Fall, Period 1, 2015
During this course we will discuss a novel fast developing interdisciplinary area called Molecular Computing and will consider both its theoretical and experimental aspects. In this area biological systems and living organisms are regarded from the Computer Science perspective, molecular-scale biological processes are considered as computations, manipulations with biologically derived materials are being designed (both in theory as well as in the lab) to perform computational functions.
This course presents the computational aspects of DNA manipulation in vitro (DNA computing) as well as in vivo (an example, gene assembly in ciliates). We review briefly the basics of DNA molecular structure and manipulation, the basic biology of ciliates and especially the gene assembly process. We then investigate several computational models to reason about DNA manipulation in vitro as well as in vivo, and will study their computational properties, including: DNA splicing and insertion/deletion, self-assembly of nano-structures by DNA, gene assembly strategies in ciliates as well as parallelism and concurrency, computing with ciliates, etc. We overview the field of Membrane Computing as a computational paradigm describing multi-compartmental membranar structure as well as distributed computations and information fluxes between different places within living systems.
In particular we will discuss:
- the benefits of this research for computer scientists – novell and challenging problems and paradigms which lead to broader and deeper understanding of the notion of computation;
- the benefits of this research for biologists – novel and uniform explanation of experimental results, new insights into DNA manipulation in vivo and in vitro, new suggestions for experiments.
- Introduction to DNA Computing;
- Formal models for DNA Computing;
- DNA-based computational devices;
- Introduction to gene assembly in ciliates;
- Formal models for gene assembly in ciliates;
- Computing through gene assembly;
- Introduction to Membrane Computing.
- The course book is Grzegorz Rozenberg, Thomas Bäck, Joost N. Kok – “Handbook of Natural Computing”, Volume II, Section IV “Molecular Computation”, Springer, ISBN 978-3-540-92910-9, 2012
- Reference on Formal Language Theory and Computability: Arto Salomaa – “Computation and Automata”, Cambridge University Press, Mathematics, 2011
- 5 study points
- 28h lectures,
- final examination
- 1st term of the academic year 2015-2016: weeks 36 – 43
- First lecture: Monday 31.09.2015, 15:15, ICT Building, Cobol (map)
- Last lecture: Thursday 22.10.2015, 10:15, ICT Building, Algol (map)
- Lectures twice per week:
- No background on Biology is required, as this will be provided throughout the course, when needed.
- Some notions and concepts of discrete mathematics and computer science, especially permutations, strings, graphs, formal languages and computability may be useful. However, those will be briefly introduced when needed.
- Vladimir Rogojin,
- Department of IT,
- Åbo Akademi University,
- vrogojin at abo.fi, room B5050, ICT-house
- August 31, 2015: Introduction 3:00 pm – 5:00 pm, ICT Building, Cobol
- September 3, 2015: Notions of Biochemistry and Molecular Biology Manipulating DNA 10:00 am – 12:00 pm, ICT Building, Algol
- September 7, 2015: Introduction to DNA Computing 3:00 pm – 5:00 pm, ICT Building, Cobol
- September 10, 2015: Computing by DNA manipulations 10:00 am – 12:00 pm, ICT Building, Algol
- September 14, 2015: Engineering Natural Computation by Autonomous DNA-Based Biomolecular Devices 3:00 pm – 5:00 pm, ICT Building, Cobol
- September 17, 2015: Computing in vivo: gene assembly in ciliates 10:00 am – 12:00 pm, ICT Building, Algol
- September 21, 2015: Gene assembly. Molecular models 3:00 pm – 5:00 pm, ICT Building, Cobol
- September 24, 2015: Computation in living cells: Formalizing gene assembly 10:00 am – 12:00 pm, ICT Building, Algol
- September 28, 2015: Gene assembly as graph reduction. Parallelism and complexity. Computing with gene assembly 3:00 pm – 5:00 pm, ICT Building, Cobol
- October 1, 2015: DNA Algorithmic Self-Assembly 10:00 am – 12:00 pm, ICT Building, Algol
- October 5, 2015: DNA Algorithmic Self-Assembly 3:00 pm – 5:00 pm, ICT Building, Cobol
- October 8, 2015: DNA Memory 10:00 am – 12:00 pm, ICT Building, Algol
- October 12, 2015: Engineering Natural Computation by Autonomous DNA-Based Biomolecular Devices 3:00 pm – 5:00 pm, ICT Building, Cobol
- October 15, 2015: Molecular Computing Machineries – Models and Wet Implementations 10:00 am – 12:00 pm, ICT Building, Algol