Model architecture for associative memory in a neural network of spiking neurons

AbstractA synaptic connectivity model is assembled on a spiking neuron network aiming to build up a dynamic pattern recognition system. The connection architecture includes gap junctions and both inhibitory and excitatory chemical synapses based on Hebb’s hypothesis. The network evolution resulting from external stimulus is sampled in a properly defined frequency space. Neurons’ responses to different current injections are mapped onto a subspace using Principal Component Analysis. Departing from the base attractor, related to a quiescent state, different external stimuli drive the network to different fixed points through specific trajectories in this subspace

Heterogeneous individual motility biases group composition in a model of aggregating cells

Aggregative life cycles are characterized by alternating phases of unicellular growth and multicellular development. Their multiple, independent evolutionary emergence suggests that they may have coopted pervasive properties of single-celled ancestors. Primitive multicellular aggregates, where coordination mechanisms were less efficient than in extant aggregative microbes, must have faced high levels of conflict between different co-aggregating populations. Such conflicts within a multicellular body manifest in the differential reproductive output of cells of different types. Here, we study how heterogeneity in cell motility affects the aggregation process and creates a mismatch between the composition of the population and that of self-organized groups of active adhesive particles. We model cells as self-propelled particles and describe aggregation in a plane starting from a dispersed configuration. Inspired by the life cycle of aggregative model organisms such as Dictyostelium discoideum or Myxococcus xanthus, whose cells interact for a fixed duration before the onset of chimeric multicellular development, we study finite-time configurations for identical particles and in binary mixes. We show that co-aggregation results in three different types of frequency-dependent biases, one of which is associated to evolutionarily stable coexistence of particles with different motility. We propose a heuristic explanation of such observations, based on the competition between delayed aggregation of slower particles and detachment of faster particles. Unexpectedly, despite the complexity and non-linearity of the system, biases can be largely predicted from the behavior of the two corresponding homogenous populations. This model points to differential motility as a possibly important factor in driving the evolutionary emergence of facultatively multicellular life-cycles

Evolution signatures in genome network properties

Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome evolution, where genes in a network are either acquired de novo using a preferential attachment rule, or duplicated, with a duplication probability that linearly grows with gene degree and decreases with its clustering coefficient. The results show that topological distributions are better described than in previous genome evolution models. This model correctly predicts that, in order to produce protein-protein association networks with number of links and number of nodes in the observed range, it is necessary 90% of gene duplication and 10% of de novo gene acquisition. If this scenario is true, it implies a universal mechanism for genome evolution

Implementação do simulador Siscot para a cidade de Porto Alegre

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Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms

Expansão perturbativa em torno do limite atômico para sistemas Kondo e de valência intermediária

Neste trabalho estudamos as propriedades eletrônicas de sistemas compostos de certos elementos de terras raras. Estes sistemas apresentam propriedades físicas anômalas em decorrência da interação entre os elétrons 4f e os elétrons de condução . Eles são conhecidos como sistemas de valência intermediária, sistemas Kondo, ou, quando a baixas temperaturas apresentam massas efetivas eletrônicas muito grandes, como sistemas de férmions pesados. O hamiltoniano modelo para a descrição teórica desses sistemas é o ilamiltoniano Periódico de Anderson. Nossa abordagem ao problema é de tratar perturbativamente a energia cinética dos elétrons de condução no hamiltoniano modelo pelo uso de funções de Green em uma aproximação que desacopla médias de operadores em um dado sítio em produtos de médias de pares de operadores neste sítio. Utilizando esta técnica calculamos a densidade de estados eletrônica, a susceptibilidade estática magnética e o calor especifico eletrônico. Os resultados concordam qualitativamente com os experimentos em sistemas de Ce.In this work we study the electronic properties of systems composed of certain rare-earth elements. These systems present anomalous physical properties due to the interaction between the 4f-electrons and the conduction electrons. They are known as intermediate valence systems, Kondo systems, or heavy-fermion systems, in the case of large electronic effective masses at low temperatures. The model Hamiltonian used in the theoretical description of these systems is the Perioclic Anderson Hamiltonian. Our approach to the problem consists in treating perturbatively the kinetic energy of the conduction electrons in the model Hamiltonian. This is done through the use of Green's functions in an approximation that decouples single site operator averages in products of operator pair averages. With this technique we calculate the electronic density of states, the static magnetic susceptibility and the electronic specific heat. The results agree qualitatively with experiments in Ce systems

Expansão perturbativa em torno do limite atômico para sistemas Kondo e de valência intermediária

Neste trabalho estudamos as propriedades eletrônicas de sistemas compostos de certos elementos de terras raras. Estes sistemas apresentam propriedades físicas anômalas em decorrência da interação entre os elétrons 4f e os elétrons de condução . Eles são conhecidos como sistemas de valência intermediária, sistemas Kondo, ou, quando a baixas temperaturas apresentam massas efetivas eletrônicas muito grandes, como sistemas de férmions pesados. O hamiltoniano modelo para a descrição teórica desses sistemas é o ilamiltoniano Periódico de Anderson. Nossa abordagem ao problema é de tratar perturbativamente a energia cinética dos elétrons de condução no hamiltoniano modelo pelo uso de funções de Green em uma aproximação que desacopla médias de operadores em um dado sítio em produtos de médias de pares de operadores neste sítio. Utilizando esta técnica calculamos a densidade de estados eletrônica, a susceptibilidade estática magnética e o calor especifico eletrônico. Os resultados concordam qualitativamente com os experimentos em sistemas de Ce.In this work we study the electronic properties of systems composed of certain rare-earth elements. These systems present anomalous physical properties due to the interaction between the 4f-electrons and the conduction electrons. They are known as intermediate valence systems, Kondo systems, or heavy-fermion systems, in the case of large electronic effective masses at low temperatures. The model Hamiltonian used in the theoretical description of these systems is the Perioclic Anderson Hamiltonian. Our approach to the problem consists in treating perturbatively the kinetic energy of the conduction electrons in the model Hamiltonian. This is done through the use of Green's functions in an approximation that decouples single site operator averages in products of operator pair averages. With this technique we calculate the electronic density of states, the static magnetic susceptibility and the electronic specific heat. The results agree qualitatively with experiments in Ce systems