Electroosmosis in nanopores: computational methods and technological applications

References

• Reuss FF. Notice sur un nouvel effect de 1ʹélectricité galvanique. Mem Soc Imp Nat Moscou. 1809;2:3227.
   Google Scholar
• Porrett R Jr. Curious galvanic experiments. Ann Philos. 1816;8:74–53.
   Google Scholar
• Biscombe CJC. The discovery of electrokinetic phenomena: setting the record straight. Angew Chem. 2017;56:8338–8340.
   Google Scholar
• Kirby BJ. Micro-and nanoscale fluid mechanics: transport in microfluidic devices. Cambridge University Press; 2010.
   Google Scholar
• Haywood DG, Saha-Shah A, Baker LA, et al. Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem. 2015;87:172–187.
   PubMedGoogle Scholar
• Yusko EC, Ran A, Mayer M. Electroosmotic flow can generate ion current rectification in nano-and micropores. ACS Nano. 2010;4:477–487.
   PubMedGoogle Scholar
• Balme S, Picaud F, Manghi M, et al. Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation. Sci Rep. 2015;5:1–14.
   Google Scholar
• Chinappi M, Cecconi F. Protein sequencing via nanopore based devices: a nanofluidics perspective. J Phys. 2018;30:204002.
   Google Scholar
• Bayley H, Braha O, Gu L-Q. Stochastic sensing with protein pores. Adv Mater. 2000;12:139–142.
   Web of Science ®Google Scholar
• Xue L, Yamazaki H, Ren R, et al. Solid-state nanopore sensors. Nat Rev Mater. 2020;5:931–951.
   Google Scholar
• Chinappi M, Yamaji M, Kawano R, et al. Analytical model for particle capture in nanopores elucidates competition among electrophoresis, electroosmosis, and dielectrophoresis. ACS Nano. 2020;14:15816–15828.
   PubMed Web of Science ®Google Scholar
• Saharia, J., Bandara, Y. N. D., Karawdeniya, B. I., Hammond, C., Alexandrakis, G., & Kim, M. J. 2021. Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore. RSC advances, 11(39), 24398–24409.
   Google Scholar
• Boukhet M, Piguet F, Ouldali H, et al. Probing driving forces in aerolysin and α-hemolysin biological nanopores: electrophoresis versus electroosmosis. Nanoscale. 2016;8:18352–18359.
   PubMedGoogle Scholar
• Huang G, Willems K, Soskine M, et al. Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with frac nanopores. Nat Commun. 2017;8:1–11.
   PubMedGoogle Scholar
• Asandei A, Schiopu I, Chinappi M, et al. Electroosmotic trap against the electrophoretic force near a protein nanopore reveals peptide dynamics during capture and translocation. ACS Appl Mater Interfaces. 2016;8:13166–13179.
   PubMed Web of Science ®Google Scholar
• Ermann N, Hanikel N, Wang V, et al. Promoting single-file dna translocations through nanopores using electro-osmotic flow. J Chem Phys. 2018;149:163311.
   PubMedGoogle Scholar
• Hsu W-L, Daiguji H. Manipulation of protein translocation through nanopores by flow field control and application to nanopore sensors. Anal Chem. 2016;88:9251–9258.
   PubMedGoogle Scholar
• Bruus H. Theoretical microfluidics. Vol. 18. Oxford university press Oxford; 2008
   Google Scholar
• Gouy M. Sur la constitution de la charge électrique à la surface d’un électrolyte. J Phys Theor Appl. 1910;9:457–468.
   Google Scholar
• Leonard Chapman D. Li. a contribution to the theory of electrocapillarity. London, Edinburgh, Dublin Philos Mag J Sci. 1913;25:475–481.
   Google Scholar
• Fogolari F, Brigo A, Molinari H. The poisson–boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recog. 2002;15:377–392.
   PubMed Web of Science ®Google Scholar
• Debye P, Hückel E. De la theorie des electrolytes. i. abaissement du point de congelation et phenomenes associes. Physikalische Zeitschrift. 1923;24:185–206.
   Google Scholar
• Smeets RMM, Keyser UF, Krapf D, et al. Salt dependence of ion transport and dna translocation through solid-state nanopores. Nano Lett. 2006;6:89–95.
