Specificity of Bionoise

Glossary Bio
Acronyms Bio

                           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. Wen Chenyu, Zeng Shuangshuang, Arstila Kai, et al.: Generalized Noise Study of Solid-State Nanopores at Low Frequencies. ACS Sensors, Vol. 2, no. 2, 2017, pp. 300 – 307. DOI 10.1021/acssensors.6b00826

  2. Sha Jingjie, Shi Hongjiao, Zhang Yin, et al.: Salt Gradient Improving Signal-to-Noise Ratio in Solid-State Nanopore. ACS Sensors, Vol. 2, no. 4, 2017, pp. 506 – 512. DOI 10.1021/acssensors.6b00718

  3. Zeng Tao, Fleming A.M., Ding Yun, et al.: Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the alpha-Hemolysin Latch. Biochemistry, Vol. 56, no. 11, 2017, pp. 1596 – 1603. DOI 10.1021/acs.biochem.6b01175

  4. Shevkunov S.V.: Mechanisms for ion retention in molecular water clusters in a planar nanopore against the background of thermal fluctuations. Colloid Journal, Vol. 79, no. 3, 2017, pp. 399 – 413. DOI 10.1134/S1061933X17030140

  5. Chen Wei, Liu Guo-Chang, Ouyang Jun, et al.: Graphene nanopores toward DNA sequencing: a review of experimental aspects. Science China - Chemistry, Vol. 60, no. 6, 2017, pp. 721 – 729. DOI 10.1007/s11426-016-9016-5

  6. Bello J., Kim Young-Rok, Kim Sun Min, et al.: Lipid bilayer membrane technologies: A review on single-molecule studies of DNA sequencing by using membrane nanopores. Microchimica Acta, Vol. 184, no. 7, 2017, pp. 1883 – 1897. DOI 10.1007/s00604-017-2321-1

  7. Wu Qiong, Kaji Noritada, Yasui Takao, et al.: A millisecond micro-RNA separation technique by a hybrid structure of nanopillars and nanoslits. Scientific Reports, Vol. 7, 2017, Article # 43877. DOI 10.1038/srep43877

  8. Zhang Jianhua, Liu Xiuling, Ying Yi-Lun, et al.: High-bandwidth nanopore data analysis by using a modified hidden Markov model. Nanoscale, Vol. 9, no. 10, 2017, pp. 3458 – 3465. DOI 10.1039/c6nr09135k

  9. Zorkot M., Golestanian R., Bonthuis D.J.: Current fluctuations in nanopores: The effects of electrostatic and hydrodynamic interactions. European Physical Journal - Special Topics, Vol. 225, no. 8-9, 2016, pp. 1583 – 1594. DOI 10.1140/epjst/e2016-60152-y

  10. Zorkot M., Golestanian R., Bonthuis D.J.: The Power Spectrum of Ionic Nanopore Currents: The Role of Ion Correlations. Nano Letters, Vol. 16, no. 4, 2016, pp. 2205 – 2212. DOI 10.1021/acs.nanolett.5b04372

  11. Agrawal K.V., Drahushuk L.W., Strano M.S.: Observation and analysis of the Coulter effect through carbon nanotube and graphene nanopores. Philosophical Transactions of the Royal Society A - Mathematical Physical & Engineering Sciences, Vol. 374, no. 2060, 2016, Article # 20150357. DOI 10.1098/rsta.2015.0357

  12. Comera J., Aksimentiev A.: DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. Nanoscale, Vol. 8, no. 18, 2016, pp. 9600 – 9613. DOI 10.1039/c6nr01061j

  13. Shevkunov S.V.: Water vapor nucleation on ion pairs under the conditions of a planar nanopore. Colloid Journal, Vol. 78, no. 4, 2016, pp. 542 – 552. DOI 10.1134/S1061933X16040177

  14. Park Kyeong-Beom, Kim Hyung-Jun, Kim Hyun-Mi, et al.: Noise and sensitivity characteristics of solid-state nanopores with a boron nitride 2-D membrane on a pyrex substrate. Nanoscale, Vol. 8, no. 10, 2016, pp. 5755 – 5763. DOI 10.1039/c5nr09085g

  15. Wen Chenyu, Zeng Shuangshuang, Zhang Zhen, et al.: On nanopore DNA sequencing by signal and noise analysis of ionic current. Nanotechnology, Vol. 27, no. 21, 2016, Article # 215502. DOI 10.1088/0957-4484/27/21/215502

  16. Swati Bhattacharya, Jejoong Yoo, Aksimentiev A.: Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore. ACS Nano, Vol. 10, no. 4, 2016, pp. 4644 – 4651. DOI 10.1021/acsnano.6b00940

  17. Secchi E., Nigučs A., Jubin L., Siria A., Bocquet L.: Scaling Behavior for Ionic Transport and its Fluctuations in Individual Carbon Nanotubes. Phys. Rev. Lett., Vol. 116, no. 15, 2016, Article # 154501. https://doi.org/10.1103/PhysRevLett.116.154501

