764 lines
No EOL
30 KiB
BibTeX
764 lines
No EOL
30 KiB
BibTeX
|
||
@article{muzy_refounding_2013,
|
||
title = {Refounding of the activity concept? {Towards} a federative paradigm for modeling and simulation},
|
||
volume = {89},
|
||
number = {2},
|
||
journal = {Simulation},
|
||
author = {Muzy, Alexandre and Varenne, Franck and Zeigler, Bernard P and Caux, Jonathan and Coquillard, Patrick and Touraille, Luc and Prunetti, Dominique and Caillou, Philippe and Michel, Olivier and Hill, David RC},
|
||
year = {2013},
|
||
pages = {156--177}
|
||
}
|
||
|
||
@phdthesis{axen_topological_1998,
|
||
address = {Champaign, IL, USA},
|
||
title = {Topological {Analysis} {Using} {Morse} {Theory} and {Auditory} {Display}},
|
||
school = {University of Illinois at Urbana-Champaign},
|
||
author = {Axen, U.},
|
||
year = {1998}
|
||
}
|
||
|
||
@article{hu_devs-fire:_2011,
|
||
title = {{DEVS}-{FIRE}: design and application of formal discrete event wildfire spread and suppression models},
|
||
volume = {88},
|
||
issn = {0037-5497, 1741-3133},
|
||
shorttitle = {{DEVS}-{FIRE}},
|
||
url = {http://sim.sagepub.com/cgi/doi/10.1177/0037549711414592},
|
||
doi = {10.1177/0037549711414592},
|
||
number = {3},
|
||
urldate = {2013-01-29},
|
||
journal = {SIMULATION},
|
||
author = {Hu, X. and Sun, Y. and Ntaimo, L.},
|
||
month = oct,
|
||
year = {2011},
|
||
pages = {259--279}
|
||
}
|
||
|
||
@article{karafyllidis_model_1997,
|
||
title = {A model for predicting forest fire spreading using cellular automata},
|
||
volume = {99},
|
||
number = {1},
|
||
journal = {Ecological Modelling},
|
||
author = {Karafyllidis, Ioannis and Thanailakis, Adonios},
|
||
year = {1997},
|
||
pages = {87--97}
|
||
}
|
||
|
||
@article{filippi_discrete_2010,
|
||
title = {Discrete event front-tracking simulation of a physical fire-spread model},
|
||
volume = {86},
|
||
number = {10},
|
||
journal = {Simulation},
|
||
author = {Filippi, Jean-Baptiste and Morandini, Frédéric and Balbi, Jacques Henri and Hill, David RC},
|
||
year = {2010},
|
||
pages = {629--646}
|
||
}
|
||
|
||
@book{toffoli_cellular_1987,
|
||
address = {Cambridge},
|
||
title = {Cellular automata machines: a new environment for modeling},
|
||
publisher = {MIT press},
|
||
author = {Toffoli, Tommaso and Margolus, Norman},
|
||
year = {1987}
|
||
}
|
||
|
||
@inproceedings{kubera_interaction-oriented_2008,
|
||
title = {Interaction-{Oriented} {Agent} {Simulations}: {From} {Theory} to {Implementation}.},
|
||
booktitle = {{ECAI}},
|
||
author = {Kubera, Yoann and Mathieu, Philippe and Picault, Sébastien and {others}},
|
||
year = {2008},
|
||
pages = {383--387}
|
||
}
|
||
|
||
@book{mamei_field-based_2006,
|
||
title = {Field-based coordination for pervasive multiagent systems},
|
||
publisher = {Springer Science \& Business Media},
|
||
author = {Mamei, Marco and Zambonelli, Franco},
|
||
year = {2006}
|
||
}
|
||
|
||
@incollection{mamei_co-fields:_2003,
|
||
title = {Co-fields: {Towards} a unifying approach to the engineering of swarm intelligent systems},
|
||
booktitle = {Engineering {Societies} in the {Agents} {World} {III}},
|
||
publisher = {Springer},
|
||
author = {Mamei, Marco and Zambonelli, Franco and Leonardi, Letizia},
|
||
year = {2003},
|
||
pages = {68--81}
|
||
}
|
||
|
||
@article{chopard_cellular_1998,
|
||
title = {Cellular automata modeling of physical systems},
|
||
journal = {Cellular automata modeling of physical systems},
|
||
author = {Chopard, Bastien and Droz, Michel},
|
||
year = {1998}
|
||
}
|
||
|
||
@incollection{giavitto_computations_2005,
|
||
title = {Computations in space and space in computations},
|
||
booktitle = {Unconventional {Programming} {Paradigms}},
|
||
publisher = {Springer},
|
||
author = {Giavitto, Jean-Louis and Michel, Olivier and Cohen, Julien and Spicher, Antoine},
|
||
year = {2005},
|
||
pages = {137--152}
|
||
}
|
||
|
||
@inproceedings{muzy_activity_2010,
|
||
title = {Activity regions for the specification of discrete event systems},
|
||
booktitle = {Proceedings of the 2010 {Spring} {Simulation} {Multiconference}},
|
||
publisher = {Society for Computer Simulation International},
|
||
author = {Muzy, Alexandre and Touraille, Luc and Vangheluwe, Hans and Michel, Olivier and Traoré, Mamadou Kaba and Hill, David RC},
|
||
year = {2010},
|
||
pages = {136}
|
||
}
|
||
|
||
@article{shi_activity-based_1999,
|
||
title = {Activity-based construction ({ABC}) modeling and simulation method},
|
||
volume = {125},
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||
number = {5},
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||
journal = {Journal of construction engineering and management},
|
||
author = {Shi, Jonathan Jingsheng},
|
||
year = {1999},
|
||
pages = {354--360}
|
||
}
|
||
|
||
@inproceedings{potier_topological_2013,
|
||
title = {Topological computation of activity regions},
|
||
url = {http://doi.acm.org/10.1145/2486092.2486136},
|
||
doi = {10.1145/2486092.2486136},
|
||
booktitle = {{SIGSIM} {Principles} of {Advanced} {Discrete} {Simulation}, {SIGSIM}-{PADS} '13, {Montreal}, {QC}, {Canada}, {May} 19-22, 2013},
|
||
author = {Potier, Martin and Spicher, Antoine and Michel, Olivier},
|
||
year = {2013},
|
||
pages = {337--342}
