FAST: A framework for simulation and analysis of large-scale protein-silicon biosensor circuits

IEEE Transactions on Biomedical Circuits and Systems

Volumn 7, Issue 4, 2013, Pages 451-459

  Gu, Ming ^a   Chakrabartty, Shantanu ^a  

^a Michigan State University   (United States)

Author keywords

Biomolecular circuit; biosensors; computer aided design; factor graphs; inverse problems; message passing; simulation

Indexed keywords

ANALYSIS AND VERIFICATIONS; BIO-MOLECULAR; EXPERIMENTAL PROCEDURE; FACTOR-GRAPHS; NON-LINEAR RELATIONSHIPS; SIMULATION; SIMULATION AND ANALYSIS; SYSTEM LEVEL OPTIMIZATION;

BIOSENSORS; COMPUTER AIDED DESIGN; DIFFERENTIAL EQUATIONS; INVERSE PROBLEMS; MESSAGE PASSING; PROTEINS; RELIABILITY ANALYSIS; SILICON; STOCHASTIC SYSTEMS; USER INTERFACES;

ELECTRIC NETWORK ANALYSIS;

IMMUNOGLOBULIN G; PROTEIN; SILICON;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETIC PROCEDURES; IMMUNOASSAY; MOUSE; RABBIT; REPRODUCIBILITY;

ALGORITHMS; ANIMALS; BIOSENSING TECHNIQUES; COMPUTER SIMULATION; IMMUNOASSAY; IMMUNOGLOBULIN G; MICE; PROTEINS; RABBITS; REPRODUCIBILITY OF RESULTS; SILICON; SOFTWARE;

EID: 84881043714     PISSN: 19324545     EISSN: None     Source Type: Journal    
DOI: 10.1109/TBCAS.2012.2222403     Document Type: Article

References (27)

