A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics

Smaldon, James; Blakes, Jonathan; Krasnogor, Natalio; Lancet, Doron

doi:10.1145/1389095.1389134

Cited by 3 publications

(3 citation statements)

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“…Evaluation of the fluorescence as a function of time showed that the vesicle cargo was slowly released, indicating a measurable response to an external stimulus. These results can be compared with those from simulations presented in our previous work (Smaldon et al 2008), in which the diffusion rate of encapsulated particles within vesicles containing different numbers of membrane pores was determined in simulation. The results are presented in Fig.…”

Section: Potential Routes To a Chemical Implementationmentioning

confidence: 97%

“…In our previous work, a prototype version of the P systems and DPD based simulation and modelling framework was used to investigate the effect of poration on the rate of diffusion of encapsulants through vesicle membranes (Smaldon et al 2008). The results from simulation indicated a linear relationship between the number of pores present in the membrane and the rate of diffusion.…”

Section: Potential Routes To a Chemical Implementationmentioning

confidence: 99%

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A computational study of liposome logic: towards cellular computing from the bottom up

et al. 2010

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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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Section: Potential Routes To a Chemical Implementationmentioning

confidence: 97%

Section: Potential Routes To a Chemical Implementationmentioning

confidence: 99%

A computational study of liposome logic: towards cellular computing from the bottom up

et al. 2010

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“…At the core of these entities are gene transcriptional systems encapsulated within self-assembled vesicles (in this case liposomes), spherical membranes which provide a selectively permeable barrier around a surrounded volume of fluid. This approach is similar in some aspects to membrane computing [18], in which computation can take place by applying reaction rules to chemicals within encapsulated volumes, and in [23] we employed a hybrid DPD-membrane computing technique to simulate diffusion in vesicles. In contrast with the most common, top-down, approach to synthetic biologic, we advocate a bottom-up approach with engineered components of manageable complexity.…”

Section: Introductionmentioning

confidence: 99%

Liposome logic

Smaldon

Krasnogor

Alexander

et al. 2009

Proceedings of the 11th Annual Conference on Genetic and Evolutionary Computation

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VLSI research, in its continuous push toward further miniaturisation, is seeking to break through the limitations of current circuit manufacture techniques by moving towards biomimetic methodologies that rely on self-assembly, selforganisation and evodevo-like processes. On the other hand, Systems and Synthetic biology's quest to achieve ever more detailed (multi)cell models are relying more and more on concepts derived from computer science and engineering such as the use of logic gates, clocks and pulse generator analogs to describe a cell's decision making behavior. This paper is situated at the crossroad of these two enterprises. That is, a novel method of non-conventional computation based on the encapsulation of simple gene regulatory-like networks within liposomes is described. Three transcription Boolean logic gates were encapsulated and simulated within liposomes self-assembled from DMPC (dimyristoylphosphatidylcholine) amphiphiles using an implementation of Dissipative Particle Dynamics (DPD) created with the NVIDIA CUDA framework, and modified to include a simple collision chemistry in a stochastic environment. The response times of the AND, OR and NOT gates were shown to be positively effected by the encapsulation within the liposome inner volume.

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