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A guide to membrane computing

Gheorghe Păun, Grzegorz Rozenberg
2002 Theoretical Computer Science  
the biological background and the mathematical formalism used, not only there are already proposed many types of P systems, but the flexibility and the versatility of P systems seem to be, in p rinciple  ...  This is a comprehensive (and -supposed -friendly) introduction to membrane computing, meant to offer both to computer scientists and to non-computer scientists an up-dated overview of the domain.  ...  A Formal Definition of a Transition P System Systems based on multiset-rewriting rules as above are usually called trans ition P systems, and we preserve here this terminology (although "transitions" are  ... 
doi:10.1016/s0304-3975(02)00136-6 fatcat:u5gj4rfjr5guva3aggjsfjozi4

Towards a Programming Language in Cellular Computing

Miguel A. Gutiérrez-Naranjo, Mario J. Pérez-Jiménez, Agustín Riscos-Núñez
2005 Electronical Notes in Theoretical Computer Science  
In this paper we present a new solution, to the Partition problem, via a family of deterministic P systems with active membranes using 2-division.  ...  Several solutions to hard numerical problems using P systems have been presented recently, and strong similarities in their designs have been noticed.  ...  Acknowledgement The support this research through the project TIC2002-04220-C03-01 of the Ministerio de Ciencia y Tecnología of Spain, cofinanced by FEDER funds, is gratefully acknowledged.  ... 
doi:10.1016/j.entcs.2004.04.044 fatcat:7pzgqrolora4lnh74jufmuf23y

MAREX: A general purpose hardware architecture for membrane computing

Daniel Cascado-Caballero, Fernando Diaz-del-Rio, Daniel Cagigas-Muñiz, Antonio Rios-Navarro, Jose-Luis Guisado-Lizar, Ignacio Pérez-Hurtado, Agustín Riscos-Núñez
2021 Information Sciences  
Membrane computing is an unconventional computing paradigm that has gained much attention in recent decades because of its massively parallel character and its usefulness to build models of complex systems  ...  In this paper, a first intrinsically parallel hardware architecture to implement generic P system models is introduced.  ...  This work opens new research lines, specially promising for the practical resolution of problems where P systems have already demonstrated their potential.  ... 
doi:10.1016/j.ins.2021.10.064 fatcat:ehlmwn5auregbe3q7e7mljkxfq

How Computational Models Enable Mechanistic Insights into Virus Infection [chapter]

Ivo F. Sbalzarini, Urs F. Greber
2018 Msphere  
We discuss how computational implementations of mathematical models can assist and enhance the quantitative measurements of infection dynamics of enveloped and non-enveloped viruses and thereby help generating  ...  We discuss how computational implementations of mathematical models can assist and enhance the quantitative measurements of infection dynamics of enveloped and non-enveloped viruses, and thereby help generating  ...  Deterministic models might be implemented for simulating the disruption of a non-enveloped virion, where the interactions between capsid proteins are known in atomic detail.  ... 
doi:10.1007/978-1-4939-8678-1_30 pmid:30151595 fatcat:7pbezksan5cv3dm5ixkcnypymi

An interactive timeline of simulators in membrane computing

Luis Valencia-Cabrera, David Orellana-Martín, Miguel Ángel Martínez-del-Amor, Mario J. Pérez-Jiménez
2019 Journal of Membrane Computing  
computing (a.k.a P systems), aiming to stay updated whenever any new practical work comes out in the discipline.  ...  This paper recalls the main stages and milestones within the evolution of simulation tools for different types and variants of P systems, along with their main related applications.  ...  search space working non-deterministically on a number of "processors".  ... 
doi:10.1007/s41965-019-00016-z fatcat:qfooqodxefbcbadrr4ealb53my

Spatial Calculus of Looping Sequences

Roberto Barbuti, Andrea Maggiolo–Schettini, Paolo Milazzo, Giovanni Pardini
2009 Electronical Notes in Theoretical Computer Science  
Such descriptions can then be used to simulate the systems, so as to obtain a faithful representation of their evolution.  ...  Handling spatial information in a simulator may have a high computational cost.  ...  In the field of natural computing, P systems [47, 11, 48] have been defined as a computational formalism based on the description of interactions inside membranes.  ... 
doi:10.1016/j.entcs.2009.02.003 fatcat:qmaaodbokfa7hh3uyiizqdoxba

Looking for Computers in the Biological Cell. After Twenty Years [chapter]

Gheorghe Păun
2016 Emergence, Complexity and Computation  
, of a computational type, can not only ensure a better use of the existing computers, the electronic ones, but they can also return to the starting point, as tools for biological investigations.  ...  Looking to the cell through the mathematician-computer scientist glasses, this is the short description of the present approach, and in this area it is placed the personal research experience which the  ...  Processing of multisets (of symbols), in parallel, in the compartments defined by a hierarchical structure of membranes -this is the short description of a "P system".  ... 
doi:10.1007/978-3-319-33924-5_30 fatcat:5un6zuvwvfchbbqazd5h4eru3y

The ReaxFF reactive force-field: development, applications and future directions

Thomas P Senftle, Sungwook Hong, Md Mahbubul Islam, Sudhir B Kylasa, Yuanxia Zheng, Yun Kyung Shin, Chad Junkermeier, Roman Engel-Herbert, Michael J Janik, Hasan Metin Aktulga, Toon Verstraelen, Ananth Grama (+1 others)
2016 npj Computational Materials  
full dynamic evolution of a system.  ...  This article provides an overview of the development, application, and future directions of the ReaxFF method.  ...  MC methods are most useful when the properties of interest in a system are dominated by thermodynamic driving forces (i.e., when kinetic factors do not limit the deterministic evolution of the system).  ... 
doi:10.1038/npjcompumats.2015.11 fatcat:iukcentvxbfxxdq5vevkd6naba

