A molecular dynamics simulation framework for predicting noise in solid-state nanopores

References

• Eijkel JCT, Berg Avd. Nanofluidics: what is it and what can we expect from it? Microfluid Nanofluidics. 2005;1:249–267. doi: 10.1007/s10404-004-0012-9
   Web of Science ®Google Scholar
• Bocquet L, Charlaix E. Nanofluidics, from bulk to interfaces. Chem Soc Rev. 2010;39:1073–1095. doi: 10.1039/B909366B
   PubMed Web of Science ®Google Scholar
• Schoch RB, Han J, Renaud P. Transport phenomena in nanofluidics. Rev Mod Phys. 2008;80:839–883. doi: 10.1103/RevModPhys.80.839
   Web of Science ®Google Scholar
• Dekker C. Solid-state nanopores. Nat Nanotechnol. 2007;2:209–216. doi: 10.1038/nnano.2007.27
   PubMed Web of Science ®Google Scholar
• Heerema SJ, Vicarelli L, Pud S, et al. Probing DNA translocations with inplane current signals in a graphene nanoribbon with a nanopore. ACS Nano. 2018;12:2623–2633. doi: 10.1021/acsnano.7b08635
   PubMed Web of Science ®Google Scholar
• Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. Nanoscale. 2016;18:9600–9613. doi: 10.1039/C6NR01061J
   Google Scholar
• Comer J, Ho A, Aksimentiev A. Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations. Electrophoresis. 2012;33:3466–3479. doi: 10.1002/elps.201200164
   PubMed Web of Science ®Google Scholar
• Farimani AB, Dibaeinia P, Aluru NR. DNA origami–graphene hybrid nanopore for DNA detection. ACS Appl Mater Interfaces. 2017;9:92–100. doi: 10.1021/acsami.6b11001
   PubMed Web of Science ®Google Scholar
• Cohen-Tanugi D, Grossman JC. Water desalination across nanoporous graphene. Nano Lett. 2012;12:3602–3608. doi: 10.1021/nl3012853
   PubMed Web of Science ®Google Scholar
• Heiranian M, Farimani AB, Aluru NR. Water desalination with a single-layer MoS2 nanopore. Nat Commun. 2015;6:8616. doi: 10.1038/ncomms9616
   PubMed Web of Science ®Google Scholar
• Surwade SP, Smirnov SN, Vlassiouk IV, et al. Water desalination using nanoporous single-layer graphene. Nature Nanotech. 2015;10:459–464. doi: 10.1038/nnano.2015.37
   PubMed Web of Science ®Google Scholar
• Boretti A, Al-Zubaidy S, Vaclavikova M, et al. Outlook for graphene-based desalination membranes. NPJ Clean Water. 2018;1:5. doi: 10.1038/s41545-018-0004-z
   Web of Science ®Google Scholar
• Karnik R, Fan R, Yue M, et al. Electrostatic control of ions and molecules in nanofluidic transistors. Nano Lett. 2005;5:943–948. doi: 10.1021/nl050493b
   PubMed Web of Science ®Google Scholar
• Radisavljevic B, Radenovic A, Brivio J, et al. Single-layer MoS2 transistors. Nature Nanotech. 2011;6:147–150. doi: 10.1038/nnano.2010.279
   PubMed Web of Science ®Google Scholar
• Lopez-Sanchez O, Lembke D, Kayci M, et al. Ultrasensitive photodetectors based on monolayer MoS2. Nature Nanotech. 2013;8:497–450. doi: 10.1038/nnano.2013.100
   PubMed Web of Science ®Google Scholar
• Siwy Z, Gu Y, Spohr HA, et al. Rectification and voltage gating of ion currents in a nanofabricated pore. Europhys Lett. 2002;60:349–355. doi: 10.1209/epl/i2002-00271-3
   Google Scholar
• Karnik R, Duan C, Castelino K, et al. Rectification of ionic current in a nanofluidic diode. Nano Lett. 2007;7:547–551. doi: 10.1021/nl062806o
   PubMed Web of Science ®Google Scholar
• Vlassiouk I, Siwy ZS. Nanofluidic diode. Nano Lett. 2007;7:552–556. doi: 10.1021/nl062924b
   PubMed Web of Science ®Google Scholar
• Yan R, Liang W, Fan R, et al. Nanofluidic diodes based on nanotube heterojunctions. Nano Lett. 2009;9:3820–3825. doi: 10.1021/nl9020123
   PubMed Web of Science ®Google Scholar
• Nandigana VVR, Jo K, Timperman A, et al. Asymmetric-fluidic-reservoirs induced high rectification nanofluidic diode. Sci Rep. 2018;8:13941. doi: 10.1038/s41598-018-32284-7
