Discrete-time signal processing with DNA

ACS Synthetic Biology

Volumn 2, Issue 5, 2013, Pages 245-254

  Jiang, Hua ^a   Salehi, Sayed Ahmad ^a   Riedel, Marc D ^a   Parhi, Keshab K ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

DNA computing; DNA strand displacement; molecular computing; recurrent circuits; sequential circuits; signal processing

Indexed keywords

DNA;

ARTICLE; CONTROLLED STUDY; DNA STRAND; FOURIER TRANSFORMATION; MASS ACTION; PRIORITY JOURNAL; SIGNAL PROCESSING; TIME;

COMPUTER SIMULATION; COMPUTERS, MOLECULAR; DNA; FOURIER ANALYSIS; LOGISTIC MODELS; MODELS, CHEMICAL; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 84878054050     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300087n     Document Type: Article

References (16)

1. Anderson, J. C., Clarke, E. J., Arkin, A. P., and Voigt, C. A. (2006) Environmentally controlled invasion of cancer cells by engineered bacteria J. Mol. Biol. 355, 619-627 (Pubitemid 41817623)
2. Venkataramana, S., Dirks, R. M., Ueda, C. T., and Pierce, N. A. (2010) Selective cell death mediated by small conditional RNAs Proc. Natl. Acad. Sci. U.S.A. 107, 16777-16782
3. Zhang, D. Y. and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange J. Am. Chem. Soc. 131, 17303-17314
4. Soloveichik, D., Seelig, G., and Winfree, E. (2010) DNA as a universal substrate for chemical kinetics Proc. Natl. Acad. Sci. U.S.A. 107, 5393-5398
5. Parhi, K. K. (1999) VLSI Digital Signal Processing Systems, John Wiley & Sons, New York.
6. Epstein, I. R. and Pojman, J. A. (1998) An Introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos, Oxford University Press, Oxford, U.K.
7. Kepper, P. D., Epstein, I. R., and Kustin, K. (2008) A systematically designed homogeneous oscillating reaction: the arsenite-iodate-chlorite system J. Am. Chem. Soc. 103, 2133-2134
8. Oppenheim, A., Schafer, R., and Buck, J. (1999) Discrete-Time Signal Processing, Prentice-Hall, Upper Saddle River, NJ.
9. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339-342 (Pubitemid 30062394)
10. Weiss, R., Basu, S., Hooshangi, S., Kalmbach, A., Karig, D., Mehreja, R., and Netravali, I. (2003) Genetic circuit building blocks for cellular computation, communications, and signal processing Nat. Comput. 2, 47-84 (Pubitemid 39137568)
11. Beneson, Y., Gil, B., Ben-Dor, U., Adar, R., and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression Nature 429, 423-429 (Pubitemid 38715134)
12. Endy, D. (2005) Foundations for engineering biology Nature 438, 449-453 (Pubitemid 41742010)
13. Ramalingam, K., Tomshine, J. R., Maynard, J. A., and Kaznessis, Y. N. (2009) Forward engineering of synthetic bio-logical AND gates Biochem. Eng. J. 47, 38-47
14. Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires' Nature 469, 212-215
15. Qian, L. and Winfree, E. (2011) Scaling up digital circuit computation with DNA strand displacement Cascades Science 332, 1196-1201
16. Nagel, L. and Pederson, D. (1973) SPICE (Simulation Program with Integrated Circuit Emphasis), University of California, Berkeley, Berkeley, CA, Memorandum ERL-M 382.