15 results on '"Besozzi D"'
Search Results
2. ginSODA: massive parallel integration of stiff ODE systems on GPUs
- Author
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Nobile, M, Cazzaniga, P, Besozzi, D, Mauri, G, Nobile, MS, Nobile, M, Cazzaniga, P, Besozzi, D, Mauri, G, and Nobile, MS
- Abstract
Ordinary differential equations (ODEs) are a widespread formalism for the mathematical modeling of natural and engineering systems, whose analysis is generally performed by means of numerical integration methods. However, real-world models are often characterized by stiffness, a circumstance that can lead to prohibitive execution times. In such cases, the practical viability of many computational tools—e.g., sensitivity analysis—is hampered by the necessity to carry out a large number of simulations. In this work, we present ginSODA, a general-purpose black-box numerical integrator that distributes the calculations on graphics processing units, and allows to run massive numbers of numerical integrations of ODE systems characterized by stiffness. By leveraging symbolic differentiation, meta-programming techniques, and source code hashing, ginSODA automatically builds highly optimized binaries for the CUDA architecture, preventing code re-compilation and allowing to speed up the computation with respect to the sequential execution. ginSODA also provides a simplified Python interface, which allows to define a system of ODEs and the test to be performed in a few lines of code. According to our results, ginSODA provides up to a 25× speedup with respect to the sequential execution
- Published
- 2019
3. Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis
- Author
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Gheorghe, M, Frisco, P, Pérez-Jiménez, M, Cazzaniga, P, Besozzi, D, Pescini, D, Mauri, G, BESOZZI, DANIELA, PESCINI, DARIO, MAURI, GIANCARLO, Gheorghe, M, Frisco, P, Pérez-Jiménez, M, Cazzaniga, P, Besozzi, D, Pescini, D, Mauri, G, BESOZZI, DANIELA, PESCINI, DARIO, and MAURI, GIANCARLO
- Abstract
In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called tau-DPP, is used for the modeling, simulation and analysis of bacterial chemotaxis. Two different models of this signal transduction pathway are presented. The first is a single volume model used to investigate the properties of bacterial chemotaxis and to analyze the effects of different perturbations (deletion of chemotactic proteins, addition of distinct amounts of external ligand, effect of different methylation states of the receptors) on the system dynamics. The second model represents a multivolume extension of the former, and it is exploited for the analysis of the diffusive processes that give rise to the formation of concentration gradients throughout the bacterial cytoplasm. The outcome of stochastic simulations of both models are exploited to analyze the process of synchronization of flagella, in order to evaluate the running and tumbling time intervals of bacterial cells
- Published
- 2014
4. cupSODA: A CUDA-Powered Simulator of Mass-Action Kinetics
- Author
-
Malyshkin, V, Nobile, M, Besozzi, D, Cazzaniga, P, Mauri, G, Pescini, D, NOBILE, MARCO SALVATORE, BESOZZI, DANIELA, MAURI, GIANCARLO, PESCINI, DARIO, Malyshkin, V, Nobile, M, Besozzi, D, Cazzaniga, P, Mauri, G, Pescini, D, NOBILE, MARCO SALVATORE, BESOZZI, DANIELA, MAURI, GIANCARLO, and PESCINI, DARIO
- Abstract
The computational investigation of a biological system often requires the execution of a large number of simulations to analyze its dynamics, and to derive useful knowledge on its behavior under physiologicaland perturbed conditions. This analysis usually turns out into very high computational costs when simulations are run on central processing units (CPUs), therefore demanding a shift to the use of high performance processors. In this work we present a simulator of biological systems, called cupSODA, which exploits the higher memory bandwidth and computational capability of graphics processing units (GPUs). This software allows to execute parallel simulations of the dynamics of biological systems, by first deriving a set of ordinary differential equations from reaction-based mechanistic models defined according to the massaction kinetics, and then exploiting the numerical integration algorithm LSODA. We show that cupSODA can achieve a 112× speedup on GPUs with respect to equivalent executions of LSODA on CPUs.
