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                           NOISE in ION CHANNEL and NANOPORE

Even today a good many distinguished minds seem unable to accept or even to understand that from

a source of noise natural selection could quite unaided have drawn all the music of the biosphere

(Jacques Monod)

  1. Lv Wenping, Liu Shengju, Li Xin, Wu Renan: Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore. Electrophoresis, Vol. 35, no. 8, 2014. DOI 10.1002/elps.201470071

  2. Fischer W.B., Li Li-Hua, Mahato D. R., Wang Yi-Ting , Chen Chin-Pei: Viral channel proteins in intracellular protein-protein communication: Vpu of HIV-1, E5 of HPV16 and p7 of HCV. Biochimica & Biophysica Acta-Biomembranes, Vol. 1838, no. 4, Special no. SI, 2014, pp. 1113 – 1121. DOI 10.1016/j.bbamem.2013.08.017

  3. Hilborn R.C.: Modeling discrete-variable stochastic dynamics: Ecological populations, gene networks, and a nanotube ion channel. American Journal of Physics, Vol. 82, no. 5, 2014. DOI 10.1119/1.4870076

  4. Qian Hong, Zhang Xue-Juan, Qian Min: Stochastic dynamics of electrical membrane with voltage-dependent ion channel fluctuations. EPL, Vol. 106, no. 1, 2014, pp. 10002 – 10002.

  5. Kim Kyung-Joong, Ahn Kang-Hun: Amplitude death of coupled hair bundles with stochastic channel noise. Physical Review E, Vol. 89, no. 4, 2014, Article # 042703. DOI 10.1103/PhysRevE.89.042703

  6. Huang Yandong, Ruediger Sten, Shuai Jianwei: Langevin approach for stochastic Hodgkin-Huxley dynamics with discretization of channel open fraction. Physics Lett. A, Vol. 377, no. 44, 2013, pp. 3223 – 3227. DOI 10.1016/j.physleta.2013.10.008

  7. Wu Xinyi, Ma Jun, Li Fan, Jia Ya: Development of spiral wave in a regular network of excitatory neurons due to stochastic poisoning of ion channels. Communications in Nonlinear Science and Numerical Simulation, Vol. 18, no. 12, 2013, pp. 3350 – 3364. DOI 10.1016/j.cnsns.2013.05.011

  8. Uzuntarla M., Uzun R. ,Yilmaz E., Ozer M., Perc M.: Noise-delayed decay in the response of a scale-free neuronal network. Chaos Solitons & Fractals, Vol. 56, Special no. SI, 2013, pp. 202 – 208. DOI 10.1016/j.chaos.2013.08.009

  9. Pizzolato N., Fiasconaro A., Adorno D.P., Spagnolo B.: Translocation dynamics of a short polymer driven by an oscillating force. Journal of Chemical Physics, Vol. 138, no. 5, 2013, Article # 054902. DOI 10.1063/1.4789016

  10. Rizzi F., Jones R.E., Debusschere B.J., Knio O.M.: Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore. Journal of Chemical Physics, Vol. 138, no. 19, 2013, Article # 194104. DOI 10.1063/1.4804666

  11. Rizzi F., Jones R. E., Debusschere B. J., Knio O.M.: Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. II. Uncertain potential parameters. Journal of Chemical Physics, Vol. 138, no. 19, 2013, Article # 194105. DOI 10.1063/1.4804669

  12. Wanzhi Qiu, Nguyen T.C., Skafidas E.: Modeling and Estimating Simulated DNA Nanopore Translocation Signals. IEEE Sensors Journal, Vol. 13, no. 4, 2013, pp.1216 – 1222. DOI 10.1109/JSEN.2012.2225044

  13. Kim Jungsuk, Pedrotti K., Dunbar W.B.: An area-efficient low-noise CMOS DNA detection sensor for multichannel nanopore applications. Sensors and Actuators - B – Chemical Biochemical Sensors, Vol. 176, 2013, pp. 1051 – 1055. DOI 10.1016/j.snb.2012.08.075

  14. Zeng S. Y., Zhang Z. Z., Wei D. Q., Luo X. S , Tang W. Y , Zeng S. W., Wang R. F: Optimal physiological structure of small neurons to guarantee stable information processing. EPL, Vol. 101, no. 3, 2013, Article # 38005. DOI 10.1209/0295-5075/101/38005

  15. Meni Wanunu: Nanopores: A journey towards DNA sequencing. Physics of Life Reviews, Vol. 9, 2012, pp 125 – 158. Available online at www.sciencedirect.com

  16. Joseph A. Billo, Waseem Asghar, Samir M. Iqbal: An Implementation for the Detection and Analysis of Negative Peaks in an Applied Current Signal across a Silicon Nanopore. Proc. of SPIE Vol. 8031, no 1, 2011, pp 80312T-1 – 80312T-7. DOI 10.1117/12.884088

  17. Powell M. R., N. Sa, M. Davenport, K. Healy, I. Vlassiouk, S. E. Létant, L. A. Baker, Z. S. Siwy: Noise Properties of Rectifying Nanopores. J. of Physical Chemistry C, 2011, Vol. 115, pp 8775 – 8783. DOI 10.1021/jp2016038

  18. Rosenstein J., Vishva Ray, M. Drndic, K. L. Shepard: Solid-State Nanopores Integrated with Low-Noise Preamplifiers for High-Bandwidth DNA Analysis. IEEE/NIH Life Science Systems and Applications Workshop (LiSSA), 2011, pp 59 – 62. DOI 10.1109/LISSA.2011.5754155

