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Simplifying Stochastic Mathematical Models of Biochemical Systems  [PDF]
Silvana Ilie, Samaneh Gholami
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.41A038
Abstract:

Stochastic modeling of biochemical reactions taking place at the cellular level has become the subject of intense research in recent years. Molecular interactions in a single cell exhibit random fluctuations. These fluctuations may be significant when small populations of some reacting species are present and then a stochastic description of the cellular dynamics is required. Often, the biochemically reacting systems encountered in applications consist of many species interacting through many reaction channels. Also, the dynamics of such systems is typically non-linear and presents multiple time-scales. Consequently, the stochastic mathematical models of biochemical systems can be quite complex and their analysis challenging. In this paper, we present a method to reduce a stochastic continuous model of well-stirred biochemical systems, the Chemical Langevin Equation, while preserving the overall behavior of the system. Several tests of our method on models of practical interest gave excellent results.

Automatic Simulation of the Chemical Langevin Equation  [PDF]
Silvana Ilie, Monjur Morshed
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.41A036
Abstract:

Biochemical systems have important practical applications, in particular to understanding critical intra-cellular processes. Often biochemical kinetic models represent cellular processes as systems of chemical reactions, traditionally modeled by the deterministic reaction rate equations. In the cellular environment, many biological processes are inherently stochastic. The stochastic fluctuations due to the presence of some low molecular populations may have a great impact on the biochemical system behavior. Then, stochastic models are required for an accurate description of the system dynamics. An important stochastic model of biochemical kinetics is the Chemical Langevin Equation. In this work, we provide a numerical method for approximating the solution of the Chemical Langevin Equation, namely the derivative-free Milstein scheme. The method is compared with the widely used strategy for this class of problems, the Milstein method. As opposed to the Milstein scheme, the proposed strategy has the advantage that it does not require the calculation of exact derivatives, while having the same strong order of accuracy as the Milstein scheme. Therefore it may be used for an automatic simulation of the numerical solution of the Chemical Langevin Equation. The tests on several models of practical interest show that our method performs very well.

