TUNA : Theory Underpinning Nanotech Assembers

Useful references

General books

• J. Griffin, S. Arif, A. Mufti.
  • Crash Course: Immunology and Haematology, 2nd edition.
  • Mosby 2003, ISBN 0-7234-3292-9.
  • It has a chapter on haemostasis and background information on blood cells and their function and operation. Curiously, it's written by students. (jcpw, alcc)

Websites

• Marc d@Inverno and others: simulting stem cells:
  Visualisation meeting
  SCML05
  Cell (stem cell) project background and publications, including eg links to Agur's CA model of stem cells.
• The Institute for Molecular Manufacturing website:
  http://www.imm.org/
  You should look for their reports, and in particular
  Robert A. Freitas Jr.,
  IMM Report Number 18: Nanomedicine Clottocytes: Artificial Mechanical Platelets
  http://www.imm.org/Reports/Rep018.html
  (jcpw)
• Luca Cardelli's slides from York, Languages for Systems Biology, http://www.luca.demon.co.uk/BioComputing.htm

Simulating biological systems

• A recent literature overview of Bioinformatics and related topics
• Cellular Automata a review of biological applications of cellular automata

Emergence and Tuna-relevant references from the Proposal

• F. Barnes, P. Welch. Prioritised dynamic communicating and mobile processes, IEE Proc. Software. 150(2):121--136, April, 2003.
• E. Bonabeau et al. Swarm Intelligence: from Natural to Artificial Systems. OUP, 1999.
• A. Cavalcanti, A. Sampaio, J. Woodcock. A refinement strategy for Circus. FACS15(2-3):146--181, 2003.
• A. Cavalcanti, J. Woodcock. ZRC - A Refinement Calculus for Z. FACS 10:267--289, 1999.
• C. Crichton, J. Davies, J. Woodcock. When to trust mobile objects. IEEE TOOLS. 1999.
• K. E. Drexler. Engines of Creation: the Coming Era of Nanotechnology. Anchor, 1986.
• K. E. Drexler. Nanosystems: Molecular Machinery, Manufacturing, and Computation. Wiley, 1992.
• R. Feynman. There's plenty of room at the bottom: an invitation to enter a new field of physics. Eng. \& Sci., Caltech, February 1960.
• R. Freitas. Exploratory design in medical nanotechnology: a mechanical artificial red blood cell. Artificial Cells, Blood Substitutes, \& Immobil. Tech. 26:411--430, 1998.
• R. Freitas. Nanomedicine. Vol 1: Basic Capabilities. Landes Bioscience, 1999.
• R. Freitas. Nanomedicine. Vol 2A: Biocompatibility. Landes Bioscience, 2003.
• R. Freitas. Clottocytes: artificial mechanical platelets. Nano-medicine. 2000. Available at http://www.imm.org/Reports/Rep018.html.
• J. Heather, G. Lowe, S. Schneider. How to prevent type flaw attacks on security protocols. J. Comp. Sec. 11(2), 2003
• C. A. R. Hoare. Communicating Sequential Processes. Prentice Hall, 1986.
• J. Martin, P. Welch. A Design Strategy for Deadlock-Free Concurrent Systems. Transputer Comms. 3(4):215--232. Wiley, 1996.
• S. Stepney. Critical Critical Systems. In Formal Aspects of Security, FASeC'02. LNCS 2629. Springer, 2003.
• X. Tang, J. Woodcock. Travelling Processes. MPC 2004. Springer. 2004.
• H. Treharne, S. Schneider. Using a Process Algebra to control B operations. IFM'99, 1999.
• H. Treharne, S. Schneider. How to drive a B Machine. ZB2000. LNCS 1878. Springer. 2000.
• H. Treharne, S. Schneider. Combining B Machines. ZB2002. LNCS 2272. Springer, 2002.
• UKCRC. In Vivo $\iff$ In Silico. Grand Challenge 1. 2003. Available at http://www.nesc.ac.uk/esi/events/Grand_Challenges/proposals/ViSoGCWebv2.pdf.
• UKCRC. Dependable Systems Evolution. Grand Challenge 6. 2003. Available at http://www.nesc.ac.uk/esi/events/Grand_Challenges/proposals/dse.pdf.
• {ukcrc-gc-7} UKCRC. Journeys in Non-Classical Computation. Grand Challenge 7. 2003. Available at http://www.nesc.ac.uk/esi/events/Grand_Challenges/proposals/stepney.pdf.
• P. Welch, D. Wood, J. Kerridge. Synchronisation Primitives for Highly Parallel Discrete Event Simulations. HICSS-3, IEEE, Jan 1999.
• P. Welch, J. Martin. A CSP Model for Java Multi-threading, ICSE 2000. IEEE, 2000.
• P. Welch, J. Aldous, J. Foster. CSP networking for Java (JCSP.net). ICCS 2002. LNCS 2330. Springer, 2002.
• J. Woodcock, A. Cavalcanti. The semantics of Circus. ZB2002. LNCS 2272. Springer. 2002
• A. Zettl. World's smallest electric rotor. Nature 424:408--410, 2003.