   PubMed Web of Science ®Google Scholar
• Tianji M, Balanzat E, Janot J-M, et al. Nanopore functionalized by highly charged hydrogels for osmotic energy harvesting. ACS Appl Mater Interfaces. 2019;11:12578–12585.
   PubMedGoogle Scholar
• Willems K, Ruić D, Lucas FLR, et al. Accurate modeling of a biological nanopore with an extended continuum framework. Nanoscale. 2020;12:16775–16795.
   PubMedGoogle Scholar
• Bétermier F, Cressiot B, Di Muccio G, et al. Single-sulfur atom discrimination of polysulfides with a protein nanopore for improved batteries. Communicat Mater. 2020;1:1–11.
   Google Scholar
• Wang X, Cheng C, Wang S, et al. Electroosmotic pumps and their applications in microfluidic systems. Microfluid Nanofluid. 2009;6:145–162.
   PubMed Web of Science ®Google Scholar
• Green Y. Conditions for electroneutrality breakdown in nanopores. J Chem Phys. 2021;155:184701.
   PubMedGoogle Scholar
• Noh Y, Aluru NR. Ion transport in electrically imperfect nanopores. ACS Nano. 2020;14:10518–10526.
   PubMed Web of Science ®Google Scholar
• Dong Z, Kennedy E, Hokmabadi M, et al. Discriminating residue substitutions in a single protein molecule using a sub-nanopore. ACS Nano. 2017;11:5440–5452.
   PubMedGoogle Scholar
• Ying C, Houghtaling J, Eggenberger OM, et al. Formation of single nanopores with diameters of 20–50 nm in silicon nitride membranes using laser-assisted controlled breakdown. ACS nano. 2018;12:11458–11470.
   PubMedGoogle Scholar
• Won Shin J, Yong Lee J, Do Hyun O, et al. Shrinkage and expansion mechanisms of sio 2 elliptical membrane nanopores. Appl Phys Lett. 2008;93:221903.
   Google Scholar
• Cressiot B, Oukhaled A, Patriarche G, et al. Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory. ACS nano. 2012;6:6236–6243.
   PubMedGoogle Scholar
• Yameen B, Ali M, Neumann R, et al. Single conical nanopores displaying ph-tunable rectifying characteristics. manipulating ionic transport with zwitterionic polymer brushes. J Am Chem Soc. 2009;131:2070–2071.
   PubMed Web of Science ®Google Scholar
• Bai J, Wang D, Nam S-W, et al. Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales. Nanoscale. 2014;6:8900–8906.
   PubMedGoogle Scholar
• Cantley L, Swett JL, Lloyd D, et al. Voltage gated inter-cation selective ion channels from graphene nanopores. Nanoscale. 2019;11:9856–9861.
   PubMedGoogle Scholar
• Yao Y, Wen C, Pham NH, et al. On induced surface charge in solid-state nanopores. Langmuir. 2020;36:8874–8882.
   PubMedGoogle Scholar
• Di Muccio G, Morozzo Della Rocca B, Chinappi M. Geometrically induced selectivity and unidirectional electroosmosis in uncharged nanopores. arXiv preprint arXiv:2104 03390. 2021. https://doi.org/10.1021/acsnano.1c03017
   Google Scholar
• Letizia Bonome E, Cecconi F, Chinappi M. Electroosmotic flow through an α-hemolysin nanopore. Microfluid Nanofluid. 2017;21:96.
   Google Scholar
• Gu L-Q, Cheley S, Bayley H. Prolonged residence time of a noncovalent molecular adapter, β-cyclodextrin, within the lumen of mutant α-hemolysin pores. J Gen Physiol. 2001;118:481–494.
   PubMed Web of Science ®Google Scholar
• Cao B, Zhao Y, Kou Y, et al. Structure of the nonameric bacterial amyloid secretion channel. Proc Nat Acad Sci. 2014;111:E5439–E5444.
   PubMed Web of Science ®Google Scholar
• Wanunu M, Meller A. Chemically modified solid-state nanopores. Nano Lett. 2007;7:1580–1585.
   PubMed Web of Science ®Google Scholar
• Lin K, Zhongwu L, Tao Y, et al. Surface charge density inside a silicon nitride nanopore. Langmuir. 2021.
   Google Scholar
• Chen P, Mitsui T, Farmer DB, et al. Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. Nano Lett. 2004;4:1333–1337.
