Volume 103, Number 1, January 2011

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  József Garay: Active centrum hypothesis: The origin of chiral homogeneity and the RNA-world. 1-12
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  Yubing Gong, Yanhang Xie, Xiu Lin, Yinghang Hao: Non-Gaussian noise-optimized intracellular cytosolic calcium oscillations. 13-17
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  Rodrick Wallace: Structure and dynamics of the 'protein folding code' inferred using Tlusty's topological rate distortion approach. 18-26
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  Steady Mushayabasa, Jean M. Tchuenche, Claver P. Bhunu, E. Ngarakana-Gwasira: Modeling gonorrhea and HIV co-interaction. 27-37
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  Yaochu Jin, Yan Meng: Emergence of robust regulatory motifs from in silico evolution of sustained oscillation. 38-44
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  Jose A. Fernandez-Leon: Evolving experience-dependent robust behaviour in embodied agents. 45-56
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  Sayed-Amir Marashi, Alexander Bockmayr: Flux coupling analysis of metabolic networks is sensitive to missing reactions. 57-66
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  Claudia Eberle, Christoph Ament: The Unscented Kalman Filter estimates the plasma insulin from glucose measurement. 67-72
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  Stamatios C. Nicolis, A. Dussutour: Resource exploitation strategies in the presence of traffic between food sources. 73-78
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  Itsuki Kunita, Shigeru Sakurazawa, Hajime Honda: Up-and-down movement of a sliding actin filament in the in vitro motility assay. 79-84
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  Atsuo Yamauchi, Jun Tanimoto, Aya Hagishima: An analysis of network reciprocity in Prisoner's Dilemma games using Full Factorial Designs of Experiment. 85-92
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  Motoya Wakiyama, Jun Tanimoto: Reciprocity phase in various 2 × 2 games by agents equipped with two-memory length strategy encouraged by grouping for interaction and adaptation. 93-104
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  Kazuhito Yamasaki, Kazuyoshi Z. Nanjo, Satoshi Chiba: Symmetry and entropy of biological patterns: Discrete Walsh functions for 2D image analysis. 105-112

Volume 103, Number 2, February 2011

Editorial

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  Abir U. Igamberdiev: Special issue: Computational models in photosynthesis. 113-114

Part I. Light harvesting and photosynthetic electron transport

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  David Safránek, Jan Cervený, Matej Klement, Jana Pospísilová, Lubos Brim, Dusan Lazar, Ladislav Nedbal: E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. 115-124
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  Oleg V. Moskvin, Dmitry Bolotin, Andrew Wang, Pavel S. Ivanov, Mark Gomelsky: Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium. 125-131
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  Fabio Pichierri: A quantum mechanical analysis of the light-harvesting complex 2 (LH2) from purple photosynthetic bacteria: Insights into the electrostatic effects of transmembrane helices. 132-137
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  Wim Vredenberg: Kinetic analyses and mathematical modeling of primary photochemical and photoelectrochemical processes in plant photosystems. 138-151
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  Ya Guo, Jinglu Tan: Modeling and simulation of the initial phases of chlorophyll fluorescence from Photosystem II. 152-157
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  Teena Tongra, Pooja Mehta, Sonal Mathur, Divya Agrawal, Sudhakar Bharti, Dmitry A. Los, Suleyman I. Allakhverdiev, Anjana Jajoo: Computational analysis of fluorescence induction curves in intact spinach leaves treated at different pH. 158-163
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  Alexey V. Vershubskii, Ilya V. Kuvykin, Vladimir I. Priklonskii, Alexander N. Tikhonov: Functional and topological aspects of pH-dependent regulation of electron and proton transport in chloroplasts in silico. 164-179
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  Ilya B. Kovalenko, Anna M. Abaturova, Galina Yu. Riznichenko, Andrei B. Rubin: Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin. 180-187
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  N. E. Belyaeva, F.-J. Schmitt, V. Z. Paschenko, G. Yu. Riznichenko, A. B. Rubin, G. Renger: PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies. 188-195
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  Oliver Ebenhöh, Torsten Houwaart, Heiko Lokstein, Stephanie Schlede, Katrin Tirok: A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence. 196-204