  18. Kyeong-Beom Park, Hyung-Jun Kim, Hyun-Mi Kim, Sang A Han, Kang Hyuck Lee, Sang-Woo Kim, Ki-Bum Kim: Noise and sensitivity characteristics of solid-state nanopores with a boron nitride 2-D membrane on a pyrex substrate. Nanoscale, Vol. 8, no. 10, 2016, pp. 5755 – 5763. DOI 10.1039/C5NR09085G

  19. Yi Li, Chang Chen, Willems K., Lagae L., Groeseneken G., Stakenborg T., Pol Van Dorpe: Asymmetric plasmonic induced ionic noise in metallic nanopores. Nanoscale, Vol. 8, no. 24, 2016, pp. 12324 – 12329. DOI 10.1039/C6NR01837H

  20. Lidón López M., Queralt-Martín M., Alcaraz A.: Stochastic pumping of ions based on colored noise in bacterial channels under acidic stress. Nanoscale, Vol. 8, no. 27, 2016, pp. 13422 – 13428. DOI 10.1039/C6NR02638A

  21. France D., Johnson W., Cordell W., Walls F.: Rapid Antimicrobial Susceptibility Testing through Phase Noise Measurements of Cellular Biophysics. Biophysical Journal, Vol. 110, no. 3, Supplement 1, 2016, page 200a. http://dx.doi.org/10.1016/j.bpj.2015.11.1116

  22. Hu Qiu, Anuj Girdhar, Schulten K., Leburton J.-P.: Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores. ACS Nano, Vol. 10, no. 4, 2016, pp. 4482 – 4488. DOI 10.1021/acsnano.6b00226

  23. Hyung-Jun Kim, Pitchford W.H., Kyeong-Beom Park, Hyun-Mi Kim, Edel J.B., Ki-Bum Kim: Photo-Induced Ionic Noise in Si and Quartz Based Solid-State Nanopore Device. Nanopore Sensing - Oct 5 2016, ECS Meeting Abstracts, Abstract 2284. Print ISSN 2151-2041.

  24. Jayesh A. Bafna, Gautam V. Soni: Fabrication of Low Noise Borosilicate Glass Nanopores for Single Molecule Sensing. PloS One, Vol. 11, no. 6, 2016, Article # e0157399. https://doi.org/10.1371/journal.pone.0157399

  25. Yusuke Goto, Itaru Yanagi, Kazuma Matsui, Takahide Yokoi, Ken-ichi Takeda: Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Scientific Reports, Vol. 6, 2016, Article # 31324. DOI 10.1038/srep31324

  26. Wang Ying, Yao Fujun, Kang Xiao-feng: Tetramethylammonium-Filled Protein Nanopore for Single-Molecule Analysis. Analytical Chemistry, Vol. 87, no. 19, 2015, pp. 9991 – 9997. DOI 10.1021/acs.analchem.5b02611

  27. Ramirez P., Gomez V., Cervera J., et al.: Energy conversion from external fluctuating signals based on asymmetric nanopores. Nano Energy, Vol. 16, 2015, pp. 375 – 382. DOI 10.1016/j.nanoen.2015.07.013

  28. Gomez V., Ramirez P., Cervera J., et al.: Converting external potential fluctuations into nonzero time-average electric currents using a single nanopore. Applied Physics Lett., Vol. 106, no. 7, 2015, Article # 073701. DOI 10.1063/1.4909532

  29. Zhai Qingfeng, Wang Jiahai, Jiang Hong, et al.: Bare conical nanopore embedded in polymer membrane for Cr(III) sensing. Talanta, Vol. 140, 2015, pp. 219 – 225. DOI 10.1016/j.talanta.2015.03.035

  30. Wang Ceming, Fu Qibin, Wang Xinwei, et al.: Atomic Layer Deposition Modified Track-Etched Conical Nanochannels for Protein Sensing. Analytical Chemistry, Vol. 87, no. 16, 2015, pp. 8227 – 8233. DOI 10.1021/acs.analchem.5b01501

  31. Rosenstein J.K., Lemay S.G., Shepard K.L.: Single-molecule bioelectronics. Wiley Interdisciplinary Reviews - Nanomedicine & Nanobiotechnology, Vol. 7, no. 4, 2015, pp. 475 – 493. DOI 10.1002/wnan.1323

  32. Hyland B., Siwy Z.S., Martens C.C.: Nanopore Current Oscillations: Nonlinear Dynamics on the Nanoscale. Journal of Physical Chemistry Lett., Vol. 6, no. 10, 2015, pp. 1800 – 1806. DOI 10.1021/acs.jpclett.5b00520

  33. Jiang Yanan, Guo Wei: Nanopore-based sensing and analysis: beyond the resistive-pulse method. Science Bulletin, Vol. 60, no. 5, 2015, pp. 491 – 502. DOI 10.1007/s11434-015-0739-6