   PubMed Web of Science ®Google Scholar
• Hoogerheide DP, Garaj S, Golovchenko JA. Probing surface charge fluctuations with solid-state nanopores. Phys Rev Lett. 2009;102:256804.
   PubMedGoogle Scholar
• Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. Nanoscale. 2019;11:19636–19657.
   PubMed Web of Science ®Google Scholar
• Lepoitevin M, Tianji M, Bechelany M, et al. Functionalization of single solid state nanopores to mimic biological ion channels: a review. Adv Colloid Interface Sci. 2017;250:195–213.
   PubMed Web of Science ®Google Scholar
• Anderson BN, Muthukumar M, Meller A. ph tuning of dna translocation time through organically functionalized nanopores. ACS nano. 2013;7:1408–1414.
   PubMedGoogle Scholar
• Karmi A, Priya Sakala G, Rotem D, et al. Durable, stable, and functional nanopores decorated by self-assembled dipeptides. ACS Appl Mater Interfaces. 2020;12:14563–14568.
   PubMedGoogle Scholar
• Mayumi Fujinami Tanimoto I, Cressiot B, Jarroux N, et al. Selective target protein detection using a decorated nanopore into a microfluidic device. Biosens Bioelectron. 2021;183:113195.
   PubMedGoogle Scholar
• Kim D, Darve E. High-ionic-strength electroosmotic flows in uncharged hydrophobic nanochannels. J Colloid Interface Sci. 2009;330:194–200.
   PubMedGoogle Scholar
• Armstrong CM, Hille B. Voltage-gated ion channels and electrical excitability. Neuron. 1998;20:371–380.
   PubMed Web of Science ®Google Scholar
• Guan W, Sylvia Xin L, Reed MA. Voltage gated ion and molecule transport in engineered nanochannels: theory, fabrication and applications. Nanotechnology. 2014;25:122001.
   PubMedGoogle Scholar
• Ren R, Zhang Y, Paulose Nadappuram B, et al. Nanopore extended field-effect transistor for selective single-molecule biosensing. Nat Commun. 2017;8:1–9.
   PubMedGoogle Scholar
• Sedra AS, Smith KC. Microelectronic circuits. In: Oxf ser elec series. Oxford University Press; 2010.
   Google Scholar
• Kalman EB, Sudre O, Vlassiouk I, et al. Control of ionic transport through gated single conical nanopores. Anal Bioanal Chem. 2009;394:413–419.
   PubMedGoogle Scholar
• Van Toan N, Inomata N, Toda M, et al. Ion transport by gating voltage to nanopores produced via metal-assisted chemical etching method. Nanotechnology. 2018;29:195301.
   PubMedGoogle Scholar
• Nam S-W, Rooks MJ, Kim K-B, et al. Ionic field effect transistors with sub-10 nm multiple nanopores. Nano Lett. 2009;9:2044–2048.
   PubMed Web of Science ®Google Scholar
• Pérez-Mitta G, Marmisollé WA, Trautmann C, et al. An all-plastic field-effect nanofluidic diode gated by a conducting polymer layer. Adv Mater. 2017;29:1700972.
   Google Scholar
• Cheng C, Jiang G, Philip Simon G, et al. Low-voltage electrostatic modulation of ion diffusion through layered graphene-based nanoporous membranes. Nat Nanotechnol. 2018;13:685–690.
   PubMedGoogle Scholar
• Wang Y, Zhang H, Kang Y, et al. Voltage-gated ion transport in two-dimensional sub-1 nm nanofluidic channels. ACS Nano. 2019;13:11793–11799.
   PubMedGoogle Scholar
• Squires TM. Induced-charge electrokinetics: fundamental challenges and opportunities. Lab Chip. 2009;9:2477–2483.
   PubMedGoogle Scholar
• Läuger P, Lesslauer W, Marti E, et al. Electrical properties of bimolecular phospholipid membranes. Biochimi Biophys Acta (BBA) Biomembr. 1967;135:20–32.
   PubMed Web of Science ®Google Scholar
• Bazant MZ, Squires TM. Induced-charge electrokinetic phenomena. Curr Opin Colloid Interface Sci. 2010;15:203–213.
   Web of Science ®Google Scholar
• Wanunu M, Morrison W, Rabin Y, et al. Electrostatic focusing of unlabelled dna into nanoscale pores using a salt gradient. Nat Nanotechnol. 2010;5:160–165.
