Signaling-pathway-based molecular computing for efficient 3-SAT problem solving

Information Sciences

Volumn 161, Issue 3-4, 2004, Pages 121-137

  Liu, Jian Qin ^a,b   Shimohara, Katsunori ^a  

^a ADVANCED TELECOMMUNICATIONS RESEARCH INSTITUTE INTERNATIONAL   (Japan)

^b CENTRAL SOUTH UNIVERSITY   (China)

Author keywords

3 SAT problem; Molecular computing; Parallel algorithm

Indexed keywords

COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; DNA SEQUENCES; ENZYMES; MOLECULAR PHYSICS; PARALLEL ALGORITHMS; PROBLEM SOLVING; ROBUSTNESS (CONTROL SYSTEMS); SIGNALING;

3-SAT PROBLEM; MOLECULAR COMPUTING;

INFORMATION SCIENCE;

EID: 1842424453     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ins.2003.05.002     Document Type: Conference Paper

References (19)

1. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science. 266:1994;1021-1024.
2. Lipton R. DNA solution of hard computational problems. Science. 268:1995;542-545.
3. Liu Q., Wang L., Frutos A.G., Condon A.E., Corn R.M., Smith L.M. DNA computing on surfaces. Nature. 403:2000;175-179.
4. Ogihara M., Ray A. DNA computing on a chip. Nature. 403:2000;143-144.
5. Sakamoto K., Gouzu H., Komiya K., Kiga D., Yokoyama S., Yokomori T., Hagiya M. Molecular computation by DNA hairpin formation. Science. 288:2000;1223-1226.
6. Braich R.S., Johnson C., Rothemund P.W.K., Hwang D., Chelyapov N., Adleman L.M. Solution of a satisfiability problem on a gel-based DNA computer. Condon A., Rozenberg G. DNA Computing (6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 13-17, 2000, Revised Papers). LNCS. 2054:2001;27-42 Springer-Verlag, Berlin, Heidelberg.
7. D́az S., Esteban J.L., Ogihara M. A DNA-based random walk method for solving k-SAT. Condon A., Rozenberg G. DNA Computing (6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 13-17, 2000, Revised Papers). LNCS. 2054:2001;209-219 Springer-Verlag, Berlin, Heidelberg.
8. Liu J.-Q., Shimohara K. Pathway graph models for molecular computing in situ. RIMS Kokyuroku (RIMS, Kyoto University). 1222:2001;128-137.
9. Liu J.-Q., Shimohara K. On arithmetic units and logic operators of kinase-based molecular computers. IPSJ SIG Notes. 2001(93):2001;25-32.
10. Liu J.-Q., Shimohara K. Kinase computing in Rho-GTPases: analysis and simulation. IPSJ SIG Notes. 2001(91):2001;29-32. (in Japanese).
11. Garey M.R., Johnson D.S. Computers and intractability - a guide to the theory of NP-completeness. 1979;Freeman, New York.
12. C. Herández, M. Granã, F.J. Torrealdea, On the study of genetic algorithms in the hard region of SAT, in: H.J. Caulfield, S.-H. Chen, H.-D. Cheng, et al. (Eds.), Proceedings of the 6th Joint Conference on Information Sciences, Research Triangle Park, North Carolina, USA, March 8-13, 2002, pp. 598-601.
13. Schöning U. A probabilistic algorithm for k-SAT and constraint satisfaction problems. Proceedings of 40th Symposium on Foundations of Computer Science. 1999;IEEE Computer Society, Los Alamitos, CA. pp. 410-414.
14. Kaibuchi K., Kuroda S., Amano M. Regulation of the cytoskeleton and cell adhesion by the Rho family GTPases in mammalian cells. Annual Review of Biochemistry. 68:1999;459-486.
15. Courcelle B. The expression of graph properties and graph transformations in monadic second-order logic. Rozenberg G. Foundations. Handbook of Graph Grammars and Computing by Graph Transformations. vol. 1:1997;313-400 World Scientific, New-Jersey, London. (Chapter 5).
16. Liu J.-Q., Shimohara K. Graph rewriting in topology I: operators and the grammar. SIG-FAI-A101. 4(9/21):2001;21-26.
17. R. Milner, Bigraphical reactive systems: basic theory, 2001. Available from 〈 http://www.cl.cam.ac.uk/users/rm135/bigraphs.ps.gz〉.
18. J.-Q. Liu, K. Shimohara, Graph rewriting in topology II: computability, in: T. Imaoka, K. Shoji (Eds.), Proceedings of the 5th Symposium on Algebra, Language and Computation, (Shimane Univ., Japan, November 17-18, 2001), pp. 63-68.
19. Scott J.D., Pawson T. Cell communication: the inside story. Scientific American. 282:2000;54-61.