Decision Trees for Applicability of Evolution Rules in Transition P Systems

Transition P Systems are a parallel and distributed computational model based on the notion of the cellular membrane structure. Each membrane determines a region that encloses a multiset of objects and evolution rules. Transition P Systems evolve through transitions between two consecutive configurations that are determined by the membrane structure and multisets present inside membranes. Moreover, transitions between two consecutive configurations are provided by an exhaustive non-deterministic and parallel application of active evolution rules subset inside each membrane of the P system. But, to establish the active evolution rules subset, it is required the previous calculation of useful and applicable rules. Hence, computation of applicable evolution rules subset is critical for the whole evolution process efficiency, because it is performed in parallel inside each membrane in every evolution step. The work presented here shows advantages of incorporating decision trees in the evolution rules applicability algorithm. In order to it, necessary formalizations will be presented to consider this as a classification problem, the method to obtain the necessary decision tree automatically generated and the new algorithm for applicability based on it.

Forming Knowledge Bases in the Computer Knowledge Bank on Medical Diagnostics

* This paper was made according to the program of FEBRAS, project "Creating methods and tools for developing intellectual information systems in medicine and public health".

Towards the Problems of an Evaluation of Data Uncertainty in Decision Support Systems

The question of forming aim-oriented description of an object domain of decision support process is outlined. Two main problems of an estimation and evaluation of data and knowledge uncertainty in decision support systems – straight and reverse, are formulated. Three conditions being the formalized criteria of aimoriented constructing of input, internal and output spaces of some decision support system are proposed. Definitions of appeared and hidden data uncertainties on some measuring scale are given.

P Systems Goedelization

This paper presents a method for assigning natural numbers to Transition P systems based on a Gödelization process. The paper states step by step the way for obtaining Gödel numbers for each one of the fundamental elements of Transition P systems –multisets of objects, evolution rules, priorities relation, membrane structure- until defining the Gödel number of a given Transition P system.

Fast Linear Algorithm for Active Rules Application in Transition P Systems

Transition P systems are computational models based on basic features of biological membranes and the observation of biochemical processes. In these models, membrane contains objects multisets, which evolve according to given evolution rules. In the field of Transition P systems implementation, it has been detected the necessity to determine whichever time are going to take active evolution rules application in membranes. In addition, to have time estimations of rules application makes possible to take important decisions related to the hardware / software architectures design. In this paper we propose a new evolution rules application algorithm oriented towards the implementation of Transition P systems. The developed algorithm is sequential and, it has a linear order complexity in the number of evolution rules. Moreover, it obtains the smaller execution times, compared with the preceding algorithms. Therefore the algorithm is very appropriate for the implementation of Transition P systems in sequential devices.

Analysis of P-Systems under a Multiagent Systems Perspective

Membrane computing is a recent area that belongs to natural computing. This field works on computational models based on nature's behavior to process the information. Recently, numerous models have been developed and implemented with this purpose. P-systems are the structures which have been defined, developed and implemented to simulate the behavior and the evolution of membrane systems which we find in nature. What we show in this paper is an application capable to simulate the P-systems based on a multiagent systems (MAS) technology. The main goal we want to achieve is to take advantage of the inner qualities of the multiagent systems. This way we can analyse the proper functioning of any given p-system. When we observe a P-system from a different perspective, we can be assured that it is a particular case of the multiagent systems. This opens a new possibility, in the future, to always evaluate the P-systems in terms of the multiagent systems technology.

CO-stabilisation mechanisms of nanoparticles and surfactants in Pickering emulsions produced by membrane emulsification

Two different membrane emulsification methods were used to study mechanisms for co-stabilisation of emulsions, by either electrostatic or steric stabilised nanoparticles with anionic, cationic or non-ionic surfactants. The experimental results demonstrated the existence of two distinct co-stabilisation mechanisms that arise from interactions of the nanoparticles and surfactant molecules. When significant interaction is not involved, independent competitive adsorption of nanoparticles and surfactant molecules occurs spontaneously to stabilise droplets in formation. The adsorption/desorption equilibrium between surfactant molecules determines the longevity of the droplet stability. When the surfactant molecule reacts with the nanoparticle surface, the resultant surface modification appears to generate faster wetting kinetics for nanoparticles at the oil/water interface and yields enhanced stabilisation. The paper discusses the implications of controlling these interactions for emulsion production membrane systems.