Nonclassical Computation — A Dynamical Systems Perspective [chapter]

Susan Stepney
2012 Handbook of Natural Computing  
My thanks to Andy Adamatzky, Leo Caves, Ed Clark, Simon Hickinbotham, Mic Lones, Adam Nellis, Ed Powley, and Jon Timmis for comments on a previous draft.  ...  Acknowledgements My thanks to Ed Powley for providing figures 1, 3, 4, and 18, and for drawing my attention to the work on exact correspondences between CAs and PDEs in section 2.3.4.  ...  P-Systems. Pȃun's P-systems [71] , and other membrane computing formalisms, are another form of rewriting systems with an underlying tree-structured topology.  ... 
doi:10.1007/978-3-540-92910-9_59 fatcat:bdmfgi5rrjcufnkigqiomece3y

Rewriting Logic Specification of Membrane Systems with Promoters and Inhibitors

Oana Agrigoroaiei, Gabriel Ciobanu
2009 Electronical Notes in Theoretical Computer Science  
Membrane systems represent a new model of computation involving parallel application of rules, communication between membranes and dissolving.  ...  Dynamic allocation allows translation of the maximal parallel application of membrane rules into sequential rewritings. An implementation in Maude is provided.  ...  We give an example of membrane system, chosen such that its evolution will be non-trivial in all three stages: 1 ' & $ % 2 ' & $ % 3 A A → δ B C B → (C, here)δ| C C → (B, here)(A, out) 4 A C A → (B, here  ... 
doi:10.1016/j.entcs.2009.05.010 fatcat:za7i4bica5ftvkmvrcjuejieey

DNA Computing — Foundations and Implications [chapter]

Lila Kari, Shinnosuke Seki, Petr Sosík
2012 Handbook of Natural Computing  
The symbol ⊥ ∈ ∆ makes it possible for an observer O to distinguish bad evolutions by a sticker system γ from good ones in a way that the observation of bad evolutions leads to the output of ⊥.  ...  Formally speaking, configurations of a sticker system, which are elements of Σ * d , are observed so that an observer is implemented as a finite automaton which works on elements of Σ * d .  ... 
doi:10.1007/978-3-540-92910-9_33 fatcat:n3zmhzpj5rgsphmurdophcg234

Journeys in non-classical computation II: initial journeys and waypoints

Susan Stepney, Samuel L. Braunstein, John A. Clark, Andy Tyrrell, Andrew Adamatzky, Robert E. Smith, Tom Addis, Colin Johnson, Jonathan Timmis, Peter Welch, Robin Milner, Derek Partridge
2006 International Journal of Parallel, Emergent and Distributed Systems  
A start was made in establishing the verification of computer programs as an activity in formal logic [32, 40] .  ...  States and their transitions tend to be predefined, and the execution of the transitions has to be explicitly implemented by the computational system.  ... 
doi:10.1080/17445760500355454 fatcat:amvihccwmvbvviswdc5344cu5m

9. Computational Chemistry Experiment Possibilities [chapter]

Bartłomiej M. Szyja, Danny Vanpoucke, Vincent Blay, Luis Francisco Bobadilla, Alejandro Cabrera García
2018 Zeolites and Metal-Organic Frameworks  
Fitting the parameters of the state equation also has the advantage of allowing a calculation of the transition pressure P t in a breathing MOF.  ...  As a result, varying the crystal momentum (p=ħk) will lead to a change in the energy of the electron.  ...  in the early days of Quantum Chemistry that a non-wave-function based description could exist.  ... 
doi:10.1515/9789048536719-010 fatcat:75wi6deitbff5cdpbifgvw5tje

Mathematical and computational modeling in biology at multiple scales

Jack A Tuszynski, Philip Winter, Diana White, Chih-Yuan Tseng, Kamlesh K Sahu, Francesco Gentile, Ivana Spasevska, Sara Omar, Niloofar Nayebi, Cassandra DM Churchill, Mariusz Klobukowski, Rabab M El-Magd
2014 Theoretical Biology and Medical Modelling  
A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms.  ...  The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed.  ...  Acknowledgements The authors are grateful to the Natural Sciences and Engineering Research Council of Canada, the Li Ka Shing Institute of Applied Virology and the Alberta Cancer Foundation for funding  ... 
doi:10.1186/1742-4682-11-52 pmid:25542608 pmcid:PMC4396153 fatcat:aq4cuo4sebhijl2hddggtixssm

Reversible Computation in Petri Nets [article]

Kyriaki Psara
2021 arXiv   pre-print
In this respect, a further aim is to control reversibility by extending our formal semantics where transitions are associated with conditions whose satisfaction allows the execution of transitions in the  ...  Reversible computation is an unconventional form of computing that extends the standard forward-only mode of computation with the ability to execute a sequence of operations in reverse at any point during  ...  Such backward deterministic systems are the foundations of an alternative computation paradigm, called Re-versible Computation [40] .  ... 
arXiv:2101.07066v1 fatcat:tsse7k3zjfaxbltu7cuj3qjrsm
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