|
||
}
|
||
|
||
@book{tocher_art_1967,
|
||
title = {The {Art} of {Simulation}},
|
||
isbn = {B0007ITI4E},
|
||
publisher = {English Universities Press},
|
||
author = {Tocher, K. D},
|
||
year = {1967}
|
||
}
|
||
|
||
@phdthesis{louail_comparer_2010,
|
||
title = {Comparer les morphogénèses urbaines en {Europe} et aux États-{Unis} par la simulation à base d'agents–{Approches} multi-niveaux et environnements de simulation spatiale},
|
||
school = {Université d'Evry-Val d'Essonne},
|
||
author = {Louail, Thomas},
|
||
year = {2010}
|
||
}
|
||
|
||
@article{bretagnolle_theory_2006,
|
||
title = {From theory to modelling: urban systems as complex systems},
|
||
journal = {Cybergeo: European Journal of Geography},
|
||
author = {Bretagnolle, Anne and Daudé, Eric and Pumain, Denise},
|
||
year = {2006}
|
||
}
|
||
|
||
@article{karr_whole-cell_2012,
|
||
title = {A whole-cell computational model predicts phenotype from genotype},
|
||
volume = {150},
|
||
number = {2},
|
||
journal = {Cell},
|
||
author = {Karr, Jonathan R and Sanghvi, Jayodita C and Macklin, Derek N and Gutschow, Miriam V and Jacobs, Jared M and Bolival, Benjamin and Assad-Garcia, Nacyra and Glass, John I and Covert, Markus W},
|
||
year = {2012},
|
||
pages = {389--401}
|
||
}
|
||
|
||
@article{lighthill_kinematic_1955,
|
||
title = {On kinematic waves. {II}. {A} theory of traffic flow on long crowded roads},
|
||
volume = {229},
|
||
number = {1178},
|
||
journal = {Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences},
|
||
author = {Lighthill, Michael J and Whitham, Gerald Beresford},
|
||
year = {1955},
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||
pages = {317--345}
|
||
}
|
||
|
||
@article{nagel_cellular_1992,
|
||
title = {A cellular automaton model for freeway traffic},
|
||
volume = {2},
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||
number = {12},
|
||
journal = {Journal de physique I},
|
||
author = {Nagel, Kai and Schreckenberg, Michael},
|
||
year = {1992},
|
||
pages = {2221--2229}
|
||
}
|
||
|
||
@article{banos_simuler_2008,
|
||
title = {Simuler les interactions piétons-automobilistes dans un environnement urbain : une approche à base d’agents},
|
||
copyright = {© Tous droits réservés},
|
||
issn = {1954-4863},
|
||
shorttitle = {Simuler les interactions piétons-automobilistes dans un environnement urbain},
|
||
url = {http://tem.revues.org/1048},
|
||
abstract = {Afin d’explorer le rôle des interactions piétons-automobilistes dans l’avènement des accidents de la circulation en milieu urbain, un modèle à base d’agents - SAMU - a été développé. SAMU permet d’explorer des dynamiques complexes à partir de règles comportementales simples. Les principaux éléments de ce modèle sont exposés et discutés., An agent-based model - SAMU - has been designed, which allows exploring pedestrians-drivers interaction in a virtual urban environment. Complex dynamics are obtained from simple behaviours. The key elements of SAMU are presented and discussed.},
|
||
language = {fr},
|
||
number = {1},
|
||
urldate = {2015-01-05},
|
||
journal = {Territoire en mouvement Revue de géographie et aménagement. Territory in movement Journal of geography and planning},
|
||
author = {Banos, Arnaud and Lassarre, Sylvain},
|
||
month = dec,
|
||
year = {2008},
|
||
note = {Afin d’explorer le rôle des interactions piétons-automobilistes dans l’avènement des accidents de la circulation en milieu urbain, un modèle à base d’agents - SAMU - a été développé. SAMU permet d’explorer des dynamiques complexes à partir de règles comportementales simples. Les principaux éléments de ce modèle sont exposés et discutés.},
|
||
keywords = {accidentologie, agent-based simulation, environnement urbain, multi-agents, risque routier, road safety, simulation, urban environment},
|
||
pages = {58--66}
|
||
}
|
||
|
||
@article{willems_paradigms_1991,
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||
title = {Paradigms and puzzles in the theory of dynamical systems},
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||
volume = {36},
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number = {3},
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journal = {Automatic Control, IEEE Transactions on},
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||
author = {Willems, Jan C},
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year = {1991},
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pages = {259--294}
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}
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||
@article{kurtz_relationship_1972,
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title = {The relationship between stochastic and deterministic models for chemical reactions},
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volume = {57},
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number = {7},
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journal = {The Journal of Chemical Physics},
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||
author = {Kurtz, Thomas G},
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year = {1972},
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pages = {2976--2978}