   PubMed Web of Science ®Google Scholar
• Tabard-Cossa V, Trivedi D, Wiggin M, et al. Noise analysis and reduction in solid-state nanopores. Nanotechnology. 2007;18:305505. doi: 10.1088/0957-4484/18/30/305505
   Web of Science ®Google Scholar
• Soskine M, Biesemans A, Moeyaert B, et al. An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. Nano Lett. 2012;12:4895–4900. doi: 10.1021/nl3024438
   PubMed Web of Science ®Google Scholar
• Mohammad MM, Iyer R, Howard KR, et al. Engineering a rigid protein tunnel for biomolecular detection. J Am Chem Soc. 2012;134:9521–9531. doi: 10.1021/ja3043646
   PubMed Web of Science ®Google Scholar
• Smeets RMM, Dekker NH, Dekker C. Low-frequency noise in solid-state nanopores. Nanotechnology. 2009;20:095501. doi: 10.1088/0957-4484/20/9/095501
   PubMed Web of Science ®Google Scholar
• Hoogerheide DP, Garaj S, Golovchenko JA. Probing surface charge fluctuations with solid-state nanopores. Phys Rev Lett. 2009;102:5–8. doi: 10.1103/PhysRevLett.102.256804
   Web of Science ®Google Scholar
• Tasserit C, Koutsioubas A, Lairez D, et al. Pink noise of ionic conductance through single artificial nanopores revisited. Phys Rev Lett. 2010;105:260602. doi: 10.1103/PhysRevLett.105.260602
   PubMed Web of Science ®Google Scholar
• Smeets RMM, Keyser UF, Wu MY, et al. Nanobubbles in solid-state nanopores. Phys Rev Lett. 2006;97:088101. doi: 10.1103/PhysRevLett.97.088101
   PubMed Web of Science ®Google Scholar
• Siwy Z, Fuliński A. Origin of 1/fα noise in membrane channel currents. Phys Rev Lett. 2002;89:158101. doi: 10.1103/PhysRevLett.89.158101
   PubMed Web of Science ®Google Scholar
• Qiao R, Aluru NR. Ion concentrations and velocity profiles in nanochannel electroosmotic flows. J Chem Phys. 2013;118:4692–4701. doi: 10.1063/1.1543140
   Google Scholar
• Comer J, Dimitrov V, Zhao Q, et al. Microscopic mechanics of hairpin DNA translocation through synthetic nanopores. Biophys J. 2009;96:593–608. doi: 10.1016/j.bpj.2008.09.023
   PubMed Web of Science ®Google Scholar
• Cruz-Chú E, Aksimentiev A, Schulten K. Ionic current rectification through silica nanopores. Phys Chem C Nanomater Interfaces. 2009;113:1850. doi: 10.1021/jp804724p
   PubMed Web of Science ®Google Scholar
• Aksimentiev A, Schulten K. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J. 2005;88:3745–3761. doi: 10.1529/biophysj.104.058727
   PubMed Web of Science ®Google Scholar
• Ho C, Qiao R, Heng JB, et al. Electrolytic transport through a synthetic nanometer-diameter pore. PNAS. 2005;102:10445–10450. doi: 10.1073/pnas.0500796102
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5
   PubMed Web of Science ®Google Scholar
• Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802. doi: 10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Lee C, Joly L, Siria A, et al. Large apparent electric size of solid-state nanopores due to spatially extended surface conduction. Nano Lett. 2012;12:4037–4044. doi: 10.1021/nl301412b
   PubMed Web of Science ®Google Scholar
• Siria A, Poncharal P, Biance A-L, et al. Giant osmotic energy conversion measured in a single transmembrane boron nitride nanotube. Nature. 2013;494:455–458. doi: 10.1038/nature11876
   PubMed Web of Science ®Google Scholar
• Feng J, Graf M, Liu K, et al. Single-layer MoS2 nanopores as nanopower generators. Nature. 2016;536:197–200. doi: 10.1038/nature18593
   PubMed Web of Science ®Google Scholar
• Macha M, Marion S, Nandigana VVR, et al. 2D materials as an emerging platform for nanopore-based power generation. Nat Rev Mater. 2019;1:1–18.
