Volume 10, Number 1, March 2011

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  Roberto Barbuti, Giuditta Franco, Gheorghe Paun: Foreword. 1-2
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  Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini, Luca Tesei: Spatial P systems. 3-16
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  Francesco Bernardini, Robert Brijder, Matteo Cavaliere, Giuditta Franco, Hendrik Jan Hoogeboom, Grzegorz Rozenberg: On aggregation in multiset-based self-assembly of graphs. 17-38
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  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
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  Alberto Castellini, Giuditta Franco, Roberto Pagliarini: Data analysis pipeline from laboratory to MP models. 55-76
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  Michael Cauchi, Luca Bianco, Conrad Bessant: The quantification of pollutants in drinking water by use of artificial neural networks. 77-90
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  Vincenzo Cutello, Giuseppe Morelli, Giuseppe Nicosia, Mario Pavone, Giuseppe Scollo: On discrete models and immunological algorithms for protein structure prediction. 91-102
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  Eugen Czeizler, Lila Kari: Towards a neighborhood simplification of tile systems: From Moore to quasi-linear dependencies. 103-117
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  Ángel Goñi Moreno, Miguel Redondo-Nieto, Fernando Arroyo, Juan Castellanos: Biocircuit design through engineering bacterial logic gates. 119-127
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  Tom Head: Computing transparently: the independent sets in a graph. 129-138
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  John Jack, Andrei Paun, Alfonso Rodríguez-Patón: A review of the nondeterministic waiting time algorithm. 139-149
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  Raluca Lefticaru, Marian Gheorghe, Florentin Ipate: An empirical evaluation of P system testing techniques. 151-165
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  Antonio E. Porreca, Alberto Leporati, Giancarlo Mauri, Claudio Zandron: P systems with active membranes: trading time for space. 167-182
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  Jon Timmis, Paul S. Andrews, Susan Stepney: Editorial for special issue on the interaction between computation and biology. 187-188
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  Wei Pang, George Macleod Coghill: An immune-inspired approach to qualitative system identification of biological pathways. 189-207
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  Heder S. Bernardino, Helio J. C. Barbosa: Grammar-based immune programming. 209-241
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  Martin Drozda, Sven Schaust, Sebastian Schildt, Helena Szczerbicka: Priming: making the reaction to intrusion or fault predictable. 243-274
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  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
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  N. C. Woolley, J. V. Milanovic: An immune system inspired clustering and classification method to detect critical areas in electrical power networks. 305-333
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  Russell Deaton: Forward. 335-336
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  Aaron Sterling: Distributed agreement in tile self-assembly. 337-355
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  Ya Meng, Navin Kashyap: The effect of malformed tiles on tile assemblies within the kinetic tile assembly model. 357-373
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  Max H. Garzon, Tit-Yee Wong: DNA chips for species identification and biological phylogenies. 375-389
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  Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon: NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. 391-405
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  Luca Cardelli: Strand algebras for DNA computing. 407-428
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  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
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  Urmi Majumder, John H. Reif: Design of a biomolecular device that executes process algebra. 447-466
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  Ashish Goel, Morteza Ibrahimi: A renewable, modular, and time-responsive DNA circuit. 467-485
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  Xiaoying Pan, Licheng Jiao, Fang Liu: An improved multi-agent genetic algorithm for numerical optimization. 487-506
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  Teng Nga Sing, Jason Teo: Evolutionary and population dynamics of 3 parents differential evolution (3PDE) using self-adaptive tuning methodologies. 507-526
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  Laura Diosan, Mihai Oltean: Friction-based sorting. 527-539
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  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
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  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
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  Vamsi Kundeti, Sanguthevar Rajasekaran: Efficient algorithms for self assembling non-rectangular nano structures. 583-594
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  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
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  Niall Murphy, Damien Woods: The computational power of membrane systems under tight uniformity conditions. 613-632

Volume 10, Number 2, June 2011

Special issue "Petri Nets for Systems and Synthetic Biology, Part I: Bridging Gaps" Part II: Special issue "Computing with Biomolecules"

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

Special Issue "Petri Nets for Systems and Synthetic Biology, Part 2: Unifying Diversity"

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  Monika Heiner: Preface: Petri nets for Systems and Synthetic Biology. 987-992
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  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
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  Louchka Popova-Zeugmann: Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks. 1017-1043
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  Ruth Lamprecht, Gregory D. Smith, Peter Kemper: Stochastic Petri net models of Ca²⁺ signaling complexes and their analysis. 1045-1075
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  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
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  Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano: Hybrid Petri net based modeling for biological pathway simulation. 1099-1120
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  Natasha Jonoska, Gregory L. McColm, Ana Staninska: On stoichiometry for the assembly of flexible tile DNA complexes. 1121-1141
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  Gerard Briscoe, Suzanne Sadedin, Philippe De Wilde: Digital Ecosystems: Ecosystem-Oriented Architectures. 1143-1194
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  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

Special Issue: Unconventional Computation (UC 2009)

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