### From BIMIB

# Cazzaniga Paolo

I graduated "cum laude" in Computer Science from the University of Milano – Bicocca, Italy, in April 2005. The title of my Thesis is *Storage Devices Inside Membrane Systems*, where I investigated membrane systems, a computational model of Natural Computing, whose aim is to abstract the way cells "compute"; in this work, I proposed a new variant of membrane systems able to store structured data.

From September 2005 to September 2006 I received a PreDoc scholarship from the University of Milano – Bicocca to work in the area of Systems Biology and Natural Computing. I mainly worked on the analysis and simulation of biochemical systems by means of stochastic algorithms implemented at the University of Milano – Bicocca lab.

I received the doctoral degree in Computer Science from the University of Milano – Bicocca in February 2010. The title of my doctoral thesis is *Stochastic algorithms for biochemical processes*.

My research activity concerns the modeling and simulation of biological, chemical and ecological systems. I am mainly interested in stochastic methods: I am currently studying and analyzing the principal stochastic simulation algorithms, such as SSA, tau leaping, slow scale SSA, adaptive tau leaping, next reaction method, next subvolume method.

Moreover, I have introduced a novel method used to simulate multiple volumes systems, called tau-Dpp. I am also implementing different stochastic procedures exploiting parallel architectures (such as MPI, grid and CUDA) to perform faster simulations.

The stochastic methods studied were applied to simulate, among others, the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae, the repressilator system, the bacterial chemotaxis and metapopulation systems.

Another research field in which I am involved is related to the use of evolutionary techniques to estimate the parameters of biological and chemical systems. In particular, I developed methods based on genetic algorithms and particle swarm optimizer to reconstruct the unknown parameters of the analyzed systems.

From January 2008 to July 2008 I spent a period at the University of Edinburgh, working under the supervision of Prof. Stephen Gilmore at the Laboratory for Foundations of Computer Science (LFCS).

## Publications

**Journals**

D. Pescini, P. Cazzaniga, D. Besozzi, G. Mauri, S. Colombo, E. Martegani. **Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states**. Biotechnology Advances, submitted

E. Mosca, I. Merelli, P. Cazzaniga, D. Pescini, G. Mauri, L. Milanesi. **Grid computing for parameter sweep applications in systems biology models**. International Journal of High Performance Computing Applications, accepted

D. Besozzi, N. Busi, P. Cazzaniga, C. Ferretti, A. Leporati, G. Mauri, D. Pescini, C. Zandron. **(Tissue) P systems with cell polarity**. Mathematical Structures in Computer Science, 19, 1141–1160, 2009

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani. **Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools**. Journal of Biotechnology, 133, 3, 377–385, 2008

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. **Modelling metapopulations with stochastic membrane Systems**. BioSystems, 91, 3, 499–514, 2008

M. Muskulus, D. Besozzi, R. Brijder, P. Cazzaniga, S. Houweling, D. Pescini, G. Rozenberg. **Cycles and communicating classes in membrane systems and molecular dynamics**. Theoretical Computer Science , Vol. 372, Issues 2-3, 15, 242–266, 2007 (doi:10.1016/j.tcs.2006.11.027)

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. **Seasonal variance in P system models for metapopulations**. Progress in Natural Science, Vol. 17, No. 4, 392–400, 2007

**Book Chapters**

P. Cazzaniga, M. Gheorghe, N. Krasnogor, G. Mauri, D. Pescini, F.J. Romero-Campero. **Probabilistic/stochastic models**. In: The Oxford Handbook of Membrane Computing, (G. Paun, G. Rozenberg, A. Salomaa, eds.), pp. 455-474, Oxford University Press, 2009

**Contributed Volumes**

D. Besozzi, P. Cazzaniga, S. Cocolo, G. Mauri, D. Pescini. **Modeling diffusion in a signal transduction pathway: the use of virtual volumes in P systems**. International Journal of Foundations of Computer Science, Volume 22, Issue 1, 89–96, 2011

