Natural Computing, Volume 10

Volume 10, Number 1, March 2011

• Roberto Barbuti, Giuditta Franco, Gheorghe Paun:
  Foreword. 1-2
  
• Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini, Luca Tesei:
  Spatial P systems. 3-16
  
• Francesco Bernardini, Robert Brijder, Matteo Cavaliere, Giuditta Franco, Hendrik Jan Hoogeboom, Grzegorz Rozenberg:
  On aggregation in multiset-based self-assembly of graphs. 17-38
  
• Mónica Cardona, M. Angels Colomer, Antoni Margalida, Antoni Palau, Ignacio Pérez-Hurtado, Mario J. Pérez-Jiménez, Delfí Sanuy:
  A computational modeling for real ecosystems based on P systems. 39-53
  
• Alberto Castellini, Giuditta Franco, Roberto Pagliarini:
  Data analysis pipeline from laboratory to MP models. 55-76
  
• Michael Cauchi, Luca Bianco, Conrad Bessant:
  The quantification of pollutants in drinking water by use of artificial neural networks. 77-90
  
• Vincenzo Cutello, Giuseppe Morelli, Giuseppe Nicosia, Mario Pavone, Giuseppe Scollo:
  On discrete models and immunological algorithms for protein structure prediction. 91-102
  
• Eugen Czeizler, Lila Kari:
  Towards a neighborhood simplification of tile systems: From Moore to quasi-linear dependencies. 103-117
  
• Ángel Goñi Moreno, Miguel Redondo-Nieto, Fernando Arroyo, Juan Castellanos:
  Biocircuit design through engineering bacterial logic gates. 119-127
  
• Tom Head:
  Computing transparently: the independent sets in a graph. 129-138
  
• John Jack, Andrei Paun, Alfonso Rodríguez-Patón:
  A review of the nondeterministic waiting time algorithm. 139-149
  
• Raluca Lefticaru, Marian Gheorghe, Florentin Ipate:
  An empirical evaluation of P system testing techniques. 151-165
  
• Antonio E. Porreca, Alberto Leporati, Giancarlo Mauri, Claudio Zandron:
  P systems with active membranes: trading time for space. 167-182
  
• Jon Timmis, Paul S. Andrews, Susan Stepney:
  Editorial for special issue on the interaction between computation and biology. 187-188
  
• Wei Pang, George Macleod Coghill:
  An immune-inspired approach to qualitative system identification of biological pathways. 189-207
  
• Heder S. Bernardino, Helio J. C. Barbosa:
  Grammar-based immune programming. 209-241
  
• Martin Drozda, Sven Schaust, Sebastian Schildt, Helena Szczerbicka:
  Priming: making the reaction to intrusion or fault predictable. 243-274
  
• Mohd Zakree Ahmad Nazri, Siti Mariyam Hj. Shamsuddin, Azuraliza Abu Bakar, Salwani Abdullah:
  A hybrid approach for learning concept hierarchy from Malay text using artificial immune network. 275-304
  
• N. C. Woolley, J. V. Milanovic:
  An immune system inspired clustering and classification method to detect critical areas in electrical power networks. 305-333
  
• Russell Deaton:
  Forward. 335-336
  
• Aaron Sterling:
  Distributed agreement in tile self-assembly. 337-355
  
• Ya Meng, Navin Kashyap:
  The effect of malformed tiles on tile assemblies within the kinetic tile assembly model. 357-373
  
• Max H. Garzon, Tit-Yee Wong:
  DNA chips for species identification and biological phylogenies. 375-389
  
• Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon:
  NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. 391-405
  
• Luca Cardelli:
  Strand algebras for DNA computing. 407-428
  
• Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre, José M. Sempere:
  Complexity-preserving simulations among three variants of accepting networks of evolutionary processors. 429-445
  
• Urmi Majumder, John H. Reif:
  Design of a biomolecular device that executes process algebra. 447-466
  
• Ashish Goel, Morteza Ibrahimi:
  A renewable, modular, and time-responsive DNA circuit. 467-485
  
• Xiaoying Pan, Licheng Jiao, Fang Liu:
  An improved multi-agent genetic algorithm for numerical optimization. 487-506
  
• Teng Nga Sing, Jason Teo:
  Evolutionary and population dynamics of 3 parents differential evolution (3PDE) using self-adaptive tuning methodologies. 507-526
  
• Laura Diosan, Mihai Oltean:
  Friction-based sorting. 527-539
  
• Masud Hasan, S. M. Shabab Hossain, Md. Mahmudur Rahman, M. Sohel Rahman:
  Solving the generalized Subset Sum problem with a light based device. 541-550
  
• Fabio R. J. Vieira, Valmir C. Barbosa:
  Optimization of supply diversity for the self-assembly of simple objects in two and three dimensions. 551-581
  
• Vamsi Kundeti, Sanguthevar Rajasekaran:
  Efficient algorithms for self assembling non-rectangular nano structures. 583-594
  
• Ion Petre, Andrzej Mizera, Claire L. Hyder, Annika Meinander, Andrey Mikhailov, Richard I. Morimoto, Lea Sistonen, John E. Eriksson, Ralph-Johan Back:
  A simple mass-action model for the eukaryotic heat shock response and its mathematical validation. 595-612
  
• Niall Murphy, Damien Woods:
  The computational power of membrane systems under tight uniformity conditions. 613-632
  

Volume 10, Number 2, June 2011

• Monika Heiner:
  Preface: Petri nets for Systems and Synthetic Biology. 633-638
  
• Wolfgang Marwan, Annegret Wagler, Robert Weismantel:
  Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks. 639-654
  
