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[Colloquium]Modeling, simulating and verifying DNA strand displacement systems

March 30, 2011

Watch Colloquium: 

M4V file (755 MB)

  • Date: Thursday, March 30, 2011
  • Time: 11:00 AM — 11:50 AM 
  • Place: Mechanical Engineering 218

Matthew Lakin
Microsoft Research Cambridge 

DNA strand displacement has been used to implement a broad range of information processing devices using nucleic acids: from logic gates, to chemical reaction networks, to architectures for universal computation. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. In this talk I will present a methodology for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. Device designs can be programmed using a common syntax and then analyzed at varying levels of detail, with or without interference. I will also discuss simulation and verification techniques for strand displacement systems which may produce unbounded numbers of species and reactions.

Bio: Matthew Lakin graduated from the University of Cambridge in 2005 with a B.A. in Computer Science. He remained in Cambridge to do his Ph.D. in programming language semantics, which he received in 2010. Since 2009 he has been a member of the Biological Computation Group at Microsoft Research Cambridge, working on programming languages, software tools and theoretical techniques for modeling and reasoning about biological systems and artificial DNA computing devices.