  34. Kaufeld T., Steinem C., Schmidt C.F.: Microporous device for local electric recordings on model lipid bilayers. Journal of Physics D - Applied Physics, Vol. 48, no. 2, 2015, Article # 025401. DOI 10.1088/0022-3727/48/2/025401

  35. Harms Z.D., Haywood D.G., Kneller A.R., et al.: Single-Particle Electrophoresis in Nanochannels. Analytical Chemistry, Vol. 87, no. 1, Special Issue: SI, 2015, pp. 699 – 705. DOI 10.1021/ac503527d

  36. Kaufman I. Kh., Gibby W., Luchinsky D.G., McClintock P.V.E., Eisenberg R.S.: Coulomb blockade oscillations in biological ion channels. Int. Conf. on Noise and Fluctuations (ICNF), 2015, pp. 1 – 4. DOI 10.1109/ICNF.2015.7288558

  37. Bian Yukun, Wang Zilin, Chen Anpu, Zhao Nanrong: Fluctuating bottleneck model studies on kinetics of DNA escape from alpha-hemolysin nanopores. Journal of Chemical Physics, Vol. 143, no. 18, 2015, Article # 184908. DOI 10.1063/1.4935118

  38. Lim Min-Cheol, Lee Min-Hyun, Kim Ki-Bum, et al.: A Mask-Free Passivation Process for Low Noise Nanopore Devices. Journal of Nanoscience and Nanotechnology, Vol. 15, no. 8, 2015, pp. 5971 – 5977. DOI 10.1166/jnn.2015.10500

  39. Balan A., Machielse B., Niedzwiecki D., et al.: Improving Signal-to-Noise Performance for DNA Trans location in Solid-State Nanopores at MHz Bandwidths. Nano Letters, Vol. 14, no. 12, 2014, pp. 7215 – 7220. DOI 10.1021/nl504345y

  40. Lee Min-Hyun, Kumar Ashvani, Park Kyeong-Beom, et al.: A Low-Noise Solid-State Nanopore Platform Based on a Highly Insulating Substrate. Scientific Reports, Vol. 4, 2014, Article # 7448. DOI 10.1038/srep07448

  41. Buyukdagli S., Ala-Nissila T.: Controlling Polymer Translocation and Ion Transport via Charge Correlations. Langmuir, Vol. 30, no. 43, 2014, pp. 12907 – 12915. DOI 10.1021/la503327j

  42. Markosyan S., De Biase P.M., Czapla L., et al.: Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore. Nanoscale, Vol. 6, no. 15, 2014, pp. 9006 – 9016. DOI 10.1039/c3nr06559f

  43. Jungsuk Kim, Dunbar W.B.: Nanopore-application CMOS potentiostat design with input parasitic compensation. Electronics Lett., Vol. 50, no. 8, 2014, pp. 578 – 579. DOI 10.1049/el.2014.0049

  44. Kalsi S., Powl A.M., Wallace B.A., et al.: Shaped Apertures in Photoresist Films Enhance the Lifetime and Mechanical Stability of Suspended Lipid Bilayers. Biophysical Journal, Vol. 106, no. 8, 2014, pp. 1650 – 1659. DOI 10.1016/j.bpj.2014.02.033

  45. Wang Yue, Yu Xufeng, Liu Yunyun, et al.: Fabrication of Graphene Nanopores and a Preliminary Study on lambda-DNA Translocation. Acta Physica Sinica, Vol. 72, no. 3, 2014, Special Issue: SI, pp. 378 – 381. DOI 10.6023/A13121208

  46. Kwok H., Briggs K., Tabard-Cossa V.: Nanopore Fabrication by Controlled Dielectric Breakdown. PLoS One, Vol. 9, no. 3, 2014, Article # e92880. DOI 10.1371/journal.pone.0092880

  47. Bressloff P.C., Newby J.M.: Stochastic hybrid model of spontaneous dendritic NMDA spikes. Physical Biology, Vol. 11, no. 1, 2014, Article # 016006. DOI 10.1088/1478-3975/11/1/016006

  48. Lee Min-Hyun, Lee Ju-Hyun, Kim Hyun-Mi, et al.: Leakage current in a Si-based nanopore structure and its influence on noise characteristics. Microfluidics and Nanofluidics, Vol. 16, no. 1-2, 2014, pp. 123 – 130. DOI 10.1007/s10404-013-1192-y

  49. 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

  50. 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

  51. 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

  52. 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. DOI 10.1209/0295-5075/106/10002

  53. 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

  54. Kim J., Maitra R., Pedrotti K.D., Dunbar W.B.: A Patch-Klamp ASIC for Nanopore-Based DNA Analysis. IEEE Trans on Biomedical Circuits and Systems, Vol. 7, no. 3, 2013, pp. 285 – 295. DOI 10.1109/TBCAS.2012.2200893

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

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  75. 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

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  77. 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

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



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