Liposome logic

ABSTRACT

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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INDEX TERMS

Primary Classification:
  I. Computing Methodologies
  I.6 SIMULATION AND MODELING
      I.6.8 Types of Simulation

Additional Classification:
  F. Theory of Computation
  F.0 GENERAL

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Design, Experimentation, Theory

Keywords:
biomolecular computing, cuda, dissipative particle dynamics, gpu computing, liposome, synthetic biology, systems biology