Published: 30th September 2013|
|Preface Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri and Marco Antoniotti|
|Invited Talk: Autocatalytic Sets and the Origin of Life Wim Hordijk||1|
|Invited Talk: The role of extrinsic bounded noises in Systems Biology, and their interplay with intrinsic stochasticity Alberto D'Onofrio||2|
|Recent developments in research on catalytic reaction networks Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani and Roberto Serra||3|
|Chemical communication between synthetic and natural cells: a possible experimental design. Giordano Rampioni, Luisa Damiano, Marco Messina, Francesca D'Angelo, Livia Leoni and Pasquale Stano||14|
|Evolution and development of complex computational systems using the paradigm of metabolic computing in Epigenetic Tracking Alessandro Fontana and Borys Wróbel||27|
|Meta-Structures: The Search of Coherence in Collective Behaviours (without Physics) Gianfranco Minati, Ignazio Licata and Eliano Pessa||35|
|Application of a Semi-automatic Algorithm for Identification of Molecular Components in SBML Models Andrea Maggiolo-Schettini, Paolo Milazzo and Giovanni Pardini||43|
|Impact of local information in growing networks Emanuele Massaro, Henrik Olsson, Andrea Guazzini and Franco Bagnoli||53|
|A Hybrid Monte Carlo Ant Colony Optimization Approach for Protein Structure Prediction in the HP Model Andrea G. Citrolo and Giancarlo Mauri||61|
|A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani and Marco Villani||70|
|A Model of Colonic Crypts using SBML Spatial Daniele Ramazzotti, Carlo Maj and Marco Antoniotti||74|
|Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts Giulio Caravagna, Alex Graudenzi, Marco Antoniotti and Giovanni de Matteis||79|
|Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles Domenico Fraccalvieri, Laura Bonati and Fabio Stella||83|
|GPU-powered Simulation Methodologies for Biological Systems Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco Nobile, Dario Pescini and Alessandro Re||87|
|An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis Chiara Damiani, Riccardo Colombo, Sara Molinari, Dario Pescini, Daniela Gaglio, Marco Vanoni, Lilia Alberghina and Giancarlo Mauri||92|
|Semi-structured data extraction and modelling: the WIA Project Gianluca Colombo, Ettore Colombo, Andrea Bonomi, Alessandro Mosca and Simone Bassis||98|
|Signed Networks, Triadic Interactions and the Evolution of Cooperation Simone Righi and Károly Takács||104|
Wivace 2013, Italian Workshop on Artificial Life and Evolutionary Computation, was held on July 1-2, 2013 at the University of Milan-Bicocca in Milan, as a satellite workshop of UCNC 2013, Unconventional Computation and Natural Computation.
Wivace 2013 gave the opportunity to researchers in Artificial Life, Evolutionary Computation and Complex Systems to present relevant novel research in a strongly multidisciplinary context.
Wivace has a rather long history, being the union of the Italian Workshop on Artificial Life (WIVA, first edition in 2003) and of the Italian Day on Evolutionary Computation (GSICE, first edition in 2005). As in the past, despite the Italian denomination, the workshop was highly international, with contributions from several European countries.
Four different sessions were organized: 'Origin of life and synthetic biology', 'Complex systems: modeling, simulation and theory', 'Bioinformatics and Systems Biology' and 'Bioinspired and evolutionary computation'.
There is no doubt that Wivace 2013 was a real success, mostly because of the valuable contributions and presentations. Furthermore, the various discussions that originated from the presentations paved the way for future national and international collaborations and for new challenging projects.
We remark that the Italian word 'vivace' means lively and so was the general atmosphere of the event, which ensures a bright future for the Wivace series.
These proceedings contain two types of accepted contributions, i.e. full papers and long abstracts, as well as the abstracts of the invited talks. In detail, 7 full papers and 8 long abstracts were selected to be included in the proceedings, on the basis of high quality and relevance criteria.
We finally want to thank all the people that made Wivace possible and successful.
First of all, we are grateful to the entire Department of Informatics, Systems and Communication of the University of Milan-Bicocca and its pricelessly efficient administrative offices.
We also thank the organizing committees of the parallel events: UCNC 2013 (Alberto Dennunzio, Teresa Gallicchio, Luca Manzoni, Antonio E. Porreca (chair), Pamela Pravettoni, Silvia Robaldo, Mariella Talia) and CiE 2013, Computability in Europe (Stefano Beretta, Paola Bonizzoni (chair), Anna Paola Carrieri, Gianluca Della Vedova, Alberto Dennunzio, Riccardo Dondi, Yuri Pirola, Marco Previtali, Raffaella Rizzi).
Warm thanks to Roberto Serra, Marco Villani, Chiara Damiani, Alessandro Filisetti and Stefano Cagnoni for their precious support and encouragement in the overall organization processes.
We also acknowledge the entire program committee and all the reviewers for their inestimable help and contribution.
Furthermore, we are deeply grateful to the invited speakers, Wim Hordijk, Alberto D'Onofrio and Enrico Formenti (joint invited speaker with UCNC 2013) for their inspirational talks and for actively participating to the discussions.
We thank all the speakers, for the brilliant presentations, and all the participants.
Finally, we want to thank the EPTCS committees for the friendly and careful assistance in the preparation of these proceedings.
The origin of life is one of the most fundamental, but also one of the most difficult problems in science. Despite differences between various proposed scenarios, one common element seems to be the emergence of an autocatalytic set or cycle at some stage. However, there has been much disagreement as to how likely it is that such self-sustaining sets could arise and evolve 'spontaneously'. This disagreement is largely caused by a lack of mathematical models that can be formally analyzed.
In this talk, after a brief introduction to the origin of life problem itself, I will introduce a formal framework of chemical reaction systems and autocatalytic sets. I will then present both theoretical and computational results which indicate that the emergence of autocatalytic sets is highly likely, even for very moderate (and chemically plausible) levels of catalysis. Furthermore, I will present a mathematical method to identify and classify autocatalytic subsets, which elucidates possible mechanisms for evolution and emergence to happen in such sets. Finally, I will show how the formal framework can be applied successfully to real (experimental) chemical systems.
After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse.
Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded implying the necessity of defining and implementing Extrinsic Bounded Noises (EBN).
In this talk, after briefly introducing bounded noises, we shall illustrate some examples of biomolecular networks affected by this kind of noise. In particular we shall illustrate:
i) The effects of EBNs in a spatiotemporal continuous model of cell polarization
ii) A simulation algorithm to analyze Gillespie-like stochastic models of nonlinear networks where the model jump rates are affected by EBNs synthesized by a suitable biochemical state-dependent Langevin system.
Applications will be illustrated for: the Michaelis-Menten approximation of noisy enzymatic reactions (which we show to be applicable also in co-presence of both intrinsic stochasticity and EBN), a model of enzymatic futile cycle and a genetic toggle switch.