   Google Scholar
• Welch D. The use of fast fourier transform for the estimation of power spectra: a method based on time averaging over short, modified periodograms. IEEE Trans Audio ElectroacousticsAU. 1967;15:70–73. doi: 10.1109/TAU.1967.1161901
   Google Scholar
• Levis RA, Rae JL. The use of quartz patch pipettes for low noise single channel recording. Biophys J. 1993;65:1666–1677. doi: 10.1016/S0006-3495(93)81224-4
   PubMed Web of Science ®Google Scholar
• Smeets RMM, Keyser UF, Dekker NH, et al. Noise in solid-state nanopores. PNAS. 2008;105:417–421. doi: 10.1073/pnas.0705349105
   PubMed Web of Science ®Google Scholar
• Kumar A, Park K-B, Kim H-M, et al. Noise and its reduction in graphene based nanopore devices. Nanotechnology. 2013;24:495503. doi: 10.1088/0957-4484/24/49/495503
   PubMed Web of Science ®Google Scholar
• Balan A, Machielse B, Niedzwiecki D, et al. Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths. Nano Lett. 2014;14:7215–7220. doi: 10.1021/nl504345y
   PubMed Web of Science ®Google Scholar
• Heerema SJ, Schneider GF, Rozemuller M, et al. 1/f noise in graphene nanopores. Nanotechnology. 2015;26:074001. doi: 10.1088/0957-4484/26/7/074001
   PubMed Web of Science ®Google Scholar
• Wen C, Zeng S, Arstila K, et al. Generalized noise study of solid-state nanopores at low frequencies. ACS Sensors. 2017;2:300–307. doi: 10.1021/acssensors.6b00826
   PubMed Web of Science ®Google Scholar
• Fragasso A, Pud S, Dekker C. 1/f noise in solid-state nanopores is governed by access and surface regions. Nanotechnology. 2019;30:395202. doi: 10.1088/1361-6528/ab2d35
   PubMed Web of Science ®Google Scholar
• Knowles SF, Keyser UF, Thorneywork AL. Noise properties of rectifying and non-rectifying nanopores. Nanotechnology. 2020;31:10LT01. doi: 10.1088/1361-6528/ab5be3
   Web of Science ®Google Scholar
• Gravelle S, Netz RR, Bocquet L. Adsorption kinetics in open nanopores as a source of low-frequency noise. Nano Lett. 2019;19:7265–7272. doi: 10.1021/acs.nanolett.9b02858
   PubMed Web of Science ®Google Scholar
• Lianga S, Xianga F, Tang Z, et al. Noise in nanopore sensors: sources, models, reduction, and benchmarking. Nanotech and Precis Eng. 2020;3:9–17. doi: 10.1016/j.npe.2019.12.008
   Google Scholar
• Hooge FN. 1/ƒ noise is no surface effect. Phys Lett. 1969;29A:139. doi: 10.1016/0375-9601(69)90076-0
   Google Scholar
• Barta J, Manela M, Fischer R. Si3N4 and Si2N2O for high performance radomes. Mater Sci Eng. 1985;71:265–272. doi: 10.1016/0025-5416(85)90236-8
   Google Scholar
• Lukianova OA, Sirota VV. Dielectric properties of silicon nitride ceramics produced by free sintering. Ceram Int. 2017;43:8284–8288. doi: 10.1016/j.ceramint.2017.03.161
   Google Scholar