- Published
- 2013
5. Computing with energy and chemical reactions
- Author
-
Leporati, A, Besozzi, D, Cazzaniga, P, Pescini, D, Ferretti, C, LEPORATI, ALBERTO OTTAVIO, CAZZANIGA, PAOLO, PESCINI, DARIO, FERRETTI, CLAUDIO, BESOZZI, DANIELA, Leporati, A, Besozzi, D, Cazzaniga, P, Pescini, D, Ferretti, C, LEPORATI, ALBERTO OTTAVIO, CAZZANIGA, PAOLO, PESCINI, DARIO, FERRETTI, CLAUDIO, and BESOZZI, DANIELA
- Abstract
Taking inspiration from some laws of Nature—energy transformation and chemical reactions—we consider two different paradigms of computation in the framework of Membrane Computing. We first study the computational power of energy-based P systems, a model of membrane systems where a fixed amount of energy is associated with each object and the rules transform objects by manipulating their energy. We show that if we assign local priorities to the rules, then energy-based P systems are as powerful as Turing machines; otherwise, they can be simulated by vector addition systems, and hence are not universal. Then, we consider stochastic membrane systems where computations are performed through chemical networks. We show how molecular species and chemical reactions can be used to describe and simulate the functioning of Fredkin gates and circuits. We conclude the paper with some research topics related to computing with energy-based P systems and with chemical reactions.
- Published
- 2010
6. Tau leaping stochastic simulation method in P Systems
- Author
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Cazzaniga, P, Pescini, D, Besozzi, D, Mauri, G, CAZZANIGA, PAOLO, PESCINI, DARIO, BESOZZI, DANIELA, MAURI, GIANCARLO, Cazzaniga, P, Pescini, D, Besozzi, D, Mauri, G, CAZZANIGA, PAOLO, PESCINI, DARIO, BESOZZI, DANIELA, and MAURI, GIANCARLO
- Abstract
Stochastic simulations based on the tau leaping method are applicable to well stirred chemical systems reacting within a single fixed volume. In this paper we propose a novel method, based on the tau leaping procedure, for the simulation of complex systems composed by several communicating regions. The new method is here applied to dynamical probabilistic P systems, which are characterized by several features suitable to the purpose of performing stochastic simulations distributed in many regions. Conclusive remarks and ideas for future research are finally presented
- Published
- 2006
7. On the power and size of extended gemmating P systems
- Author
-
Besozzi, D, Csuhaj Varjù, E, Mauri, G, Zandron, C, BESOZZI, DANIELA, MAURI, GIANCARLO, ZANDRON, CLAUDIO, Besozzi, D, Csuhaj Varjù, E, Mauri, G, Zandron, C, BESOZZI, DANIELA, MAURI, GIANCARLO, and ZANDRON, CLAUDIO
- Abstract
In [3] P systems with gemmation of mobile membranes were examined. It was shown that (extended) systems with eight membranes are as powerful as the Turing machines. Moreover, it was proved that extended gemmating P systems with only pre-dynamical rules are still computationally complete: In this case nine membranes are needed to obtain this computational power. In this paper we improve the above results concerning the size bound of extended gemmating P systems, namely we prove that these systems with at most five membranes (with meta-priority relations and without communication rules) form a class of universal computing devices, while in the case of extended systems with only pre-dynamical rules six membranes are enough to determine any recursively enumerable language.
- Published
- 2005
8. Parallel Rewriting P systems without Target Conflicts
- Author
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PĂun, G, Rozenberg, G, Salomaa, A, Zandron, C, Besozzi, D, Mauri, G, BESOZZI, DANIELA, MAURI, GIANCARLO, ZANDRON, CLAUDIO, PĂun, G, Rozenberg, G, Salomaa, A, Zandron, C, Besozzi, D, Mauri, G, BESOZZI, DANIELA, MAURI, GIANCARLO, and ZANDRON, CLAUDIO
- Abstract
We consider rewriting P systems with parallel application of evolution rules, where no conflicts on the communication of objects can arise. Different parallelism methods are used and only rules which have the same target indication can be simultaneously applied to a common string. The computational power is analyzed, with respect to Lindenmayer systems, and some relations among different parallel rewriting P systems are studied. Some open problems are also formulated.