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||
}
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||
@article{gillespie_exact_1977,
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||
title = {Exact stochastic simulation of coupled chemical reactions},
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volume = {81},
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number = {25},
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journal = {The journal of physical chemistry},
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author = {Gillespie, Daniel T},
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year = {1977},
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pages = {2340--2361}
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||
}
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||
@book{mainzer_local_2013,
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||
title = {Local {Activity} {Principle}: {The} {Cause} of {Complexity} and {Symmetry} {Breaking}},
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||
isbn = {978-1-908977-09-0},
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||
publisher = {Imperial College Press},
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||
author = {Mainzer, Klaus and Chua, Leon O.},
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||
year = {2013},
|
||
lccn = {2013427768}
|
||
}
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||
|
||
@incollection{abbott_model_1990,
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||
title = {Model {Neurons}: from {Hodgkin}-{Huxley} to {Hopfield}},
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booktitle = {Statistical mechanics of neural networks},
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publisher = {Springer},
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author = {Abbott, LF and Kepler, Thomas B},
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year = {1990},
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pages = {5--18}
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}
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@article{burkitt_review_2006,
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title = {A review of the integrate-and-fire neuron model: {I}. {Homogeneous} synaptic input},
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volume = {95},
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number = {1},
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journal = {Biological cybernetics},
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author = {Burkitt, Anthony N},
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year = {2006},
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pages = {1--19}
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||
}
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@article{hindmarsh_model_1984,
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title = {A model of neuronal bursting using three coupled first order differential equations},
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volume = {221},
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number = {1222},
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journal = {Proceedings of the Royal society of London. Series B. Biological sciences},
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author = {Hindmarsh, JL and Rose, RM},
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year = {1984},
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pages = {87--102}
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}
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@article{fitzhugh_impulses_1961,
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title = {Impulses and physiological states in theoretical models of nerve membrane},
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volume = {1},
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number = {6},
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journal = {Biophysical journal},
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author = {FitzHugh, Richard},
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year = {1961},
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pages = {445}
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}
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@article{stein_improved_1974,
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||
title = {Improved neuronal models for studying neural networks},
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volume = {15},
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number = {1},
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journal = {Kybernetik},
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author = {Stein, RB and Leung, KV and Mangeron, D and Oğuztöreli, MN},
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year = {1974},
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pages = {1--9}
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}
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@article{abarbanel_synchronisation_1996,
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title = {Synchronisation in neural networks},
