A computational study of liposome logic: towards cellular computing from the bottom up |
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Authors: | James Smaldon Francisco J Romero-Campero Francisco Fernández Trillo Marian Gheorghe Cameron Alexander Natalio Krasnogor |
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Institution: | (1) School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, UK;(2) Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, Sheffield, S1 4DP, UK;(3) School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK |
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Abstract: | In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated
within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs,
e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations
feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic
circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set
of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling
techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates
to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means
of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically
translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s
stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase.
This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem
of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation
of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation
for membrane computing from the bottom-up. |
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Keywords: | Simulation and modelling Vesicle computing Cellular computing Synthetic biology Dissipative particle dynamics Stochastic simulation Model checking Logic gates Chells Protocells |
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