- Published
- 2003
9. Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis
- Author
-
Giancarlo Mauri, Daniela Besozzi, Dario Pescini, Paolo Cazzaniga, Gheorghe, M, Frisco, P, Pérez-Jiménez, M, Cazzaniga, P, Besozzi, D, Pescini, D, and Mauri, G
- Subjects
Settore INF/01 - Informatica ,membrane system ,INF/01 - INFORMATICA ,Chemotaxis ,Compartmentalization (psychology) ,Flagellum ,Biology ,Ligand (biochemistry) ,simulation ,Cell biology ,bacterial chemotaxis ,Membrane ,Cytoplasm ,Signal transduction ,Intracellular - Abstract
In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called \(\tau \)-DPP, is used for the modeling, simulation and analysis of bacterial chemotaxis. Two different models of this signal transduction pathway are presented. The first is a single volume model used to investigate the properties of bacterial chemotaxis and to analyze the effects of different perturbations (deletion of chemotactic proteins, addition of distinct amounts of external ligand, effect of different methylation states of the receptors) on the system dynamics. The second model represents a multivolume extension of the former, and it is exploited for the analysis of the diffusive processes that give rise to the formation of concentration gradients throughout the bacterial cytoplasm. The outcome of stochastic simulations of both models are exploited to analyze the process of synchronization of flagella, in order to evaluate the running and tumbling time intervals of bacterial cells.
- Published
- 2014
10. cupSODA: a CUDA-powered simulator of mass-action kinetics
- Author
-
Giancarlo Mauri, Marco S. Nobile, Dario Pescini, Daniela Besozzi, Paolo Cazzaniga, Malyshkin, V, Nobile, M, Besozzi, D, Cazzaniga, P, Mauri, G, and Pescini, D
- Subjects
Speedup ,Memory hierarchy ,Settore INF/01 - Informatica ,Computer science ,Memory bandwidth ,Parallel computing ,Computational science ,GPU computing, simulation ,CUDA ,Shared memory ,SIMD ,General-purpose computing on graphics processing units ,Graphics ,Simulation - Abstract
The computational investigation of a biological system often requires the execution of a large number of simulations to analyze its dynamics, and to derive useful knowledge on its behavior under physiological and perturbed conditions. This analysis usually turns out into very high computational costs when simulations are run on central processing units (CPUs), therefore demanding a shift to the use of high-performance processors. In this work we present a simulator of biological systems, called cupSODA, which exploits the higher memory bandwidth and computational capability of graphics processing units (GPUs). This software allows to execute parallel simulations of the dynamics of biological systems, by first deriving a set of ordinary differential equations from reaction-based mechanistic models defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm LSODA. We show that cupSODA can achieve a 112x speedup on GPUs with respect to equivalent executions of LSODA on CPUs.
- Published
- 2013
11. Computing with energy and chemical reactions
- Author
-
Daniela Besozzi, Alberto Leporati, Paolo Cazzaniga, Dario Pescini, Claudio Ferretti, Leporati, A, Besozzi, D, Cazzaniga, P, Pescini, D, and Ferretti, C
- Subjects
Energy-based P systems ,Theoretical computer science ,Settore INF/01 - Informatica ,Computer science ,Computation ,Complex system ,INF/01 - INFORMATICA ,Chemical reactions networks ,Computer Science Applications1707 ,Membrane Computing ,Object (computer science) ,Computer Science Applications ,Turing machine ,symbols.namesake ,Transformation (function) ,Membrane computing ,Computer Vision and Pattern Recognition ,Theory of computation ,symbols ,Energy (signal processing) - Abstract
Taking inspiration from some laws of Nature--energy transformation and chemical reactions--we consider two different paradigms of computation in the framework of Membrane Computing. We first study the computational power of energy-based P systems, a model of membrane systems where a fixed amount of energy is associated with each object and the rules transform objects by manipulating their energy. We show that if we assign local priorities to the rules, then energy-based P systems are as powerful as Turing machines; otherwise, they can be simulated by vector addition systems, and hence are not universal. Then, we consider stochastic membrane systems where computations are performed through chemical networks. We show how molecular species and chemical reactions can be used to describe and simulate the functioning of Fredkin gates and circuits. We conclude the paper with some research topics related to computing with energy-based P systems and with chemical reactions.