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volume = {39},
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number = {4},
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journal = {Physics-Uspekhi},
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author = {Abarbanel, HDI and Rabinovich, Mikhail Izrailevich and Selverston, A and Bazhenov, MV and Huerta, R and Sushchik, MM and Rubchinskii, LL},
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year = {1996},
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pages = {337--362}
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}
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@article{golomb_reduction_1993,
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title = {Reduction of a channel-based model for a stomatogastric ganglion {LP} neuron},
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volume = {69},
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number = {2},
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journal = {Biological cybernetics},
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author = {Golomb, David and Guckenheimer, John and Gueron, Shay},
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year = {1993},
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pages = {129--137}
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}
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@article{morris_voltage_1981,
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title = {Voltage oscillations in the barnacle giant muscle fiber.},
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volume = {35},
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journal = {Biophysical journal},
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author = {Morris, Catherine and Lecar, Harold},
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}
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@article{prusinkiewicz_introduction_2003,
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title = {Introduction to {Modeling} with {L}-systems},
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journal = {L-systems and Beyond-SIGGRAPH 2003 Course Notes},
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author = {Prusinkiewicz, Przemyslaw},
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year = {2003},
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pages = {1--26}
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}
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@inproceedings{kovalevsky_algorithms_2001,
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title = {Algorithms and data structures for computer topology},
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booktitle = {Digital and image geometry},
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publisher = {Springer},
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author = {Kovalevsky, Vladimir},
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year = {2001},
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pages = {38--58}
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}
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@incollection{polack_architecture_2005,
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title = {An architecture for modelling emergence in {CA}-like systems},
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booktitle = {Advances in {Artificial} {Life}},
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publisher = {Springer},
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author = {Polack, Fiona and Stepney, Susan and Turner, Heather and Welch, Peter and Barnes, Fred},
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year = {2005},
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||
pages = {433--442}
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||
}
|
||
|
||
@phdthesis{louail_comparer_2010-1,
|
||
type = {Theses},
|
||
title = {Comparer les morphogénèses urbaines en {Europe} et aux États-{Unis} par la simulation à base d'agents – {Approches} multi-niveaux et environnements de simulation spatiale},
|
||
url = {https://tel.archives-ouvertes.fr/tel-00584495},
|
||
school = {Université d'Evry-Val d'Essonne},
|
||
author = {Louail, Thomas},
|
||
month = dec,
|
||
year = {2010},
|
||
keywords = {agent based simulation, city, environnements de simulation, modélisation multi-niveaux, morphogenèses urbaines, multilevel modeling, simulation à base d'agents, simulation environements, urban morphogenesis, ville}
|
||
}
|
||
|
||
@article{codd_relational_1970,
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title = {A relational model of data for large shared data banks},
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volume = {13},
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number = {6},
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journal = {Communications of the ACM},
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author = {Codd, Edgar F},
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year = {1970},
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pages = {377--387}