1. A. Hassibi, H. Vikalo, and A. Hajimiri, "On noise processes and limits of performance in biosensors," J. Appl. Phys., vol. 102, no. 1, p. 014909, 2007
2. A. Hassibi, S. Zahedi, R. Navid, R.W. Dutton, and T. H. Lee, "Biological shot-noise and quantum-limited signal-to-noise ratio in affinitybased biosensors," J. Appl. Phys., vol. 97, no. 8, p. 084701, 2005
3. Y. Liu, S. Chakrabartty, and E. C. Alocilja, "Fundamental building blocks for molecular bio-wire based forward-error correcting biosensors," Nanotechnol., no. 18, p. 4240172, 2007
4. Y. Liu and S. Chakrabartty, "Factor graph based biomolecular circuit analysis for designing forward error correcting biosensors," IEEE Trans. Biomed. Circuits Syst., vol. 3, no. 3, pp. 150-159, Jun. 2009
5. W. E. Ryan, "An introduction to LDPC codes," in CRC Handbook for Coding and Signal Processing for Recoding Systems. Boca Raton, FL: CRC Press, 2004, ch. 36
6. Y. Liu, M. Gu, E. C. Alocilja, and S. Chakrabartty, "Co-detection: Ultra-reliable nanoparticle-based electrical detection of biomolecules in the presence of large background interference," Biosens. Bioelectron., vol. 26, no. 3, pp. 1087-1092, Sep. 2010
7. F. Kschischang, B. J. Frey, and H.-A. Loeliger, "Factor graphs and the sum-product algorithm," IEEE Trans. Inf. Theory, vol. 47, no. 2, pp. 498-519, Feb. 2001 (Pubitemid 32318087)
8. R. G. Gallager, "Low-density parity check codes," IRE Trans. Inf. Theory, vol. IT-8, no. 1, pp. 21-28, Jan. 1962
9. N. Wiberg, "Codes and decoding on general graphs," Ph.D. dissertation, Linkoping Univ., Linkoping, Sweden, 1996
10. T. Richardson, M. Shokrollahi, and R. Urbanke, "Design of capacity approaching irregular low-density parity-check codes," IEEE Trans. Inf. Theory, vol. 47, no. 2, pp. 619-637, Feb. 2001 (Pubitemid 32318093)
11. T. Richardson and R. Urbanke, "The capacity of low-density parity check codes under message-passing decoding," IEEE Trans. Inf. Theory, vol. 47, pp. 599-618, 2001 (Pubitemid 32318092)
12. D. J. C. MacKay, Information Theory, Inference and Learning Algorithms. Cambridge, U.K.: Cambridge Univ. Press, 2003, ch. 6, pp. 557-572 [Online]. Available: http://www.inference.phy.cam.ac.uk/ mackay/itila
13. Y. Liu, D. Zhang, E. C. Alocilja, and S. Chakrabartty, "Biomolecules detection using a silver-enhanced gold nanoparticle-based biochip," Nano Res. Lett., 2010, DOI: 10.1007/s11671- 010-9542-0
14. K. T. Liao and H. J. Huang, "Femtomolar immunoassay based on coupling gold nanoparticle enlargement with square wave stripping voltammetry," Analytica Chimica Acta, vol. 538, no. 1-2, pp. 159-164, 2005
15. S. Gupta, S. Huda, P. K. Kilpatrick, and O. D. Velev, "Characterization and optimization of gold nanoparticle-based silver-enhanced immunoassays," Anal. Chem., vol. 79, no. 10, pp. 3810-3820, 2007 (Pubitemid 46799078)
16. R. Almog, S. Zaitsev, O. Shtempluck, and E. Buks, "Signal amplification in a nanomechanical duffing resonator via stochastic resonance," Appl. Phys. Lett., vol. 90, 2007
17. K. Wiesenfeld and F. Moss, "Stochastic resonance and the benefits of noise: From ice ages to crayfish and SQUIDs," Nature, vol. 373, pp. 33-36, 1995
18. D. F. Russell, L. A. Wilkens, and F. Moss, Nature, vol. 402, 1999
19. S. Jones, B. Jumarhon, S. McKee, and J. A. Scott, "A mathematical model of a biosensor," J. Eng.Math., vol. 30, no. 3, pp. 321-337, 1996 (Pubitemid 126708099)
20. C. Heitzinger, R. Kennell, G. Klimeck, N. Mauser, M. McLennan, and C. Ringhofer1, "Modeling and simulation of field-effect biosensors (BioFETs) and their deployment on the NanoHUB," in J. Phys., Conf. Ser., 2008, vol. 107, p. 012004
21. F. Ivanauskas and R. Baronas, "Modelling an amperometric biosensor acting in a flowing liquid," Int. J. Numer. Methods Fluids, vol. 56, no. 8, pp. 1313-1319, 2007 (Pubitemid 351385472)
22. Y. Liu and Q. Wang, "Mathematical and computational modeling of biosensors: Modeling for enzyme-substrate interaction and biomolecular interaction," in Proc. 2nd WSEAS Int. Conf. Computational Chemistry Table of Contents, Recent Advances In Biology and Biomedicine, 2008, pp. 38-42
23. N. D. Botkin, M. Schlensog, M. Tewes, and V. L. Turova, "A mathematical model of a biosensor," Nanotech., vol. 1, pp. 231-234, 2001
24. B. M. Patre and V. G. Sangam, "Mathematical model of an amperometric biosensor for the design of an appropriate instrumentation system," J. Med. Eng. Technol., vol. 31, no. 5, pp. 351-360, 2007 (Pubitemid 47295335)
25. V. Rossokhaty and N. Rossokhataja, "A mathematical model of silicon- based thermobiosensors," IMA J. Manage. Math., vol. 10, no. 1, pp. 41-53, 1999
26. P. Rachela, N. Amir, and S. D. Yosi, "Mathematical model of whole cell based bio-chip: An electrochemical biosensor for water toxicity detection," J. Electroanal. Chem., vol. 602, no. 1, pp. 17-23, 2007
27. M. Schlosshauer and D. Baker, "Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness," Protein Sci., vol. 13, pp. 1660-1669, 2004 (Pubitemid 38669253)