• Annegret Wagler, Robert Weismantel:
  The combinatorics of modeling and analyzing biological systems. 655-681
  
• Kurt Lautenbach, Alexander Pinl:
  A Petri net representation of Bayesian message flows: importance of Bayesian networks for biological applications. 683-709
  
• Anastasia Pagnoni:
  Error-correcting Petri nets. 711-725
  
• Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry:
  Petri net representation of multi-valued logical regulatory graphs. 727-750
  
• David Angeli:
  Boundedness analysis for open Chemical Reaction Networks with mass-action kinetics. 751-774
  
• Erzsébet Csuhaj-Varjú, Kai Salomaa:
  Editorial: Computing with biomolecules. 775-776
  
• Bogdan Aman, Gabriel Ciobanu:
  Mutual mobile membranes with objects on surface. 777-793
  
• Mark Daley, Ian McQuillan, James M. McQuillan, Kalpana Mahalingam:
  Theoretical and computational properties of transpositions. 795-804
  
• Giuditta Franco, Vincenzo Manca:
  Algorithmic applications of XPCR. 805-819
  
• Rudolf Freund, Sergey Verlan:
  (Tissue) P systems working in the k-restricted minimally or maximally parallel transition mode. 821-833
  
• Alexander Krassovitskiy, Yurii Rogozhin, Sergey Verlan:
  Computational power of insertion-deletion (P) systems with rules of size two. 835-852
  
• Matthew J. Patitz, Scott M. Summers:
  Self-assembly of decidable sets. 853-877
  
• Elena Rivero-Gil, Miguel A. Gutiérrez-Naranjo, Álvaro Romero Jiménez, Agustin Riscos-Núñez:
  A software tool for generating graphics by means of P systems. 879-890
  
• Sarab Al Muhaideb, Mohamed El-bachir Menai:
  Evolutionary computation approaches to the Curriculum Sequencing problem. 891-920
  
• Marcin Budka, Bogdan Gabrys:
  Electrostatic field framework for supervised and semi-supervised learning from incomplete data. 921-945
  
• Fusheng Xiong, Wayne D. Frasch:
  Padlock probe-mediated qRT-PCR for DNA computing answer determination. 947-959
  
• Hans-Jörg Kreowski, Sabine Kuske:
  Graph multiset transformation: a new framework for massively parallel computation inspired by DNA computing. 961-986
  

Volume 10, Number 3, September 2011

• Monika Heiner:
  Preface: Petri nets for Systems and Synthetic Biology. 987-992
  
• Eva M. Rodriguez, Anita Rudy, Ricardo C. H. del Rosario, Angelika M. Vollmar, Eduardo R. Mendoza:
  A discrete Petri net model for cephalostatin-induced apoptosis in leukemic cells. 993-1015
  
• Louchka Popova-Zeugmann:
  Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks. 1017-1043
  
• Ruth Lamprecht, Gregory D. Smith, Peter Kemper:
  Stochastic Petri net models of Ca²⁺ signaling complexes and their analysis. 1045-1075
  
• Ming Chen, Sridhar Hariharaputran, Ralf Hofestädt, Benjamin Kormeier, Sarah Spangardt:
  Petri net models for the semi-automatic construction of large scale biological networks. 1077-1097
  
• Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
  Hybrid Petri net based modeling for biological pathway simulation. 1099-1120
  
• Natasha Jonoska, Gregory L. McColm, Ana Staninska:
  On stoichiometry for the assembly of flexible tile DNA complexes. 1121-1141
  
• Gerard Briscoe, Suzanne Sadedin, Philippe De Wilde:
  Digital Ecosystems: Ecosystem-Oriented Architectures. 1143-1194
  
• Andrew Adamatzky, Genaro Juárez Martínez, Sergio V. Chapa Vergara, René Asomoza-Palacio, Christopher R. Stephens:
  Approximating Mexican highways with slime mould. 1195-1214
  

Volume 10, Number 4, December 2011

• José Félix Costa, Nachum Dershowitz:
  Introduction. 1215-1217
  
• Masashi Aono, Yoshito Hirata, Masahiko Hara, Kazuyuki Aihara:
  Greedy versus social: resource-competing oscillator network as a model of amoeba-based neurocomputer. 1219-1244
  
• Ed Blakey:
  Unconventional complexity measures for unconventional computers. 1245-1259
  
• Jérôme Durand-Lose:
  Abstract geometrical computation 5: embedding computable analysis. 1261-1273
  
• Enrico Formenti, Jarkko Kari, Siamak Taati:
  On the hierarchy of conservation laws in a cellular automaton. 1275-1294
  
• Daniel S. Graça, Ning Zhong:
  Computability in planar dynamical systems. 1295-1312
  
• Ellie D'Hondt, Yves Vandriessche:
  Distributed quantum programming. 1313-1343
  
• Jeff Jones:
  Influences on the formation and evolution of Physarum polycephalum inspired emergent transport networks. 1345-1369
  
• Karl Svozil:
  Quantum value indefiniteness. 1371-1382
  
• Benjamin Wells:
  Unwinding performance and power on Colossus, an unconventional computer. 1383-1405
  
• Karthik Sindhya, Kalyanmoy Deb, Kaisa Miettinen:
  Improving convergence of evolutionary multi-objective optimization with local search: a concurrent-hybrid algorithm. 1407-1430
  
• Paskorn Champrasert, Junichi Suzuki, Tetsuo Otani:
  Evolutionary high-dimensional QoS optimization for safety-critical utility communication networks. 1431-1458
  

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