Sustainable energy systems for seawater reverse osmosis desalination

Desalination of seawater driven by solar and other sustainable energy sources could in principle fulfil the growing needs of the world's most water-stressed countries. Reverse osmosis (RO) has become the most efficient process for desalination, making it the technology of choice for use with solar energy, and photovoltaics (PV) has become the most successful technology for solar energy conversion. But despite recent gains in the efficiency of PV-RO, substantial improvements are still possible because of the numerous energy losses occurring between input of sunlight and output of freshwater. This chapter gives an overview of some of the research activities and recent advances that could ultimately result in solar-powered RO systems becoming more than 10 times efficient than today. It also describes advances in waste heat recovery for RO desalination that are yielding greatly improved performance over desalination processes based on distillation.

Computational modeling of intermediate temperature proton exchange membrane (PEM) fuel cells

A two-phase three-dimensional computational model of an intermediate temperature (120--190°C) proton exchange membrane (PEM) fuel cell is presented. This represents the first attempt to model PEM fuel cells employing intermediate temperature membranes, in this case, phosphoric acid doped polybenzimidazole (PBI). To date, mathematical modeling of PEM fuel cells has been restricted to low temperature operation, especially to those employing Nafion ® membranes; while research on PBI as an intermediate temperature membrane has been solely at the experimental level. This work is an advancement in the state of the art of both these fields of research. With a growing trend toward higher temperature operation of PEM fuel cells, mathematical modeling of such systems is necessary to help hasten the development of the technology and highlight areas where research should be focused.^ This mathematical model accounted for all the major transport and polarization processes occurring inside the fuel cell, including the two phase phenomenon of gas dissolution in the polymer electrolyte. Results were presented for polarization performance, flux distributions, concentration variations in both the gaseous and aqueous phases, and temperature variations for various heat management strategies. The model predictions matched well with published experimental data, and were self-consistent.^ The major finding of this research was that, due to the transport limitations imposed by the use of phosphoric acid as a doping agent, namely low solubility and diffusivity of dissolved gases and anion adsorption onto catalyst sites, the catalyst utilization is very low (∼1--2%). Significant cost savings were predicted with the use of advanced catalyst deposition techniques that would greatly reduce the eventual thickness of the catalyst layer, and subsequently improve catalyst utilization. The model also predicted that an increase in power output in the order of 50% is expected if alternative doping agents to phosphoric acid can be found, which afford better transport properties of dissolved gases, reduced anion adsorption onto catalyst sites, and which maintain stability and conductive properties at elevated temperatures.^

Membrane protein production in the Yeast, S. cerevisiae

The first crystal structures of recombinant mammalian membrane proteins were solved in 2005 using protein that had been produced in yeast cells. One of these, the rabbit Ca2+-ATPase SERCA1a, was synthesized in Saccharomyces cerevisiae. All host systems have their specific advantages and disadvantages, but yeast has remained a consistently popular choice in the eukaryotic membrane protein field because it is quick, easy and cheap to culture, whilst being able to post-translationally process eukaryotic membrane proteins. Very recent structures of recombinant membrane proteins produced in S. cerevisiae include those of the Arabidopsis thaliana NRT1.1 nitrate transporter and the fungal plant pathogen lipid scramblase, TMEM16. This chapter provides an overview of the methodological approaches underpinning these successes.

Experiment: Acidified seawater impacts sea urchin larvae pH regulatory systems relevant for calcification

Calcifying echinoid larvae respond to changes in seawater carbonate chemistry with reduced growth and developmental delay. To date, no information exists on how ocean acidification acts on pH homeostasis in echinoderm larvae. Understanding acid-base regulatory capacities is important because intracellular formation and maintenance of the calcium carbonate skeleton is dependent on pH homeostasis. Using H(+)-selective microelectrodes and the pH-sensitive fluorescent dye BCECF, we conducted in vivo measurements of extracellular and intracellular pH (pH(e) and pH(i)) in echinoderm larvae. We exposed pluteus larvae to a range of seawater CO(2) conditions and demonstrated that the extracellular compartment surrounding the calcifying primary mesenchyme cells (PMCs) conforms to the surrounding seawater with respect to pH during exposure to elevated seawater pCO(2). Using FITC dextran conjugates, we demonstrate that sea urchin larvae have a leaky integument. PMCs and spicules are therefore directly exposed to strong changes in pH(e) whenever seawater pH changes. However, measurements of pH(i) demonstrated that PMCs are able to fully compensate an induced intracellular acidosis. This was highly dependent on Na(+) and HCO(3)(-), suggesting a bicarbonate buffer mechanism involving secondary active Na(+)-dependent membrane transport proteins. We suggest that, under ocean acidification, maintained pH(i) enables calcification to proceed despite decreased pH(e). However, this probably causes enhanced costs. Increased costs for calcification or cellular homeostasis can be one of the main factors leading to modifications in energy partitioning, which then impacts growth and, ultimately, results in increased mortality of echinoid larvae during the pelagic life stage.

