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Search Results: 1 - 10 of 2545 matches for " Silvana Ilie "
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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
Seeds for effective oligonucleotide design
Lucian Ilie, Silvana Ilie, Shima Khoshraftar, Anahita Bigvand
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-280
Abstract: We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.An oligonucleotide is a short DNA or RNA sequence. It is usually designed to hybridize with a unique position in a target sequence. In this way the target sequence can be uniquely identified using the oligonucleotide as a probe. DNA oligonucleotides have many applications such as gene identification, PCR (polymerase chain reaction) amplification, or DNA microarrays.Many software programs have been written to construct good DNA oligonucleotides, such as ProbeSelect [1], PROBESEL [2], ProMide [3], OligoArray [4,5], ArrayOligoSelector [6], OligoWiz [7], ROSO [8], GoArrays [9], and ProDesign [10]. One crucial issue in designing good oligonucleotides is to minimize the chance of cross-hybridization. Unsuitable regions are filtered out before checking for cross-hybridization. The underlying algorithms of these software programs are based on one or more of the following tools: suffix trees, suffix arrays, sequence alignments, seeds. Those based on seeds are very good, due to the increased accuracy and efficiency. However, their performance depends heavily on the seeds they use and our main goal here is to find the best seeds for oligonucleotide design.Seeds were made highly popu
The inheritance rights of the surviving spouse provided by the romanian law
Urs,Ilie;
Revista de derecho (Valparaíso) , 2009, DOI: 10.4067/S0718-68512009000100005
Abstract: in the old romanian law succession, the transmission was governed by legislation that was under the influence of roman law. the surviving spouse was quite at a disadvantage compared to the blood relatives of the defunct. the unfair succession situation of the surviving spouse was the object of vehement criticism in the romanian doctrine. nowadays, the inheritance rights of the surviving spouse are regulated by law nr. 319 of 10th june 1944 for the inheritance right of the surviving spouse that implicitly abrogated the dispositions of article 679, 681-684 of the romanian civil code. thus, according to law nr. 319 of 10th june 1944, the surviving spouse has three distinctive succession rights: i) a general inheritance right, in competition with any of the classes of heirs i-iv; ii) a special inheritance right over the movable goods and objects belonging to the household and over the wedding gifts; iii) a temporary right of occupancy of the house.
The Sale with Repurchase Clause
Urs,Ilie;
Revista de derecho (Valparaíso) , 2010, DOI: 10.4067/S0718-68512010000200002
Abstract: the sale with repurchase clause was regulated in 1864 by the civil code, within the meaning of articles 1371-1387, as a variety of sale affected by a cancellation condition. the sale with repurchase clause was frequently used in practice in order to breach the public provisions of article 1689 of the romanian civil code, on mortgage matters. taking into consideration that the sale with repurchase clause was actually a way to breach the provisions of article 1689 of the romanian civil code, giving birth to a lot of abuses on the part of the creditors, the romanian legislator decided to prohibit this type of sale. we also consider that, de lege ferenda, the implementation of a new prohibition law of the sale with repurchase clause is both necessary and useful.
NATO CONCEPT EVOLUTION – CONSEQUENCE OF THE CHANGES OCCURRED IN THE INTERNATIONAL SECURITY ENVIRONMENT
Marin ILIE
Journal of Defense Resources Management , 2010,
Abstract: We initiated our endeavor staring from an undisputed reality, that is, NATO changes its strategies and, implicitly, concepts, according to the developments occurred in the international security environment, in order to be able to respond to any challenge operatively and adequately. We would like to emphasize that regardless of the concepts formulation and application, the Organization’s fundamental values, and particularly its purely defensive character and the principle of collective defense do not alter.
THE NEW STRATEGIC CONCEPT NATO 2010
Marin ILIE
Journal of Defense Resources Management , 2011,
Abstract: NATO (The North Atlantic Treaty Organization) – OTAN (Organisation du Traité de l’Atlantique Nord) has been, since its estabslishment, oustandingly receptive to the international security environment developments and has always altered its strategy and strategic concepts in order to meet the afferent challenges, with an emphasis on its purely defensive character. The most favorable moment of this kind have been its summits: Rome (1991), Washington (1999) and Lisbon (2010), on which our paper will focus. The greats mutations in the last decade have called for the creation of the new strategic concept NATO 2010, developed in the Lisbon summit declaration of 19-20 November 2010.
PUBLIC TREASURY IN THE CONTEXT OF GLOBALIZED FINANCIAL MARKETS
Drago? Ilie
Studia Universitatis Vasile Goldis Arad, Seria Stiinte Economice , 2011,
Abstract: In the development and functioning process of the economy, the financing of current andinvestment activities is a key factor, the mobilization of necessary funds being possible bythe existence of financial markets. In the financial markets, public treasury plays a key role.The economic crisis has left economies without cash and the banking system was unable tosecure, through the mechanism of credit, the necessary resources for the normal functioningof economy. In these circumstances the Public Treasury must take seriously intoconsideration, as an option for the future, the development of banking operations and toattract available state funds on the financial markets.
Aspects of Implementation of European Law in the Legal System of the Republic of Moldova within the European Integration Process
Ilie Mamaliga
Acta Universitatis Danubius : Administratio , 2011,
Abstract: The author researches in this paper the political, economic and legal trends, concerning the integration of Moldova into the European Union. The greet The researcher pays attention to the principles of freedom and pluralistic democracy, supremacy of national European law over the law, in the non-discrimination and equality before the law, reflected in the European and national acts, as well as the principles of the market economy.
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