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}
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@techreport{gratie_quantitative_2013,
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title = {Quantitative model refinement in four different frameworks, with applications to the heat shock response},
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institution = {Technical Report 1067, TUCS},
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author = {Gratie, Diana-Elena and Iancu, Bogdan and Azimi, Sepinoud and Petre, Ion},
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year = {2013}
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||
}
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@article{grace_integrative_2016,
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title = {Integrative modelling reveals mechanisms linking productivity and plant species richness},
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volume = {529},
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number = {7586},
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journal = {Nature},
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author = {Grace, James B and Anderson, T Michael and Seabloom, Eric W and Borer, Elizabeth T and Adler, Peter B and Harpole, W Stanley and Hautier, Yann and Hillebrand, Helmut and Lind, Eric M and Pärtel, Meelis and {others}},
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year = {2016},
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||
pages = {390--393}
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||
}
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||
|
||
@article{karr_whole-cell_2012-1,
|
||
title = {A whole-cell computational model predicts phenotype from genotype},
|
||
volume = {150},
|
||
number = {2},
|
||
journal = {Cell},
|
||
author = {Karr, Jonathan R and Sanghvi, Jayodita C and Macklin, Derek N and Gutschow, Miriam V and Jacobs, Jared M and Bolival, Benjamin and Assad-Garcia, Nacyra and Glass, John I and Covert, Markus W},
|
||
year = {2012},
|
||
pages = {389--401}
|
||
}
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||
|
||
@article{mens_taxonomy_2006,
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title = {A taxonomy of model transformation},
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volume = {152},
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journal = {Electronic Notes in Theoretical Computer Science},
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author = {Mens, Tom and Van Gorp, Pieter},
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year = {2006},
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pages = {125--142}
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||
}
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@article{adamek_abstract_2004,
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title = {Abstract and concrete categories. {The} joy of cats},
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author = {Adámek, Jiří and Herrlich, Horst and Strecker, George E},
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||
year = {2004}
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||
}
|
||
|
||
@incollection{ehresmann_mens:_2012,
|
||
address = {Berlin, Heidelberg},
|
||
title = {{MENS}: {From} {Neurons} to {Higher} {Mental} {Processes} up to {Consciousness}},
|
||
isbn = {978-3-642-28111-2},
|
||
url = {http://dx.doi.org/10.1007/978-3-642-28111-2_3},
|
||
booktitle = {Integral {Biomathics}: {Tracing} the {Road} to {Reality}},
|
||
publisher = {Springer Berlin Heidelberg},
|
||
author = {Ehresmann, Andrée C.},
|
||
editor = {Simeonov, L. Plamen and Smith, S. Leslie and Ehresmann, C. Andrée},
|
||
year = {2012},
|
||
pages = {29--30}
|
||
}
|
||
|
||
@article{jang_specification_2012,
|
||
title = {Specification and simulation of synthetic multicelled behaviors},
|
||
volume = {1},
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||
number = {8},
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||
journal = {ACS synthetic biology},
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||
author = {Jang, Seunghee S and Oishi, Kevin T and Egbert, Robert G and Klavins, Eric},
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||
year = {2012},
|
||
pages = {365--374}
|
||
}
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||
|
||
@article{hallatschek_genetic_2007,
|
||
title = {Genetic drift at expanding frontiers promotes gene segregation},
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||
volume = {104},
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number = {50},
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||
journal = {Proceedings of the National Academy of Sciences},
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author = {Hallatschek, Oskar and Hersen, Pascal and Ramanathan, Sharad and Nelson, David R},
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||
year = {2007},
|
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pages = {19926--19930}
|
||
}
|
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|
||
@article{mittal_motility_2003,
|
||
title = {Motility of {Escherichia} coli cells in clusters formed by chemotactic aggregation},