   PubMedGoogle Scholar
• Chinappi M, Luchian T, Cecconi F. Nanopore tweezers: voltage-controlled trapping and releasing of analytes. Phys Rev E. 2015;92:032714.
   Google Scholar
• Marbach S, Dean DS, Bocquet L. Transport and dispersion across wiggling nanopores. Nat Phys. 2018;14:1108–1113.
   Web of Science ®Google Scholar
• Ming M, Grey F, Shen L, et al. Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction. Nat Nanotechnol. 2015;10:692–695.
   PubMedGoogle 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.
   PubMedGoogle Scholar
• Thorneywork AL, Gladrow J, Qing Y, et al. Direct detection of molecular intermediates from first-passage times. Sci Adv. 2020;6:eaaz4642.
   PubMedGoogle Scholar
• Marbach S. Intrinsic fractional noise in nanopores: the effect of reservoirs. J Chem Phys. 2021;154:171101.
   PubMedGoogle Scholar
• Tai Andrew Wong C, Muthukumar M. Polymer capture by electro-osmotic flow of oppositely charged nanopores. J Chem Phys. 2007;126:164903.
   PubMedGoogle Scholar
• Grosberg AY, Rabin Y. Dna capture into a nanopore: interplay of diffusion and electrohydrodynamics. J Chem Phys. 2010;133:10B617.
   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.
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Muzard J, Payet L, et al. Rectification of the current in α-hemolysin pore depends on the cation type: the alkali series probed by molecular dynamics simulations and experiments. J Phys Chem C. 2011;115:4255–4264.
   PubMedGoogle 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.
   PubMedGoogle Scholar
• Schmid S, Stömmer P, Dietz H, et al. Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations. bioRxiv. 2021.
   Google Scholar
• Mukherjee S, Goswami P, Dhar J, et al. Ion-size dependent electroosmosis of viscoelastic fluids in microfluidic channels with interfacial slip. Phys Fluids. 2017;29:072002.
   Google Scholar
• Kim S, Karrila SJ. Microhydrodynamics: principles and selected applications. Courier Corporation; 2013.
   Google Scholar
• Prohl A, Schmuck M. Convergent finite element discretizations of the navier-stokes-nernst-Planck-poisson system. ESAIM Math Modell Numer Anal. 2010;44:531–571.
   Google Scholar
• Sherwood JD, Mao M, Ghosal S. Electrically generated eddies at an eightfold stagnation point within a nanopore. Phys Fluids. 2014;26:112004.
   PubMedGoogle Scholar
• Cho C-C, Chen C-L, et al. Characteristics of combined electroosmotic flow and pressure-driven flow in microchannels with complex-wavy surfaces. Int J Ther Sci. 2012;61:94–105.
   Web of Science ®Google Scholar
• Lauga E, Brenner M, Stone H. Microfluidics: the no-slip boundary condition. In: Springer handbooks. Springer; 2007. p. 1219–1240.
   Google Scholar
• Collis JF, Olcum S, Chakraborty D, et al. Measurement of navier slip on individual nanoparticles in liquid. Nano Lett. 2021.
   PubMedGoogle Scholar
• Bazant MZ, Vinogradova OI. Tensorial hydrodynamic slip. J Fluid Mech. 2008;613:125–134.
   Web of Science ®Google Scholar
• Sendner C, Horinek D, Bocquet L, et al. Interfacial water at hydrophobic and hydrophilic surfaces: slip, viscosity, and diffusion. Langmuir. 2009;25:10768–10781.
   PubMed Web of Science ®Google Scholar
• Huang DM, Sendner C, Horinek D, et al. Water slippage versus contact angle: a quasiuniversal relationship. Phys Rev Lett. 2008;101:226101.
   PubMed Web of Science ®Google Scholar
• Chinappi M, Casciola CM. Intrinsic slip on hydrophobic self-assembled monolayer coatings. Phys Fluids. 2010;22:042003.
   Google Scholar
• Bakli C, Chakraborty S. Slippery to sticky transition of hydrophobic nanochannels. Nano Lett. 2015;15:7497–7502.
   PubMedGoogle Scholar
• Joly L, Ybert C. Emmanuel T, et al. Liquid friction on charged surfaces: from hydrodynamic slippage to electrokinetics. J Chem Phys. 2006;125:204716.
