Competitividad TIN2012-3743