- Published
- 2010
12. BioSimWare: A software for the modeling, simulation and analysis of biological systems
- Author
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Dario Pescini, Giancarlo Mauri, Daniela Besozzi, Paolo Cazzaniga, M. Gheorghe, Besozzi, D, Cazzaniga, P, Mauri, G, and Pescini, D
- Subjects
education.field_of_study ,Theoretical computer science ,Settore INF/01 - Informatica ,Computer science ,Stochastic modelling ,business.industry ,Distributed computing ,Population ,Membrane systems ,Message Passing Interface ,INF/01 - INFORMATICA ,Stochastic simulation ,Variation (game tree) ,Modeling and simulation ,Software ,SBML ,education ,business - Abstract
BioSim Ware is a novel software that provides a user-friendly framework for the modeling and stochastic simulation of complex biological systems, ranging from cellular processes to population phenomena. BioSim Ware implements several stochastic algorithms to simulate the dynamics of single or multivolume models, as well as automatic tools to analyze the effect of variation of the system parameters. BioSim Ware supports SBML format, and can automatically convert stochastic models into the corresponding deterministic formulation. The main features of BioSim Ware are presented in this paper, together with some applications which highlight the most relevant aspects of the computational tools that it provides.
- Published
- 2010
13. On the power and size of extended gemmating P systems
- Author
-
Daniela Besozzi, Claudio Zandron, Giancarlo Mauri, Erzsébet Csuhaj-Varjú, Besozzi, D, Csuhaj Varjù, E, Mauri, G, and Zandron, C
- Subjects
Discrete mathematics ,Class (set theory) ,Computer science ,formal languages ,Theoretical Computer Science ,Power (physics) ,Turing machine ,symbols.namesake ,Membrane ,Recursively enumerable language ,Gemmating P system ,Formal language ,symbols ,Geometry and Topology ,Membrane computing ,Software - Abstract
In [3] P systems with gemmation of mobile membranes were examined. It was shown that (extended) systems with eight membranes are as powerful as the Turing machines. Moreover, it was proved that extended gemmating P systems with only pre-dynamical rules are still computationally complete: in this case nine membranes are needed to obtain this computational power. In this paper we improve the above results concerning the size bound of extended gemmating P systems, namely we prove that these systems with at most five membranes (with meta-priority relations and without communication rules) form a class of universal computing devices, while in the case of extended systems with only pre-dynamical rules six membranes are enough to determine any recursively enumerable language.
- Published
- 2005
14. Parallel Rewriting P systems without Target Conflicts
- Author
-
Daniela Besozzi, Claudio Zandron, Giancarlo Mauri, Paun, G, Rozenberg, G, Salomaa, A, Zandron, C, Besozzi, D, and Mauri, G
- Subjects
Theoretical computer science ,Computer science ,String (computer science) ,P systems ,Parallelism (grammar) ,INF/01 - INFORMATICA ,Rewriting ,Membrane computing ,P system ,Register machine - Abstract
We consider rewriting P systems with parallel application of evolution rules, where no conflicts on the communication of objects can arise. Different parallelism methods are used and only rules which have the same target indication can be simultaneously applied to a common string. The computational power is analyzed, with respect to Lindenmayer systems, and some relations among different parallel rewriting P systems are studied. Some open problems are also formulated.
- Published
- 2003
15. The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae.
- Author
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Besozzi D, Cazzaniga P, Pescini D, Mauri G, Colombo S, and Martegani E
- Abstract
: In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regulated by multiple feedback loops, exerted by the protein kinase A (PKA) on a few pivotal components of the pathway. In this article, we investigate the dynamics of the second messenger cAMP by performing stochastic simulations and parameter sweep analysis of a mechanistic model of the Ras/cAMP/PKA pathway, to determine the effects that the modulation of these feedback mechanisms has on the establishment of stable oscillatory regimes. In particular, we start by studying the role of phosphodiesterases, the enzymes that catalyze the degradation of cAMP, which represent the major negative feedback in this pathway. Then, we show the results on cAMP oscillations when perturbing the amount of protein Cdc25 coupled with the alteration of the intracellular ratio of the guanine nucleotides (GTP/GDP), which are known to regulate the switch of the GTPase Ras protein. This multi-level regulation of the amplitude and frequency of oscillations in the Ras/cAMP/PKA pathway might act as a fine tuning mechanism for the downstream targets of PKA, as also recently evidenced by some experimental investigations on the nucleocytoplasmic shuttling of the transcription factor Msn2 in yeast cells.
- Published
- 2012
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