   PubMed Web of Science ®Google Scholar
• Melnikov DV, Hulings ZK, Gracheva ME. Electro-osmotic flow through nanopores in thin and ultrathin membranes. Phys Rev E. 2017;95:063105.
   PubMedGoogle Scholar
• Malgaretti P, Pagonabarraga I, Miguel Rubi J. Entropic electrokinetics: recirculation, particle separation, and negative mobility. Phys Rev Lett. 2014;113:128301.
   PubMedGoogle Scholar
• Chinappi M, Malgaretti P. Charge polarization, local electroneutrality breakdown and eddy formation due to electroosmosis in varying-section channels. Soft Matter. 2018;14:9083–9087.
   PubMedGoogle Scholar
• Malgaretti P, Janssen M, Pagonabarraga I, et al. Driving an electrolyte through a corrugated nanopore. J Chem Phys. 2019;151:084902.
   PubMed Web of Science ®Google Scholar
• Benzhuo L, Zhou YC. Poisson-nernst-Planck equations for simulating biomolecular diffusion-reaction processes ii: size effects on ionic distributions and diffusion-reaction rates. Biophys J. 2011;100:2475–2485.
   PubMedGoogle Scholar
• Davidson SM, Andersen MB, Mani A. Chaotic induced-charge electro-osmosis. Phys Rev Lett. 2014;112:128302.
   PubMedGoogle Scholar
• Laohakunakorn N, Keyser UF. Electroosmotic flow rectification in conical nanopores. Nanotechnology. 2015;26:275202.
   PubMedGoogle Scholar
• Laohakunakorn N, Thacker VV, Muthukumar M, et al. Electroosmotic flow reversal outside glass nanopores. Nano Lett. 2015;15:695–702.
   PubMedGoogle Scholar
• Ai Y, Zhang M, Joo SW, et al. Effects of electroosmotic flow on ionic current rectification in conical nanopores. J Phys Chem C. 2010;114:3883–3890.
   Google Scholar
• Manghi M, Palmeri J, Henn F, et al. Ionic conductance of carbon nanotubes: confronting literature data with nanofluidic theory. J Phys Chem C. 2021;125:22943–22950.
   Google Scholar
• Sherwood JD, Mao M, Ghosal S. Electroosmosis in a finite cylindrical pore: simple models of end effects. Langmuir. 2014;30:9261–9272.
   PubMedGoogle Scholar
• Dreyer W, Guhlke C, Müller R. Overcoming the shortcomings of the nernst–Planck model. Phys Chem Chem Phys. 2013;15:7075–7086.
   PubMed Web of Science ®Google Scholar
• Marbach S, Yoshida H, Bocquet L. Osmotic and diffusio-osmotic flow generation at high solute concentration. i. mechanical approaches. J Chem Phys. 2017;146:194701.
   PubMedGoogle Scholar
• Ruurds De Groot S, Mazur P. Non-equilibrium thermodynamics. Courier Corporation; 2013.
   Google Scholar
• Fuhrmann J. Comparison and numerical treatment of generalised nernst–Planck models. Comput Phys Commun. 2015;196:166–178.
   Google Scholar
• Bandopadhyay A, Chakraborty S. Ionic size dependent electroosmosis in ion-selective microchannels and nanochannels. Electrophoresis. 2013;34:2193–2198.
   PubMedGoogle Scholar
• Hameed Chaudhry J, Comer J, Aksimentiev A, et al. A stabilized finite element method for modified poisson-nernst-Planck equations to determine ion flow through a nanopore. Commun Computat Phys. 2014;15:93–125.
   Google Scholar
• Qiao Y, Bin T, Benzhuo L. Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified pnp equations. J Chem Phys. 2014;140:174102.
   PubMedGoogle Scholar
• Siddiqua F, Wang Z, Zhou S. A modified poisson–nernst–Planck model with excluded volume effect: theory and numerical implementation. arXiv preprint arXiv:1801 00751, 2017.
   Google Scholar
• Sabri Kilic M, Bazant MZ, Ajdari A. Steric effects in the dynamics of electrolytes at large applied voltages. i. double-layer charging. Phys Rev E. 2007;75:021502.