Efficient computation of spaced seeds
Silvana Ilie
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-123
Abstract: SpEED uses a hill climbing method based on the overlap complexity heuristic. We propose a new algorithm for this heuristic that improves its speed by over one order of magnitude. We use the new implementation to compute improved seeds for several software programs. We compute as well multiple seeds of the same weight as MegaBLAST, that greatly improve its sensitivity.Multiple spaced seeds are being successfully used in bioinformatics software programs. Enabling researchers to compute very fast high quality seeds will help expanding the range of their applications.The most frequently used tools in bioinformatics are those searching for similarities, or local alignments, between biological sequences. This problem can be solved exactly using the dynamic programming algorithm of Smith-Waterman in quadratic time. Many instances, including all database searches, are too large for this approach to be feasible and heuristic algorithms are used instead [1,2]. The most widely used program in bioinformatics, BLAST [2,3], is one such tool. It uses the so-called "hit and extend" approach: a hit consists of 11 consecutive matches between two sequences and represents a potential local alignment. The hit is then extended both ways in search for similarity.It is clear that not all local alignments have to include an identical stretch of length 11. It has been already noticed in [4] and then again in [5] that requiring that the matches are not consecutive increases the chances of finding alignments. The idea of optimizing the way the required matches are placed has been investigated in [6,7], the latter having used it in a similarity search software, PatternHunter. Much work has been dedicated to spaced seeds. For a survey of earlier work, we refer the reader to [8].The 11 consecutive matches of BLAST are called a contiguous seed, denoted 11111111111 (for 11 consecutive matches), whereas the one of PatternHunter is a spaced seed, 111*1**1*1**11*111; a 1 represents a match and * a don
Corpos, cadeiras, colares: Charlotte Perriand e Lina Bo Bardi
Rubino, Silvana;
Cadernos Pagu , 2010, DOI: 10.1590/S0104-83332010000100013
Abstract: the article explores the crossroads of the trajectories of two professional women linked to the production of space: the italian architect lina bo bardi, who worked in brazil, and the french designer charlotte perriand. the article begins by comparing two photographs and then investigates the performance of these two well-known professionals, their moments of exclusion, disqualification as well as success throughout their careers. as they both had long and diversified careers, we capture two moments when they produced the emblematic chairs, that they exhibited using their own bodies, albeit in a quite anonymous way, as an ergonometric measure.
Cristianismo y neoplatonismo en San Agustín: la crítica heideggeriana
Filippi,Silvana;
Enfoques , 2010,
Abstract: heidegger believes to find in st. augustine, as in the case of paul, the expression of human existence as a historic fact, and of history as non objectively or available fate. this radical facticity of self belongs to the christian earliest form of experience that appears with strong clearness in st. augustine's confessions, particularly in book x. there are two relevant aspects that stand out in the heideggerian reading of confessions: for one, the phenomenology of self, and secondly, the understanding of dasein as time. however, in st. augustine, the dramatic finitude of existence is metaphysically and theologically transcended and grounded; while in heidegger's reflection, the finitude of human existence tends to close itself on its own limits.
Gelassenheit: el desapego como forma de vida en la mística eckhartiana
Filippi,Silvana;
Enfoques , 2010,
Abstract: the notorious importance that eckhart gives to the detachment from things (gelassenheit) may suggest that the mystical german disdains active life. inversely, eckhart understands that the detachment in respect of the created being is perfectly compatible with the action and he even interprets the attitude of martha and mary towards jesus in a way which is opposite to the habitual.
Os resultados do Ideb no cotidiano escolar
Mesquita, Silvana;
Ensaio: Avalia??o e Políticas Públicas em Educa??o , 2012, DOI: 10.1590/S0104-40362012000300009
Abstract: this work is part of the master's research on " intra-school factors and school performance: what makes the difference?" this text presents the data collected during the investigation show that the impact of the disclosure of the results of the ideb on everyday life of a public school in rio de janeiro. aiming to integrate quantitative data, brought by the statistics of external evaluations, with the qualitative data from school of everyday life, if adopted as methodology the ethnographic approach. the researcher remained immersed in the field for six months gathering data through participant observation, interviews with managers and teachers, and track the activities in the classroom and analyze documents from school. it was adopted as theoretical studies of the sociology school establishments, in addition to research on effective schools in brazil, united states and england. it was possible to identify that data, collected through research of external evaluation are redirected within the school environment for their actors, but they nevertheless contribute to the understanding of the education system. it becomes evident that bringing the quantitative data with the point of view of the actors of the school community, one can understand the contributions of these two fields of research to reflect on the school and search for more quality.
Las Mo?ras y el Laberinto en la lírica borgeana: la fusión de dos mitos griegos
Pfeiffer,Silvana;
Synthesis (La Plata) , 2005,
Abstract: the literary originality of jorge luis borges is notable in his peculiar employment of myths proceeding from diverse cultural ambits. the purpose of this paper is to analyze the innovations that borges effect when he links two hellenics myths: the myth of the mo?ras and the myth of the labyrinth.
Antologia: escrita compilada, discurso e capital simbólico
Serrani, Silvana;
Alea : Estudos Neolatinos , 2008, DOI: 10.1590/S1517-106X2008000200008
Abstract: this article discusses, from a discourse analysis perspective, general properties of anthologies, as paradigmatic realizations of compiled writing. formal distinctions (such as miscellany/anthology) and general characteristics attributed to the genre (for instance, the decontextualization of contents) are questioned and discursive effects of geopolitical-cultural representations in anthologies are also examined. the main claim is that conceiving anthologies as discourse allows us to go further in the comprehension of the genre's materiality and functioning. illustrations are mainly drawn from anthologies belonging to hispanic studies, but references to other contexts are also made. the proposal of a discursive comparative analysis is presented, searching to deepen the comprehension of the anthology's functions as a memory and cultural legacy, an instrument of criticism and a symbolic capital. results from a case study on bilingual anthologies of argentinian poetry are presented. to conclude, the relevance of the anthology regarding the notion of cultural trans-nationality is underlined.
La representación de las relaciones interétnicas en el discurso de Antonio Viedma (Patagonia Meridional, sigLo XVIII)
BUSCAGLIA,SILVANA;
Magallania (Punta Arenas) , 2011, DOI: 10.4067/S0718-22442011000200002
Abstract: the aim of this paper is to analyze the interethnic relationship construction at the spanish colony of floridablanca (san julián, santa cruz province, 18th century). our analytic perspective integrates the discourses and daily practices from information provided by historical sources. in particular, we evaluate the representation of local tehuelches (aonikenk) in antonio viedma′s discourse, considering the implications of contact and indigenous practices for the implementation of the ideal society which sought to promote in the colony.
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