  19. Rosenstein J., Ray V., Drndic M., Shepard K.L.: Nanopore DNA sensors in CMOS with on-chip low-noise preamplifiers. 16th Int. Solid-State Sensors, Actuators and Microsystems Conf. (TRANSDUCERS), 2011, pp. 874 – 877. DOI 10.1109/TRANSDUCERS.2011.5969316

  20. Tasserit C, Koutsioubas A, Lairez D, Zalczer G, Clochard M.-C.: Pink Noise of Ionic Conductance through Single Artificial Nanopores Revisited. Physical Review Letters, 2010, Vol. 105, no 26, pp. 260602 (4 pages) DOI 10.1103/PhysRevLett.105.260602

  21. Powell M., Vlassiouk I., Letant S., Siwy Z.: Studying Voltage Dependent Noise in Polymer and Solid State Nanopores. Biophysical Journal, 2010, Vol. 98, no 3, pp. 601a. DOI 10.1016/j.bpj.2009.12.3271

  22. Wanga Gang, Dunbarb W. B.: An integrated, low noise patch-klamp amplifier for biological nanopore applications. 2010 Annual Int. Conf of the IEEE Engineering in Medicine and Biology Society, EMBC'10, 2010, pp. 2718 – 2721. DOI 10.1109/IEMBS.2010.5626570

  23. V. Dimitrov, U. Mirsaidov, D. Wang, T. Sorsch, W. Mansfield, J. Miner, F. Klemens, R Cirelli, S. Yemenicioglu, G. Timp: Nanopores in solid-state membranes engineered for single molecule detection. Nanotechnology, Vol. 21, 2010, pp 065502 (11 pages). DOI 10.1088/0957-4484/21/6/065502

  24. Powell M. R., Vlassiouk I., Martens C., Siwy Z.: Nonequilibrium 1/f noise in rectifying nanopores. Physical Review Letters, 2009, Vol. 103, no 24, pp. 248104 DOI 10.1103/PhysRevLett.103.248104

  25. D. P. Hoogerheide, S. Garaj, J. A. Golovchenko: Probing surface charge fluctuations with solid-state nanopores. Physical Review Letters, 2009, Vol. 102, no 25, pp. 256804 – 256808. DOI 10.1103/PhysRevLett.102.256804

  26. Smeets R. M. M., Dekker N. H., Dekker C.: Low-frequency noise in solid-state nanopores. Nanotechnology, 2009, Vol. 20, no 9, pp. 095501 DOI 10.1088/0957-4484/20/9/095501

  27. D. G. Luchinsky, R Tindjong, I Kaufman, P V E McClintock, R S Eisenberg: Charge fluctuations and their effect on conduction in biological ion channels. J. Stat. Mech., 2009, P01010. DOI 10.1088/1742-5468/2009/01/P01010

  28. Uram J. D., Ke Kevin, Mayer M. L.: Noise and bandwidth of current recordings from submicrometer pores and nanopores. ACS Nano, 2008, Vol. 2, no 5, pp. 857-872 DOI 10.1021/nn700322m

  29. R. M. M. Smeets, U. F. Keyser, N. H. Dekker, C. Dekker: Noise in solid-state nanopores. PNAS, Jan 15th, 2008, Vol 105, no 2, pp 417 – 421. DOI 10.1073/pnas.0705349105 http://www.pnas.org/content/105/2/417.full.pdf

  30. Zitserman V.Y., Berezhkovskii A.M., Pustovoit M.A., Bezrukov S.M.: Relaxation and fluctuations of the number of particles in a membrane channel at arbitrary particle-channel interaction. The Journal of Chemical Physics, Vol. 129, no 9, 2008, pp 095101. DOI 10.1063/1.2972981

  31. V. Tabard-Cossa, D. Trivedi, M. Wiggin, N. N Jetha, A. Marziali : Noise analysis and reduction in solid-state nanopores. Nanotechnology, Vol. 18, 2007, pp 305505 (6 pages) DOI 10.1088/0957-4484/18/30/305505

  32. J. W. Shuai, P. Jung: The dynamics of small excitable ion channel clusters. Chaos, Vol. 16, no 2, 2006, pp 026104 (10 pages). DOI 10.1063/1.2210827 http://lsp.xmu.edu.cn/physics/shuaiweb/ShuaiPub/Chaos16.pdf

  33. Z. Siwy, A. Fulinski: 1/f Noise in ion transport through nanopores: Origins and mechanism. CP665, Unsolved Problems of Noise and Fluctuations: UpoN2002 Third Int. Conf. (edited by S. M. Bezrukov), American Inst. of Physics, 2003, pp 273 – 282. DOI 10.1063/1.1584901

  34. S. M. Bezrukov, A. M. Berezhkovskii, M. A. Pustovoit, A. Szabo: Particle number fluctuations in a membrane channel. J. of Chem. Physics, Vol. 113, No. 18, 8 Nov. 2000, pp 8206 – 8211. DOI 10.1063/1.1314862

 

Links:

http://www.nslij-genetics.org/wli/1fnoise/ (A bibliography on 1/f noise in biosystems)

http://papers.cnl.salk.edu/PDFs/

http://iopscience.iop.org/1742-5468/focus/extra.focus5


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