|
||
volume = {100},
|
||
number = {23},
|
||
journal = {Proceedings of the National Academy of Sciences},
|
||
author = {Mittal, Nikhil and Budrene, Elena O and Brenner, Michael P and van Oudenaarden, Alexander},
|
||
year = {2003},
|
||
pages = {13259--13263}
|
||
}
|
||
|
||
@misc{thesoundofscience_motions_2010,
|
||
title = {Motions of {Swarming} {E} coli {Bacteria}},
|
||
url = {https://www.youtube.com/watch?v=q27Jn3h4kpE&feature=youtube_gdata_player},
|
||
abstract = {A dense group of E. coli swims in the roughly two dimensional space at an air water interface. Their collective motion is significantly different from their motion as single cells. Under these conditions they behave more like an active fluid, hence changing the way that nutrients are shared within the group. Notice the appearance of turbulence-like flow fields. Groups of cells form and swim together, other groups split and join, the average trajectory of a single cell can be quite erratic as shown by the cell labeled in red.
|
||
|
||
Video courtesy Matthew Copeland, University of Wisconsin, Madison.},
|
||
urldate = {2015-01-05},
|
||
collaborator = {{thesoundofscience}},
|
||
month = feb,
|
||
year = {2010}
|
||
}
|
||
|
||
@book{toffoli_cellular_1987-1,
|
||
title = {Cellular automata machines: a new environment for modeling},
|
||
publisher = {MIT press},
|
||
author = {Toffoli, Tommaso and Margolus, Norman},
|
||
year = {1987}
|
||
}
|
||
|
||
@article{margolus_physics-like_1984,
|
||
title = {Physics-like models of computation},
|
||
volume = {10},
|
||
number = {1},
|
||
journal = {Physica D: Nonlinear Phenomena},
|
||
author = {Margolus, Norman},
|
||
year = {1984},
|
||
pages = {81--95}
|
||
}
|
||
|
||
@article{morita_computation_1989,
|
||
title = {Computation universality of one-dimensional reversible (injective) cellular automata},
|
||
volume = {72},
|
||
number = {6},
|
||
journal = {IEICE TRANSACTIONS (1976-1990)},
|
||
author = {Morita, Kenichi and Harao, Masateru},
|
||
year = {1989},
|
||
pages = {758--762}
|
||
}
|
||
|
||
@article{kari_reversibility_1994,
|
||
title = {Reversibility and surjectivity problems of cellular automata},
|
||
volume = {48},
|
||
number = {1},
|
||
journal = {Journal of Computer and System Sciences},
|
||
author = {Kari, Jarkko},
|
||
year = {1994},
|
||
pages = {149--182}
|
||
}
|
||
|
||
@phdthesis{michel_representations_1996,
|
||
title = {Représentations dynamiques de l'espace dans un langage déclaratif de simulation},
|
||
school = {Université de Paris-Sud, centre d'Orsay},
|
||
author = {Michel, O.},
|
||
month = dec,
|
||
year = {1996}
|
||
}
|
||
|
||
@article{pascalie_morphogenetic_2016,
|
||
title = {Morphogenetic {Engineering} in {Synthetic} {Biology}},
|
||
journal = {ACS Synthetic Biology},
|
||
author = {Pascalie, Jonathan and Potier, Martin and Kowaliw, Taras and Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine and Doursat, René},
|
||
year = {2016}
|
||
}
|
||
|
||
@article{blattner_complete_1997,
|
||
title = {The complete genome sequence of {Escherichia} coli {K}-12},
|
||
volume = {277},
|
||
number = {5331},
|
||
journal = {Science},
|
||
author = {Blattner, Frederick R and Plunkett, Guy and Bloch, Craig A and Perna, Nicole T and Burland, Valerie and Riley, Monica and Collado-Vides, Julio and Glasner, Jeremy D and Rode, Christopher K and Mayhew, George F and {others}},
|
||
year = {1997},
|
||
pages = {1453--1462}
|
||
}
|
||
|
||
@article{bremer_modulation_1996,
|
||
title = {Modulation of chemical composition and other parameters of the cell by growth rate},
|
||
author = {Bremer, Hans and Dennis, Patrick P.},
|
||
year = {1996},
|
||
file = {[PDF] à partir de researchgate.net:/home/eeva/work/thesis/biblio/zotero/storage/7SUBW2MM/Bremer et Dennis - 1996 - Modulation of chemical composition and other param.pdf:application/pdf}
|
||
}
|
||
|
||
@article{kubitschek_cell_1990,
|
||
title = {Cell volume increase in {Escherichia} coli after shifts to richer media.},
|
||
volume = {172},
|
||
number = {1},
|
||
journal = {Journal of bacteriology},
|
||
author = {Kubitschek, HE},
|
||
year = {1990},
|
||
pages = {94--101}
|
||
}
|
||
|
||
@article{zaritsky_growth_1982,
|
||
title = {Growth and form in bacteria},
|
||
volume = {1},
|
||
journal = {Comments Mol. Cell. Biophys},
|
||
author = {Zaritsky, A and Grover, NB and Naaman, J and Woldringh, CL and Rosenberger, RF},
|
||
year = {1982},
|
||
pages = {237--260}
|
||
}
|
||
|
||
@article{skarstad_cell_1983,
|
||
title = {Cell cycle parameters of slowly growing {Escherichia} coli {B}/r studied by flow cytometry.},
|
||
volume = {154},
|
||
number = {2},
|
||
journal = {Journal of Bacteriology},
|
||
author = {Skarstad, Kirsten and Steen, Harold B and Boye, Erik},
|
||
year = {1983},
|
||
pages = {656--662}
|
||
}
|
||
|
||
@misc{britanica_online_encyclopedia_bacteria_2016,
|
||
title = {Bacteria article},
|
||
url = {http://www.britannica.com/print/article/48203},
|
||
urldate = {2016-01-30},
|
||
author = {Britanica Online Encyclopedia},
|
||
year = {2016}
|
||
}
|
||
|
||
@article{trueba_changes_1980,
|
||
title = {Changes in cell diameter during the division cycle of {Escherichia} coli.},
|
||
volume = {142},
|