Antimicrobial activity of prodigiosin is attributable to plasma-membrane damage

The bacterial pigment prodigiosin has various biological activities; it is, for instance, an effective antimicrobial. Here, we investigate the primary site targeted by prodigiosin, using the cells of microbial pathogens of humans as model systems: Candida albicans, Escherichia coli, Staphylococcus aureus. Inhibitory concentrations of prodigiosin; leakage of intracellular K+ ions, amino acids, proteins and sugars; impacts on activities of proteases, catalases and oxidases; and changes in surface appearance of pathogen cells were determined. Prodigiosin was highly inhibitory (30% growth rate reduction of C. albicans, E. coli, S. aureus at 0.3, 100 and 0.18 μg ml−1, respectively); caused leakage of intracellular substances (most severe in S. aureus); was highly inhibitory to each enzyme; and caused changes to S. aureus indicative of cell-surface damage. Collectively, these findings suggest that prodigiosin, log Poctanol–water 5.16, is not a toxin but is a hydrophobic stressor able to disrupt the plasma membrane via a chaotropicity-mediated mode-of-action.

How curvature-generating proteins build scaffolds on membrane nanotubes

Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex sub-cellular structures, and many other cellular phenomena. They form three-dimensional assemblies, which act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we employ various experimental, theoretical and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube’s length. Our work implies that the nature of local protein-membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30–40% of a tube’s surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes. 

Catalytic reactions with palladium supported on mesocellular foam : Applications in hydrogenation, isomerization, and C-C bond forming reactions

The major part of this thesis concerns the development of catalytic methodologies based on palladium nanoparticles immobilized on aminopropyl-functionalized siliceous mesocellular foam (Pd0-AmP-MCF). The catalytic activity of the precursor to the nanocatalyst, PdII-AmP-MCF is also covered by this work. In the first part the application of Pd0-AmP-MCF in Suzuki-Miyaura cross-coupling reactions and transfer hydrogenation of alkenes under microwave irradiation is described. Excellent reactivity was observed and a broad range of substrates were tolerated for both transformations. The Pd0-AmP-MCF exhibited high recyclability as well as low metal leaching in both cases. The aim of the second part was to evaluate the catalytic efficiency of the closely related PdII-AmP-MCF for cycloisomerization of various acetylenic acids. The catalyst was able to promote formation of lactones under mild conditions using catalyst loadings of 0.3 - 0.5 mol% at temperatures of up to 50 oC in the presence of Et3N. By adding 1,4-benzoquinone to the reaction, the catalyst could be recycled four times without any observable decrease in the activity. The selective arylation of indoles at the C-2 position using Pd-AmP-MCF and symmetric diaryliodonium salts is presented in the third part. These studies revealed that Pd0-AmP-MCF was more effective than PdII-AmP-MCF for this transformation. Variously substituted indoles as well as diaryliodonium salts were tolerated, giving arylated indoles in high yields within 15 h at 20 - 50 oC in H2O. Only very small amounts of Pd leaching were observed and in this case the catalyst exhibited moderate recyclability. The final part of the thesis describes the selective hydrogenation of the C=C in different α,β-unsaturated systems. The double bond was efficiently hydrogenated in high yields both under batch and continuous-flow conditions. High recyclability and low metal leaching were observed in both cases.

Nonlinear Dynamics Near the Cell Membrane of Chara Corallina

The phenomenon of patterned distribution of pH near the cell membrane of the algae Chara corallina upon illumination is well-known. In this paper, we develop a mathematical model, based on the detailed kinetic analysis of proton fluxes across the cell membrane, to explain this phenomenon. The model yields two coupled nonlinear partial differential equations which describe the spatial dynamics of proton concentration changes and transmembrane potential generation. The experimental observation of pH pattern formation, its period and amplitude of oscillation, and also its hysteresis in response to changing illumination, are all reproduced by our model. A comparison of experimental results and predictions of our theory is made. Finally, a mechanism for pattern formation in Chara corallina is proposed.