scholarly journals On the Concepts of Parallelism in Biomolecular Computing

Triangle ◽  
2018 ◽  
pp. 109
Author(s):  
Remco Loos ◽  
Bendek Nagy

In this paper we consider DNA and membrane computing, both as theoretical models and as problem solving devices. The basic motivation behind these models of natural computing is using parallelism to make hard problems tractable. In this paper we analyze the concept of parallelism. We will show that parallelism has very different meanings in these models.We introduce the terms ’or-parallelism’ and ’and-parallelism’ for these two basic types of parallelism.

Author(s):  
Gheorghe Paun

Membrane computing is a branch of natural computing whose initial goal was to abstract computing models from the structure and the functioning of living cells. The research was initiated about five years ago (at the end of 1998), and since that time the area has been developed significantly from a mathematical point of view. The basic types of results of this research concern the computability power (in comparison with the standard Turing machines and their restrictions) and the efficiency (the possibility to solve computationally hard problems, typically NP-complete problems, in a feasible time and typically polynomial). However, membrane computing has recently become attractive also as a framework for devising models of biological phenomena, with the tendency to provide tools for modelling the cell itself, not only the local processes. This chapter surveys the basic elements of membrane computing, somewhat in its “historical” evolution: from biology to computer science and mathematics and back to biology. The presentation is informal, without any technical detail, and an invitation to membrane computing intended to acquaint the nonmathematician reader with the main directions of research of the domain, the type of central results, and the possible lines of future development, including the possible interest of the biologist looking for discrete algorithmic tools for modelling cell phenomena.


2014 ◽  
Vol 22 (1) ◽  
pp. 18-33 ◽  
Author(s):  
Mario J. Pérez-Jiménez

In the last few decades several computing models using powerful tools from Nature have been developed (because of this, they are known as bio-inspired models). Commonly, the space-time trade-off method is used to develop efficient solutions to computationally hard problems. According to this, implementation of such models (in biological, electronic, or any other substrate) would provide a significant advance in the practical resolution of hard problems. Membrane Computing is a young branch of Natural Computing initiated by Gh. Păun at the end of 1998. It is inspired by the structure and functioning of living cells, as well as from the organization of cells in tissues, organs, and other higher order structures. The devices of this paradigm, called P systems or membrane systems, constitute models for distributed, parallel and non-deterministic computing. In this paper, a computational complexity theory within the framework of Membrane Computing is introduced. Polynomial complexity classes associated with different models of cell-like and tissue-like membrane systems are defined and the most relevant results obtained so far are presented. Different borderlines between efficiency and non-efficiency are shown, and many attractive characterizations of the P ≠ NP conjecture within the framework of this bio-inspired and non-conventional computing model are studied.


2021 ◽  
Vol 182 (3) ◽  
pp. 243-255
Author(s):  
Yu Jin ◽  
Bosheng Song ◽  
Yanyan Li ◽  
Ying Zhu

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of living cells. The computation models obtained in the field of membrane computing are usually called P systems. P systems have been used to solve computationally hard problems efficiently on the assumption that the execution of each rule is completed in exactly one time-unit (a global clock is assumed for timing and synchronizing the execution of rules). However, in biological reality, different biological processes take different times to be completed, which can also be influenced by many environmental factors. In this work, with this biological reality, we give a time-free solution to independent set problem using P systems with active membranes, which solve the problem independent of the execution time of the involved rules.


2020 ◽  
pp. 026666692097618
Author(s):  
Consuelo Garcia ◽  
Esther Argelagós ◽  
Jesús Privado

Many of the current tests that evaluate information problem-solving skills suffer from ecological validity weakness and from library-bias. The Procedural Information Problem-Solving Knowledge Evaluation in Education test (PIKE-E) aims to assess information problem-solving skills of college students in relation to an academic literature review task in educational sciences. It entails a confirmatory analysis of the PIKE-P test in which it is based. The PIKE-E was completed by 700 students from three different Spanish-speaking countries. In our research, we do not assume that information problem solving skills at the international and cultural level are equal, but Internet access is practically the same in higher education. Results show the existence of five first-order factors, Defining the research question, Search strategies planning, Searching and locating sources, Selecting and processing information and Organizing and presenting information, and a general single second-order factor, Information problem-solving, which coincide with contemporary theoretical models on information literacy. The PIKE-E can be used to tackle in which specific areas concerning information skills development, students entering education degrees need to improve to succeed in their studies.