||
number = {3},
|
||
journal = {Journal of bacteriology},
|
||
author = {Trueba, Frank J and Woldringh, Conrad L},
|
||
year = {1980},
|
||
pages = {869--878}
|
||
}
|
||
|
||
@article{diluzio_escherichia_2005,
|
||
title = {Escherichia coli swim on the right-hand side},
|
||
volume = {435},
|
||
issn = {0028-0836},
|
||
url = {http://dx.doi.org/10.1038/nature03660},
|
||
doi = {10.1038/nature03660},
|
||
number = {7046},
|
||
journal = {Nature},
|
||
author = {DiLuzio, Willow R. and Turner, Linda and Mayer, Michael and Garstecki, Piotr and Weibel, Douglas B. and Berg, Howard C. and Whitesides, George M.},
|
||
year = {2005},
|
||
pages = {1271--1274}
|
||
}
|
||
|
||
@article{berg_chemotaxis_1972,
|
||
title = {Chemotaxis in {Escherichia} coli analysed by three-dimensional tracking},
|
||
volume = {239},
|
||
number = {5374},
|
||
journal = {Nature},
|
||
author = {Berg, Howard C and Brown, Douglas A and {others}},
|
||
year = {1972},
|
||
pages = {500--504}
|
||
}
|
||
|
||
@article{bourgoin_spoc:_2012,
|
||
title = {{SPOC}: {GPGPU} programming through stream processing with {OCaml}},
|
||
volume = {22},
|
||
number = {02},
|
||
journal = {Parallel Processing Letters},
|
||
author = {Bourgoin, Mathias and Chailloux, Emmanuel and Lamotte, Jean-Luc},
|
||
year = {2012},
|
||
pages = {1240007}
|
||
}
|
||
|
||
@incollection{medvedev_multi-particle_2010,
|
||
title = {Multi-particle cellular-automata models for diffusion simulation},
|
||
booktitle = {Methods and tools of parallel programming multicomputers},
|
||
publisher = {Springer},
|
||
author = {Medvedev, Yu},
|
||
year = {2010},
|
||
pages = {204--211}
|
||
}
|
||
|
||
@article{bray_chemotactic_2007,
|
||
title = {The chemotactic behavior of computer-based surrogate bacteria},
|
||
volume = {17},
|
||
number = {1},
|
||
journal = {Current biology},
|
||
author = {Bray, Dennis and Levin, Matthew D and Lipkow, Karen},
|
||
year = {2007},
|
||
pages = {12--19}
|
||
}
|
||
|
||
@article{goeddel_expression_1979,
|
||
title = {Expression in {Escherichia} coli of chemically synthesized genes for human insulin},
|
||
volume = {76},
|
||
number = {1},
|
||
journal = {Proceedings of the National Academy of Sciences},
|
||
author = {Goeddel, David V and Kleid, Dennis G and Bolivar, Francisco and Heyneker, Herbert L and Yansura, Daniel G and Crea, Roberto and Hirose, Tadaaki and Kraszewski, Adam and Itakura, Keiichi and Riggs, Arthur D},
|
||
year = {1979},
|
||
pages = {106--110}
|
||
}
|
||
|
||
@article{darnton_torque_2007,
|
||
title = {On torque and tumbling in swimming {Escherichia} coli},
|
||
volume = {189},
|
||
url = {http://jb.asm.org/content/189/5/1756.short},
|
||
number = {5},
|
||
urldate = {2016-02-05},
|
||
journal = {Journal of bacteriology},
|
||
author = {Darnton, Nicholas C. and Turner, Linda and Rojevsky, Svetlana and Berg, Howard C.},
|
||
year = {2007},
|
||
pages = {1756--1764},
|
||
file = {[HTML] à partir de asm.org:/home/eeva/work/thesis/biblio/zotero/storage/CGEI8NH7/1756.html:text/html;Snapshot:/home/eeva/work/thesis/biblio/zotero/storage/JK49X6HH/1756.html:text/html}
|
||
}
|
||
|
||
@article{turner_real-time_2000,
|
||
title = {Real-{Time} {Imaging} of {Fluorescent} {Flagellar} {Filaments}},
|
||
volume = {182},
|
||
issn = {0021-9193, 1098-5530},
|
||
url = {http://jb.asm.org/content/182/10/2793},
|
||
doi = {10.1128/JB.182.10.2793-2801.2000},
|
||
abstract = {Bacteria swim by rotating flagellar filaments that are several micrometers long, but only about 20 nm in diameter. The filaments can exist in different polymorphic forms, having distinct values of curvature and twist. Rotation rates are on the order of 100 Hz. In the past, the motion of individual filaments has been visualized by dark-field or differential-interference-contrast microscopy, methods hampered by intense scattering from the cell body or shallow depth of field, respectively. We have found a simple procedure for fluorescently labeling cells and filaments that allows recording their motion in real time with an inexpensive video camera and an ordinary fluorescence microscope with mercury-arc or strobed laser illumination. We report our initial findings with cells of Escherichia coli. Tumbles (events that enable swimming cells to alter course) are remarkably varied. Not every filament on a cell needs to change its direction of rotation: different filaments can change directions at different times, and a tumble can result from the change in direction of only one. Polymorphic transformations tend to occur in the sequence normal, semicoiled, curly 1, with changes in the direction of movement of the cell body correlated with transformations to the semicoiled form.},
|
||
language = {en},
|
||
number = {10},
|
||
urldate = {2016-02-05},
|
||
journal = {Journal of Bacteriology},
|
||
author = {Turner, Linda and Ryu, William S. and Berg, Howard C.},
|
||
month = may,
|
||
year = {2000},
|
||
pmid = {10781548},
|
||
pages = {2793--2801},
|
||
file = {Full Text PDF:/home/eeva/work/thesis/biblio/zotero/storage/MQ5R6TIB/Turner et al. - 2000 - Real-Time Imaging of Fluorescent Flagellar Filamen.pdf:application/pdf;Snapshot:/home/eeva/work/thesis/biblio/zotero/storage/NA5FUS4J/2793.html:text/html}
|
||
