### Non-Standard Computation & Biocomputation

### Overview

Most of the systems today are based on on Von-Neumann's model of computation - execution of instructions sequentially on few shared resources. Alternatively, other forms of computational models and architectures are being concieved and studied in the recent years with emphasis on understanding the properties of self- healing, configuring, optimizing and protecting.Of particular interest here, are the models that are inspired from analogies in Nature (Complex Adaptive and Emergent Systems) and that are inspired from studies in Physics, Biology and Chemistry. Non-standard computation takes different forms: Quantum computing, Optical Computing, Biocomputing...etc

Also look at the biocomputing part in the Biosystem Design: BioSystems and Design

**Biocomputation/Biocomputing** : In this category efforts include using knowledge and models of biological entities to enhance computer science and engineering. This broadly could be seen as applying knowledge of biological sciences to computer science and engineering (Biology -> Comp sci) in the form of generalized computing platforms. As we know such a platform has few crucial aspects: computing, storage, communication. (i/o is covered in the first category of Biochips).

One sub-category is related to **computing**. This include efforts to use biological entities as the basic building blocks to make **computers** (instead of semiconductors). Our conventional computers are based on the Von Neumann model. There is a whole computing paradigm build around Von Neumann which is used to build the computers. Current computers are built using transistors (semiconductors). Instead of semiconductors, can we build computers (with different models of computation) using the biological entities instead? This is the essential question being addressed in this field.

Another sub-category related to computing, which is relatively new, include efforts to come up with **new computing models**. Von Neumann model has been very successful abstract machine. But how does biological entities perform computation? What is the model for biological and chemical processes? Can this model be used to perform computation, can this provide a new computing paradigm? Can we write "programs" using this new paradigm.

There are other sub-categories where biological models are used to come up with new and improved ways for **storing** information and as **communication** medium between different entities.

### Journals & Conferences

- Journal of Unconventional Computing
- Conference on Unconventional Computing
- International Meeting on DNA Computing & Molecular Programming
- Workshop on Membrane Computing

### Relevant Books

- [2008]
*New Computational Paradigms Changing Conceptions of What is Computable*. Barry Cooper, Benedikt Lowe and Andrea Sorbi, Springer, 2008 - [2008]
*Molecular Devices and Machines: Concepts and Perspectives for the Nanoworld*, by Vincenzo Balzani, Alberto Credi, Margherita Venturi, 2008 - [2008]
*Systematic Design for Emergence in Cellular Nonlinear Networks: With Applications in Natural Computing and Signal Processing*, by Radu Dogaru, 2008 - [2007]
*Unconventional Computing 2007*, by Andrew Adamatzky, Larry Bull, Ben De Lacy Costello, Susan Stepney, Christof Teuscher, 2007 - [2007]
*Nano and Molecular Electronics Handbook (Nano- and Microscience, Engineering, Technology, and Medicines Series)*, by Sergey Edward Lyshevski, 2007 - [2006]
*Nanotechnology: Science and Computation (Natural Computing Series)*, by Junghuei Chen, Natasha Jonoska, Grzegorz Rozenberg, 2006 - [2006]
*Biomolecular Computation for Bionanotechnology*, by Jian-qin Liu, Katsunori Shimohara, 2006 - [2006]
*DNA Computing: New Computing Paradigms (Texts in Theoretical Computer Science. An EATCS Series)*, by Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa, 2006 - [2005]
*Reaction-Diffusion Computers*, by Andrew Adamatzky, Benjamin De Lacy Costello, Tetsuya Asai, 2005 - [2005]
*Theoretical and Experimental DNA Computation (Natural Computing Series)*, by Martyn Amos, 2005 - [2005]
*Unconventional Computing 2005: From Cellular Automata to Wetware*, by Christof Teuscher, Andrew Adamatzky, 2005 - [2005]
*Applications of Membrane Computing (Natural Computing Series)*, by Gabriel Ciobanu, Mario J. Pérez-Jiménez, Gheorghe Paun, 2005 - [2004]
*Computation in Living Cells: Gene Assembly in Ciliates*, by Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg, 2004 - [2004]
*Cellular Computing (Genomics and Bioinformatics)*, by Barbara Hanawalt, Martyn Amos, 2004 - [2004]
*Aspects of Molecular Computing: Essays Dedicated to Tom Head on the Occasion of His 70th Birthday*, by Natasha Jonoska, Gheorghe Paun, Grzegorz Rozenberg, 2004 - [2004]
*Computation in Cells and Tissues: Perspectives and Tools of Thought (Natural Computing Series)*, by R. Paton, H. Bolouri, M. Holcombe, J.H. Parish, R. Tateson, 2004 - [2003]
*Molecular Computing*, by Tanya Sienko, Andrew Adamatzky, Nicholas G. Rambidi, Michael Conrad, 2003 - [2002]
*Membrane Computing*, by Gheorghe Paun, 2002 - [2001]
*Computing in Nonlinear Media & Automata Collectives*, by Andrew Adamatzky, 2001 - [2001]
*Non-Standard Computation: Molecular Computation Cellular Automata Evolutionary Algorithms and Quantum Computers*. Tino Grams et.al., Wiley-vch, 2001. - [2000]
*Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing*, by Cris Calude, Gheorghe Paun, 2000

### Articles

- [2010] DNA could be backbone of next generation logic chips
- [2008] Living Machines, by Kirk L. Kroeker, Communications of the ACM, Volume 51 , Issue 12 (December 2008)
- [2008] Biocomputer Systems and Healthcare
- [2008] Molecular Computing, A layer of logic @Nature, Jul 2008
- [2005] Biocomputation, by J. Craig Venter, Ray Kurzweil, Rodney Brooks
- [2003] Some interesting collection of course material
- [2002] Beyond Computation: by Rodney Brooks
- [1994] Molecular Computation Of Solutions To Combinatorial Problems, by Leonard M. Adleman, 1994
- How DNA computer works from howstuffworks

### Useful links

- FP7 Proactive CHEM-IT Program 3 interesting European Commission Funded projects
- International Center of Unconventional Computing
- Journeys in Non-Standard Computation (Grand Challenge 7)
- An overview of non-standard computation, by Susan Stepney
- Grand Challenge in Non-Standard Computation, April 2005
- Computational Genomics @MIT
- Biological computation @MIT
- Course on Biomolecular computation @Caltech
- DNA Computing
- E. Shapiro et.al @Weizmann Institute
- Martin Amos (interesting references)
- Christof Teuscher (some references)

### Others

- Artificial Life
- Autonomic Computing (IBM and other industrial initiatives)
- Organic Computing (German Univ initiatives)
- Calresco
- Complex Adaptive Systems Research
- BLOB Computing
- Amorphous Computing
- Physical Limits of Computation
- References