Author(s):  
Gabriel Ciobanu

<p>Essentially writing is form of thinking on paper, and a way of learning. According to Winston Churchill, writing a book is an adventure. "To begin with, it is a toy and an amusement; then it becomes a mistress, and then it becomes a master, and then a tyrant. The last phase is that just as you are about to be reconciled to your servitude, you kill the monster, and fling him out to the public." On the other hand, writing could be a form of freedom by escaping the madness of a period, and reducing the anxiety. In many situations the authors write to save themselves, to survive as individuals.</p><p>Gheorghe Păun is an example of a person affirming his own existence by writing. He is a prolific writer with a huge number of papers: tens of scientific books, hundreds of articles, several novels, poems, and books on games. A list of his scientific publications is posted at http://www.imar.ro/~gpaun/papers.php [2], while his books are listed at http://www.imar. ro/~gpaun/books.php [1] His way of distributing information is not by speaking, but by writing. Gheorghe Păun did not like very much to teach in universities. He preferred a form of "teaching by researching", combining ideas with nice metaphors and distributing his knowledge in articles and books. In this way he wrote several papers having a high impact in the scientific community. His seminal paper "Computing with membranes" published in Journal of Computers and System Sciences in 2000 and his fundamental book on computation theory "Membrane Computing" (Springer, 2003) has over 1,000 citations [6] (and his author was recognized as an "ISI highly cited researcher" [5]). He has defined new branches, new theories. The field of membrane computing was initiated by Gheorghe Păun as a branch of natural computing [3]; P systems are inspired by the hierarchical membrane structure of eukaryotic cells [4]. An impressive handbook of membrane computing was published recently (2010) by Oxford University Press.</p><p> </p><p>After 1990 he becomes a traveling scientist, visiting several countries and receiving many research fellowships and awards. Fruitful scientific collaboration at Magdeburg University (Germany), and at University of Turku (Finland). The trio Gheorghe Păun, Grzegorz Rozenberg and Arto Salomaa is well-known for several successful books. The last years were spent in Spain, first in Tarragona and now in Sevilla. Several collaborations were possible during his trips, and there are over 100 co-authors from many countries. His scientific reputation is related to the large number of invited talks provided at many international conferences and universities. He is a member of the editorial boards for several international journals, corresponding member of the Romanian Academy (from 1997), and member of Academia Europaea (from 2006).<br /> It is not possible to understand the personality of Gheorghe Păun without mentioning his activity as writer of novels and poems; he is a member of the Romanian Writers Association for a long time. Another aspect of his life is related to the intellectual seduction of games; he was the promoter of GO in Romania, writing many books about GO and other "mathematical" games.</p><p><br /> Personally, I am impressed by the speed of his mind (it is enough to say few words about some new results, and he is able to complete quickly the whole approach), his wide-ranging curiosity and intelligence, rich imagination and humor, talent and passion. He is highly motivated by challenging projects, and work hard to conclude them successfully. There are very few scientists having such an interesting profile, and I am very happy to learn a lot from him.</p><p><br /> Celebrating his 60th birthday, we wish him a good health, long life, and new interesting achievements!</p>


Author(s):  
Giancarlo Mauri ◽  
Gheorghe Păun ◽  
Agustín Riscos-Núñez

<p>The present volume contains a selection of papers resulting from the Seventh Brainstorming Week on Membrane Computing (BWMC7), held in Sevilla, from February 2 to February 6, 2009. The meeting was organized by the Research Group on Natural Computing (RGNC) from Department of Computer Science and Artificial Intelligence of Sevilla University. The previous editions of this series of meetings were organized in Tarragona (2003), and Sevilla (2004 – 2008). After the first BWMC, a special issue of Natural Computing – volume 2, number 3, 2003, and a special issue of New Generation Computing – volume 22, number 4, 2004, were published; papers from the second BWMC have appeared in a special issue of Journal of Universal Computer Science – volume 10, number 5, 2004, as well as in a special issue of Soft Computing – volume 9, number 5, 2005; a selection of papers written during the third BWMC has appeared in a special issue of International Journal of Foundations of Computer Science – volume 17, number 1, 2006); after the fourth BWMC a special issue of Theoretical Computer Science was edited – volume 372, numbers 2-3, 2007; after the fifth edition, a special issue of International Journal of Unconventional Computing was edited – volume 5, number 5, 2009; finally, a selection of papers elaborated during the sixth BWMC has appeared in a special issue of Fundamenta Informaticae</p>


2020 ◽  
pp. 659-678
Author(s):  
Andrei George Florea ◽  
Cătălin Buiu

In order to use membrane computing models for real life applications there is a real need for software that can read a model from some form of input media and afterwards execute it according to the execution rules that are specified in the definition of the model. Another requirement of this software application is for it to be capable of interfacing the computing model with the real world. This chapter discusses how this problem was solved along the years by various researchers around the world. After presenting notable examples from the literature, the discussion continues with a detailed presentation of three membrane computing simulators that have been developed by the authors at the Laboratory of Natural Computing and Robotics at the Politehnica University of Bucharest, Romania.


2017 ◽  
Vol 7 (3) ◽  
pp. 183-200 ◽  
Author(s):  
Corina Rotar ◽  
Laszlo Barna Iantovics

Abstract Recently, we have witnessed an infusion of calculating models based on models offered by nature, models with more or less fidelity to the original that have led to the development of various problem-solving computational procedures. Starting from the observation of natural processes at the macroscopic or microscopic level, various methods have been developed. Technological progress today allows the accelerated reproduction of natural phenomena in the laboratory, which is why a new niche has arisen in the landscape of nature-inspired methods. This niche is devoted to the emulation of artificial biological processes in computational problem-solving methods. This paper proposes a novel approach, which is to develop novel computational methods in the field of Natural Computing based on the semi-natural process, namely Directed Evolution. In the first step we explain Directed Evolution, defined as the artificial reproduction of the process of evolution in the laboratory in order to obtain performing biological entities. For computer scientists, this provide a strong source of inspiration in the search for efficient methods of optimization. The computational model that proposed here largely overlaps with the Directed Evolution protocol, and the results obtained in the numerical experiments confirm the viability of such techniques inspired by processes which are more artificial than natural. The paper describes a novel general algorithm, inspired by Directed Evolution, which is able to solve different optimization problems, such as single optimization, multiobjective optimization and combinatorial optimization problems.


2013 ◽  
Vol 655-657 ◽  
pp. 1761-1764 ◽  
Author(s):  
Hai Na Rong ◽  
Xiao Li Huang

As a branch of natural computing, membrane computing has attracted much attention in various disciplines. But the programmability of membrane computing models is an ongoing and challenging issue in this area. This paper develops the automatic design of membrane computing models through predefining the membrane structure and initial objects and introducing a modified quantum-inspired evolutionary algorithm with a local disturbance to select an appropriate subset from a redundant evolution rule set. The main idea of the presented method is that multiple membrane computing models, instead of only one model like in the literature, can be designed by applying one redundant evolution rule set. The effectiveness of the design method is verified by the experiments.


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