}
|
||
|
||
@article{sourjik_receptor_2004,
|
||
title = {Receptor clustering and signal processing in {E}. coli chemotaxis},
|
||
volume = {12},
|
||
url = {http://www.sciencedirect.com/science/article/pii/S0966842X04002343},
|
||
number = {12},
|
||
urldate = {2016-02-06},
|
||
journal = {Trends in microbiology},
|
||
author = {Sourjik, Victor},
|
||
year = {2004},
|
||
pages = {569--576},
|
||
file = {[PDF] à partir de psu.edu:/home/eeva/work/thesis/biblio/zotero/storage/PEM88DQE/Sourjik - 2004 - Receptor clustering and signal processing in E. co.pdf:application/pdf;Snapshot:/home/eeva/work/thesis/biblio/zotero/storage/K65JZAUM/S0966-842X(04)00234-3.html:text/html}
|
||
}
|
||
|
||
@article{shimizu_spatially_2003,
|
||
title = {A {Spatially} {Extended} {Stochastic} {Model} of the {Bacterial} {Chemotaxis} {Signalling} {Pathway}},
|
||
volume = {329},
|
||
issn = {00222836},
|
||
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603004376},
|
||
doi = {10.1016/S0022-2836(03)00437-6},
|
||
language = {en},
|
||
number = {2},
|
||
urldate = {2016-02-06},
|
||
journal = {Journal of Molecular Biology},
|
||
author = {Shimizu, Thomas S. and Aksenov, Sergej V. and Bray, Dennis},
|
||
month = may,
|
||
year = {2003},
|
||
pages = {291--309}
|
||
}
|
||
|
||
@article{mello_quantitative_2003,
|
||
title = {Quantitative modeling of sensitivity in bacterial chemotaxis: {The} role of coupling among different chemoreceptor species},
|
||
volume = {100},
|
||
issn = {0027-8424, 1091-6490},
|
||
shorttitle = {Quantitative modeling of sensitivity in bacterial chemotaxis},
|
||
url = {http://www.pnas.org/content/100/14/8223},
|
||
doi = {10.1073/pnas.1330839100},
|
||
abstract = {We propose a general theoretical framework for modeling receptor sensitivity in bacterial chemotaxis, taking into account receptor interactions, including those among different receptor species. We show that our model can quantitatively explain the recent in vivo measurements of receptor sensitivity at different ligand concentrations for both mutant and wild-type strains. For mutant strains, our model can fit the experimental data exactly. For the wild-type cell, our model is capable of achieving high gain while having modest values of Hill coefficient for the response curves. Furthermore, the high sensitivity of the wild-type cell in our model is maintained for a wide range of ambient ligand concentrations, facilitated by near-perfect adaptation and dependence of ligand binding on receptor activity. Our study reveals the importance of coupling among different chemoreceptor species, in particular strong interactions between the aspartate (Tar) and serine (Tsr) receptors, which is crucial in explaining both the mutant and wild-type data. Predictions for the sensitivity of other mutant strains and possible improvements of our model for the wild-type cell are also discussed.},
|
||
language = {en},
|
||
number = {14},
|
||
urldate = {2016-02-06},
|
||
journal = {Proceedings of the National Academy of Sciences},
|
||
author = {Mello, Bernardo A. and Tu, Yuhai},
|
||
month = jul,
|
||
year = {2003},
|
||
pmid = {12826616},
|
||
pages = {8223--8228},
|
||
file = {Full Text PDF:/home/eeva/work/thesis/biblio/zotero/storage/SNG3NCZX/Mello et Tu - 2003 - Quantitative modeling of sensitivity in bacterial .pdf:application/pdf;Snapshot:/home/eeva/work/thesis/biblio/zotero/storage/PIGH9TS7/8223.html:text/html}
|
||
}
|
||
|
||
@article{stewart_aging_2005,
|
||
title = {Aging and {Death} in an {Organism} {That} {Reproduces} by {Morphologically} {Symmetric} {Division}},
|
||
volume = {3},
|
||
url = {http://dx.doi.org/10.1371/journal.pbio.0030045},
|
||
doi = {10.1371/journal.pbio.0030045},
|
||
abstract = {Detailed time lapse photography reveals that organisms that divide symmetrically, such as the bacterium E. coli, can indeed age and consequently that no organism is immune to mortality.},
|
||
number = {2},
|
||
urldate = {2016-02-07},
|
||
journal = {PLoS Biol},
|
||
author = {Stewart, Eric J and Madden, Richard and Paul, Gregory and Taddei, François},
|
||
month = feb,
|
||
year = {2005},
|
||
pages = {e45},
|
||
file = {PLoS Full Text PDF:/home/eeva/work/thesis/biblio/zotero/storage/IP932H39/Stewart et al. - 2005 - Aging and Death in an Organism That Reproduces by .pdf:application/pdf}
|
||
}
|
||
|
||
@incollection{hoekstra_complex_2010,
|
||
title = {Complex automata: multi-scale modeling with coupled cellular automata},
|
||
booktitle = {Simulating complex systems by cellular automata},
|
||
publisher = {Springer},
|
||
author = {Hoekstra, Alfons G and Caiazzo, Alfonso and Lorenz, Eric and Falcone, Jean-Luc and Chopard, Bastien},
|
||
year = {2010},
|
||
pages = {29--57}
|
||
}
|
||
|
||
@article{bray_javascript_2014,
|
||
title = {The javascript object notation (json) data interchange format},
|
||
author = {Bray, Tim},
|
||
year = {2014}
|
||
}
|
||
|
||
@article{dilao_validation_1998,
|
||
title = {Validation and calibration of models for reaction–diffusion systems},
|
||
volume = {8},
|
||
number = {06},
|
||
journal = {International Journal of Bifurcation and Chaos},
|
||
author = {Dilão, Rui and Sainhas, Joaquim},
|
||
year = {1998},
|
||
pages = {1163--1182}
|
||
} |