Part II. Photosynthetic carbon assimilation

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  Mabrouk A. El-Sharkawy: Overview: Early history of crop growth and photosynthesis modeling. 205-211
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  Sergio Grimbs, Anne Arnold, Aneta Koseska, Jürgen Kurths, Joachim Selbig, Zoran Nikoloski: Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities. 212-223
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  Abir U. Igamberdiev, Leszek A. Kleczkowski: Optimization of CO₂ fixation in photosynthetic cells via thermodynamic buffering. 224-229
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  Marc R. Roussel, Abir U. Igamberdiev: Dynamics and mechanisms of oscillatory photosynthesis. 230-238
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  Marcel J. André: Modelling ¹⁸O₂ and ¹⁶O₂ unidirectional fluxes in plants: I. Regulation of pre-industrial atmosphere. 239-251
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  Marcel J. André: Modelling ¹⁸O₂ and ¹⁶O₂ unidirectional fluxes in plants: II. Analysis of Rubisco evolution. 252-264
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  Hadi Farazdaghi: The single-process biochemical reaction of Rubisco: A unified theory and model with the effects of irradiance, CO₂ and rate-limiting step on the kinetics of C₃ and C₄ photosynthesis from gas exchange. 265-284
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  Andrey Yu. Dubinsky, Alexander A. Ivlev: Computational analysis of the oscillatory dynamics in the processes of CO₂ assimilation and photorespiration. 285-290
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  Olav Keerberg, Hiie Ivanova, Hille Keerberg, Tiit Pärnik, Peeter Talts, Per Gardeström: Quantitative analysis of photosynthetic carbon metabolism in protoplasts and intact leaves of barley. Determination of carbon fluxes and pool sizes of metabolites in different cellular compartments. 291-301
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  Henning Tschiersch, Ljudmilla Borisjuk, Twan Rutten, Hardy Rolletschek: Gradients of seed photosynthesis and its role for oxygen balancing. 302-308
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  Dan Bruhn, Teis N. Mikkelsen, Mathias Herbst, Werner L. Kutsch, Marilyn C. Ball, Kim Pilegaard: Estimating daytime ecosystem respiration from eddy-flux data. 309-313

Volume 103, Number 3, March 2011

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  Carsten Herrmann-Pillath, Stanley N. Salthe: Triadic conceptual structure of the maximum entropy approach to evolution. 315-330
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  Soichiro Tsuda, Jeff Jones: The emergence of synchronization behavior in Physarum polycephalum and its particle approximation. 331-341
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  Kumiko Kihara, Kotaro Mori, Shingo Suzuki, Kazufumi Hosoda, Akito Yamada, Shin-Ichi Matsuyama, Akiko Kashiwagi, Tetsuya Yomo: Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli. 342-347
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  Shigehiro Namiki, Ryohei Kanzaki: Offset response of the olfactory projection neurons in the moth antennal lobe. 348-354
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  Martin Bier, Francisco J. Cao: How occasional backstepping can speed up a processive motor protein. 355-359
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  Hyun Mo Yang, Maria de Lourdes da Graça Macoris, Karen Cristina Galvani, Maria Teresa Macoris Andrighetti: Follow up estimation of Aedes aegypti entomological parameters and mathematical modellings. 360-371
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  Greg Lemon, Daniel Howard, Felicity R. A. J. Rose, John R. King: Individual-based modelling of angiogenesis inside three-dimensional porous biomaterials. 372-383
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  Kazunari Iwamoto, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto: Mathematical modeling of cell cycle regulation in response to DNA damage: Exploring mechanisms of cell-fate determination. 384-391
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  Anthony J. T. Lee, Ming-Chih Lin, Chia-Ming Hsu: Mining Dense Overlapping Subgraphs in weighted protein-protein interaction networks. 392-399
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  Ken-ichiro Ogawa, Yoshihiro Miyake: Generation model of positional values as cell operation during the development of multicellular organisms. 400-409
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  Sabine Pérès, François Vallée, Marie Beurton-Aimar, Jean-Pierre Mazat: ACoM: A classification method for elementary flux modes based on motif finding. 410-419
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  Shiro Saito, Osamu Narikiyo: Scale-free dynamics of somatic adaptability in immune system. 420-424
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  Zaher Dawy, Elias Yaacoub, Marcel Nassar, Rami Abdallah, Hady Ali Zeineddine: A multiorganism based method for Bayesian gene network estimation. 425-434

Application notes in systems biology

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  Paulo Vilaça, Isabel Rocha, Miguel Rocha: A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. 435-441
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  Catalin Buiu, Octavian Arsene, Corina Cipu, Monica Patrascu: A software tool for modeling and simulation of numerical P systems. 442-447