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257 results on '"Mavelli, Fabio"'

2. Single Compartment Approach for Assembling Photosynthetic Protocells

Author

Altamura, Emiliano, Albanese, Paola, Milano, Francesco, Trotta, Massimo, Stano, Pasquale, Mavelli, Fabio, Lovell, Nigel H., Advisory Editor, Oneto, Luca, Advisory Editor, Piotto, Stefano, Advisory Editor, Samsonovich, Alexei V., Advisory Editor, Babiloni, Fabio, Advisory Editor, Liwo, Adam, Advisory Editor, Magjarevic, Ratko, Advisory Editor, Concilio, Simona, editor, Sessa, Lucia, editor, and Rossi, Federico, editor

Published
2020
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3. Modelling a Light Transducing Protocell Population

Author

Mavelli, Fabio, Albanese, Paola, Altamura, Emiliano, Lovell, Nigel H., Advisory Editor, Oneto, Luca, Advisory Editor, Piotto, Stefano, Advisory Editor, Samsonovich, Alexei V., Advisory Editor, Babiloni, Fabio, Advisory Editor, Liwo, Adam, Advisory Editor, Magjarevic, Ratko, Advisory Editor, Concilio, Simona, editor, Sessa, Lucia, editor, and Rossi, Federico, editor

Published
2020
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5. Modelling Lipid Competition Dynamics in Heterogeneous Protocell Populations

Author

Shirt-Ediss, Ben, Ruiz-Mirazo, Kepa, Mavelli, Fabio, and Solé, Ricard V.

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Subcellular Processes
Abstract

In addressing the origins of Darwinian evolution, recent experimental work has been focussed on the discovery of simple physical effects which would provide a relevant selective advantage to protocells competing with each other for a limited supply of lipid. In particular, data coming from Szostak's lab suggest that the transition from simple prebiotically plausible lipid membranes to more complex and heterogeneous ones, closer to real biomembranes, may have been driven by changes in the fluidity of the membrane and its affinity for the available amphiphilic compound, which in turn would involve changes in vesicle growth dynamics. Earlier work from the same group reported osmotically-driven competition effects, whereby swelled vesicles grow at the expense of isotonic ones. In this paper, we try to expand on these experimental studies by providing a simple mathematical model of a population of competing vesicles, studied at the level of lipid kinetics. In silico simulations of the model are able to reproduce qualitatively and often quantitatively the experimentally reported competition effects in both scenarios. We also develop a method for numerically solving the equilibrium of a population of competing model vesicles, which is quite general and applicable to different vesicle kinetics schemes., Comment: 15 pages, 6 figures, 1 table

Published
2014
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6. Towards the Synthesis of Photo-Autotrophic Protocells

Author

Altamura, Emiliano, Albanese, Paola, Marotta, Roberto, Stano, Pasquale, Milano, Francesco, Trotta, Massimo, Mavelli, Fabio, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Bartoletti, Massimo, editor, Barla, Annalisa, editor, Bracciali, Andrea, editor, Klau, Gunnar W., editor, Peterson, Leif, editor, Policriti, Alberto, editor, and Tagliaferri, Roberto, editor

Published
2019
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7. Experimental Evidences Suggest High Between-Vesicle Diversity of Artificial Vesicle Populations: Results, Models and Implications

Author

Stano, Pasquale, Marangoni, Roberto, Mavelli, Fabio, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Bartoletti, Massimo, editor, Barla, Annalisa, editor, Bracciali, Andrea, editor, Klau, Gunnar W., editor, Peterson, Leif, editor, Policriti, Alberto, editor, and Tagliaferri, Roberto, editor

Published
2019
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9. Current Directions in Synthetic Cell Research

Author

Stano, Pasquale, Rampioni, Giordano, D’Angelo, Francesca, Altamura, Emiliano, Mavelli, Fabio, Marangoni, Roberto, Rossi, Federico, Damiano, Luisa, Piotto, Stefano, editor, Rossi, Federico, editor, Concilio, Simona, editor, Reverchon, Ernesto, editor, and Cattaneo, Giuseppe, editor

Published
2018
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11. Giant Vesicles as Compartmentalized Bio-reactors: A 3D Modelling Approach

Author

Mavelli, Fabio, Altamura, Emiliano, Stano, Pasquale, Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Liu, Ting, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Rossi, Federico, editor, Mavelli, Fabio, editor, Stano, Pasquale, editor, and Caivano, Danilo, editor

Published
2016
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22. On the Transition from Prebiotic to Proto-biological Membranes: From ‘Self-assembly’ to ‘Self-production’

Author

Piedrafita, Gabriel, Mavelli, Fabio, Morán, Federico, Ruiz-Mirazo, Kepa, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Kampis, George, editor, Karsai, István, editor, and Szathmáry, Eörs, editor

Published
2011
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26. Current Directions in Synthetic Cell Research

Author

Stano, Pasquale, primary, Rampioni, Giordano, additional, D’Angelo, Francesca, additional, Altamura, Emiliano, additional, Mavelli, Fabio, additional, Marangoni, Roberto, additional, Rossi, Federico, additional, and Damiano, Luisa, additional

Published
2017
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38. Stochastic simulations of minimal cells: the Ribocell model

Author

Mavelli Fabio

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Over the last two decades, lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models. In particular, simple and complex biomolecular reactions have been carried out inside these self-assembled micro- and nano-sized compartments, leading to the synthesis of RNA and functional proteins inside liposomes. Despite this experimental progress, a detailed physical understanding of the underlying dynamics is missing. In particular, the combination of solute compartmentalization, reactivity and stochastic effects has not yet been clarified. A combination of experimental and computational approaches can reveal interesting mechanisms governing the behavior of micro compartmentalized systems, in particular by highlighting the intrinsic stochastic diversity within a population of "synthetic cells". Methods In this context, we have developed a computational platform called ENVIRONMENT suitable for studying the stochastic time evolution of reacting lipid compartments. This software - which implements a Gillespie Algorithm - is an improvement over a previous program that simulated the stochastic time evolution of homogeneous, fixed-volume, chemically reacting systems, extending it to more general conditions in which a collection of similar such systems interact and change over the course of time. In particular, our approach is focused on elucidating the role of randomness in the time behavior of chemically reacting lipid compartments, such as micelles, vesicles or micro emulsions, in regimes where random fluctuations due to the stochastic nature of reacting events can lead an open system towards unexpected time evolutions. Results This paper analyses the so-called Ribocell (RNA-based cell) model. It consists in a hypothetical minimal cell based on a self-replicating minimum RNA genome coupled with a self-reproducing lipid vesicle compartment. This model assumes the existence of two ribozymes, one able to catalyze the conversion of molecular precursors into lipids and the second able to replicate RNA strands. The aim of this contribution is to explore the feasibility of this hypothetical minimal cell. By deterministic kinetic analysis, the best external conditions to observe synchronization between genome self-replication and vesicle membrane reproduction are determined, while its robustness to random fluctuations is investigated using stochastic simulations, and then discussed.

Published
2012
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46. Racemic Phospholipids for Origin of Life Studies

Author

Altamura, Emiliano, primary, Comte, Arnaud, additional, D’Onofrio, Alice, additional, Roussillon, Charlotte, additional, Fayolle, Dimitri, additional, Buchet, René, additional, Mavelli, Fabio, additional, Stano, Pasquale, additional, Fiore, Michele, additional, and Strazewski, Peter, additional

Published
2020
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