Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

<p>Abstract</p> <p>Background</p> <p>Network inference methods reconstruct mathematical models of molecular or genetic networks directly from experimental data sets. We have previously reported a mathematical method which is exclusively data-driven, does not involve any heuristic decisions within the reconstruction process, and deliveres all possible alternative minimal networks in terms of simple place/transition Petri nets that are consistent with a given discrete time series data set.</p> <p>Results</p> <p>We fundamentally extended the previously published algorithm to consider catalysis and inhibition of the reactions that occur in the underlying network. The results of the reconstruction algorithm are encoded in the form of an extended Petri net involving control arcs. This allows the consideration of processes involving mass flow and/or regulatory interactions. As a non-trivial test case, the phosphate regulatory network of enterobacteria was reconstructed using <it>in silico</it>-generated time-series data sets on wild-type and <it>in silico </it>mutants.</p> <p>Conclusions</p> <p>The new exact algorithm reconstructs extended Petri nets from time series data sets by finding all alternative minimal networks that are consistent with the data. It suggested alternative molecular mechanisms for certain reactions in the network. The algorithm is useful to combine data from wild-type and mutant cells and may potentially integrate physiological, biochemical, pharmacological, and genetic data in the form of a single model.</p

TRANSWESD: inferring cellular networks with transitive reduction

Motivation: Distinguishing direct from indirect influences is a central issue in reverse engineering of biological networks because it facilitates detection and removal of false positive edges. Transitive reduction is one approach for eliminating edges reflecting indirect effects but its use in reconstructing cyclic interaction graphs with true redundant structures is problematic

Estudo do conversor zeta em condu??o simult?nea dos semicondutores aplicada ? alimenta??o de LEDs de pot?ncia

Submitted by Setor de Tratamento da Informa??o - BC/PUCRS ([email protected]) on 2015-06-17T12:02:56Z No. of bitstreams: 1 470517 - Texto Completo.pdf: 3643142 bytes, checksum: 1f5335f433b80cbcbe58f559422c4f72 (MD5)Made available in DSpace on 2015-06-17T12:02:56Z (GMT). No. of bitstreams: 1 470517 - Texto Completo.pdf: 3643142 bytes, checksum: 1f5335f433b80cbcbe58f559422c4f72 (MD5) Previous issue date: 2015-01-07Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPESThis work presents the simultaneous conduction mode (SCM), which is applied to the operation of the Zeta converter. This mode has the ability to implement an ideal power factor corrector (PFC) employing only one feedback control loop. In SCM, the current in the main switch and in the diode flows simultaneously within one of the operation stages. In SCM, the power converter presents characteristics of both conduction modes: continuous conduction mode (CCM) and discontinuous conduction mode (DCM). In SCM, the currents in the inductors of the power converter are never nullified, which is a typical behavior of the CCM. Nevertheless, the SCM does that while obtaining an ideal PFC with just one control loop. The SCM maintains its features, regardless of its control variable being the output current or the output voltage of the power converter. The solely application of a fixed duty cycle controller is enough to attain all these advantages, which is usually a feature of the DCM for PFCs of the flyback family. In order to validate the proposed technique, a complete study of the Zeta converter working in this new operation mode was performed.This study has included a qualitative and a quantitative power converter analysis. These analyses resulted in the development of a design methodology for the Zeta power converter working as a PFC in the SCM. In order to validate the present study, a prototype of the Zeta PFC for operation in the SCM was designed and built. This prototype was developed, as a case of study, to drive a power LED lamp (180?W). Thus, it was obtained the desired experimental confirmation for the research. The main advantage of the SCM, in comparison to the CCM, lies in its ability to maintain the input current of the PFC sinusoidal and in phase with the input voltage, which is imposed by the mains through the use of just a single PWM controller with fixed duty cycle. These results have, also, shown that the current peaks in the main semiconductors of the power converter are lower than their respective values in the DCM. However, this new operation mode results in the increase of the voltages on the main switch and diode in relation to the conventional power converter operation. The research of the application of the proposed method to other power converters is suggested to further works.Este trabalho prop?e a opera??o do conversor Zeta no modo de condu??o simult?nea (MCS), cujo interesse reside na capacidade de implementa??o de um pr?-regulador do fator de pot?ncia (PFP) ideal empregando apenas um la?o de realimenta??o. Quando o conversor trabalha no MCS, a chave principal e o diodo conduzem simultaneamente em um de seus est?gios de opera??o. Neste modo de condu??o, o conversor est?tico apresenta caracter?sticas de ambos os modos de condu??o conhecidos at? agora: o modo de condu??o cont?nua (MCC) e o modo de condu??o descont?nua (MCD). A opera??o no MCS resulta em um conversor est?tico operando como se estivesse no MCC, uma vez que a corrente nos indutores nunca se anula. Embora mantenha o conversor est?tico trabalhando com esta caracter?stica do MCC, o MCS permite a obten??o de um comportamento quase ideal do PFP, utilizando apenas um ?nico controlador, seja ele de corrente ou de tens?o, o qual mant?m a raz?o c?clica do conversor constante, assim como usualmente ocorre com os PFPs da fam?lia redutor-elevador quando operam no MCD.Visando validar esta t?cnica, foi realizado um estudo do conversor operando desta forma que incluiu o desenvolvimento das an?lises qualitativa e quantitativa do conversor, as quais culminaram na elabora??o de uma metodologia de projeto. Assim, realizou-se o projeto de um PFP, baseado no conversor Zeta, para energizar uma lumin?ria LED de 180 W, operando no MCS, como estudo de caso. A lumin?ria utilizada ? o modelo High Power LED Baylight da empresa Luckysunny?. Os resultados obtidos experimentalmente validaram a estrat?gia proposta, uma vez que, com a opera??o do conversor Zeta no MCS reduz-se a ondula??o (ripple) da corrente nos semicondutores em rela??o ? opera??o no MCD. A principal vantagem da opera??o no MCS reside no fato deste manter a corrente de entrada do PFP senoidal em fase com a tens?o imposta pela rede el?trica com apenas uma malha de controle da vari?vel de sa?da de interesse seja ela tens?o ou corrente como no estudo de caso em quest?o. Isto reduz o custo e a complexidade do controlador do conversor. Entretanto, esta estrat?gia apresenta sobretens?o na chave principal e no diodo como principal desvantagem. Sugere-se a investiga??o da aplica??o da metodologia de projeto proposta a outros conversores