A. Leporati, D. Besozzi, P. Cazzaniga, D. Pescini, C. Ferretti. **Computing with energy and chemical reactions**. Natural Computing Series, Springer-Verlag, Volume 9, Number 2, 493–512, 2009

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. **A multivolume approach to stochastic modelling with membrane systems**. In: Algorithmic Bioprocesses, (A. Condon, D. Harel, J.N. Kok, A. Salomaa, E. Winfree, eds.), Natural Computing Series, Springer-Verlag, 519-542, 2009

**Conference and Workshop Proceedings**

E. Mosca, P. Cazzaniga, D. Pescini, G. Mauri, L. Milanesi. **Modelling spatial heterogeneity and macromolecular crowding with membrane systems**. Proceedings of CMC11 - Eleventh International Conference on Membrane Computing, 24-27 August 2010 - Jena, Germany, to appear in LNCS

D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini. **BioSimWare: A P Systems–based Simulation Environment for Biological Systems**. Proceedings of CMC11 - Eleventh International Conference on Membrane Computing, 24-27August 2010 - Jena, Germany, to appear in LNCS

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri. **An analysis on the influence of network topologies on local and global dynamics of metapopulation systems**. Proceedings of the First Workshop on Applications of Membrane computing, Concurrency and Agent-based modelling in POPulation biology, EPCTS 33, 1–17, 2010

E. Mosca, P. Cazzaniga, D. Pescini, I. Merelli, G. Mauri, L. Milanesi. **Stochastic simulations on a grid framework for parallel sweep applications in biological models**. International Workshop on High Performance Computational Systems Biology, HiBi09, IEEE Computer Society, 0, 33-42, 2009

P. Cazzaniga, G. Mauri, L. Milanesi, E. Mosca, D. Pescini. **A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems**. Proceedings of the 10th International Workshop on Membrane Computing, WMC 2009 (G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, G. Rozenberg, A. Salomaa, eds.), LNCS 5957, 210–226, 2009

D. Besozzi, P. Cazzaniga, M. Dugo, D. Pescini, G. Mauri. **A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis**. Proceedings of CompMod2009 - 2nd International Workshop on Computational Models for Cell Processes (R.J. Back, I. Petre, E. de Vink, eds.), EPTCS 6, 47-62, 2009

P. Cazzaniga, D. Pescini, L. Vanneschi, D. Besozzi, G. Mauri. **A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems**. Proceedings of EvoBio 2009, LNCS 5483, 116-127, 2009

D. Pescini, P. Cazzaniga, C. Ferretti, G. Mauri. **First steps towards a wet implementation for tau-DPP**. Proceedings of the 9th International Workshop on Membrane Computing, WMC 2008 (D. Corne et al. eds.), LNCS 5391, 355-373, 2009

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri. **Tau leaping stochastic simulation method in P systems**. Proceedings of the 7th International Workshop on Membrane Computing, WMC 2006 (H.J. Hoogeboom, G. Paun, G. Rozenberg, A. Salomaa, eds.), LNCS 4361, 298-313, 2006

P. Cazzaniga, A. Leporati, G. Mauri, C. Zandron, **P Systems with Memory**. Proceedings of the 6th International Workshop on Membrane Computing, WMC 2005, Vienna, Austria, July 18-21, 2005, Revised Selected and Invited Papers, (R. Freund, Gh. Paun, G. Rozenberg, A. Salomaa, eds.), LNCS 3850,165-180, 2006

## Contacts

**Address**

Dipartimento di Informatica, Sistemistica e Comunicazione (DISCo)

Università degli studi di Milano - Bicocca, Edificio U14 - Stanza 1004

Viale Sarca 336, 20126 - Milano, Italy

**email**: cazzaniga [at] disco [dot] unimib [dot] it

**tel**: +39 02 6448 7879

## Links

Download BioSimWare here