   Google Scholar
• Sabri Kilic M, Bazant MZ, Ajdari A. Steric effects in the dynamics of electrolytes at large applied voltages. ii. modified poisson-nernst-Planck equations. Phys Rev E. 2007;75:021503.
   Google Scholar
• Fuhrmann J, Clemens Guhlke AL, Merdon C, et al. Induced charge electroosmotic flow with finite ion size and solvation effects. Electrochim Acta. 2019;317:778–785.
   Google Scholar
• Mouterde T, Ashok Keerthi ARP, Dar SA, et al. Molecular streaming and its voltage control in ångström-scale channels. Nature. 2019;567:87–90.
   PubMedGoogle Scholar
• Schlaich A, Knapp EW, Netz RR. Water dielectric effects in planar confinement. Phys Rev Lett. 2016;117:048001.
   PubMed Web of Science ®Google Scholar
• Fumagalli L, Esfandiar A, Fabregas R, et al. Anomalously low dielectric constant of confined water. Science. 2018;360:1339–1342.
   PubMedGoogle Scholar
• Kavokine N, Marbach S, Siria A, et al. Ionic Coulomb blockade as a fractional wien effect. Nat Nanotechnol. 2019;14:573–578.
   PubMedGoogle Scholar
• Sokoloff JB. Enhancement of the water flow velocity through carbon nanotubes resulting from the radius dependence of the friction due to electron excitations. Phys Rev E. 2018;97:033107.
   PubMed Web of Science ®Google Scholar
• Kavokine N, Robert A. Marie-Laure B, et al. Fluctuation-induced quantum friction in nanoscale water flows. arXiv preprint arXiv:2105 03413. 2021.
   Google Scholar
• Siwy Z, Fuliński A. Origin of 1/f α noise in membrane channel currents. Phys Rev Lett. 2002;89:158101.
   PubMedGoogle Scholar
• Secchi E, Niguès A, Jubin L, et al. Scaling behavior for ionic transport and its fluctuations in individual carbon nanotubes. Phys Rev Lett. 2016;116:154501.
   PubMedGoogle Scholar
• Knowles SF, Weckman NE, Lim VJY, et al. Current fluctuations in nanopores reveal the polymer-wall adsorption potential. Phys Rev Lett. 2021;127:137801.
   PubMedGoogle Scholar
• Kavokine N, Netz RR, Bocquet L. Fluids at the nanoscale: from continuum to subcontinuum transport. Annu Rev Fluid Mech. 2021;53:377–410.
   Google Scholar
• Murad S, Oder K, Lin J. Molecular simulation of osmosis, reverse osmosis, and electro-osmosis in aqueous and methanolic electrolyte solutions. Mol Phys. 1998;95:401–408.
   Web of Science ®Google Scholar
• Zhou W, Qiu H, Guo Y, et al. Molecular insights into distinct detection properties of α-hemolysin, mspa, csgg, and aerolysin nanopore sensors. J Phys Chem A. 2020;124:1611–1618.
   Google Scholar
• Aksimentiev A, Heng JB, Timp G, et al. Microscopic kinetics of dna translocation through synthetic nanopores. Biophys J. 2004;87:2086–2097.
   PubMed Web of Science ®Google Scholar
• Hummer G, Rasaiah JC, Noworyta JP. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 2001;414:188–190.
   PubMed Web of Science ®Google Scholar
• Zhu F, Tajkhorshid E, Schulten K. Collective diffusion model for water permeation through microscopic channels. Phys Rev Lett. 2004;93:224501.
   PubMed Web of Science ®Google Scholar
• Shankla M, Aksimentiev A. Step-defect guided delivery of dna to a graphene nanopore. Nat Nanotechnol. 2019;14:858–865.
   PubMedGoogle Scholar
• Letizia Bonome E, Lepore R, Raimondo D, et al. Multistep current signal in protein translocation through graphene nanopores. J Phys Chem A. 2015.
   Google Scholar
• Barati Farimani A, Heiranian M, Aluru NR. Identification of amino acids with sensitive nanoporous mos2: towards machine learning-based prediction. Nat 2D Mater. 2018;2.
   Google Scholar
• Shankla M, Aksimentiev A. Molecular transport across the ionic liquid–aqueous electrolyte interface in a mos2 nanopore. ACS Appl Mater Interfaces. 2020;12:26624–26634.
   PubMedGoogle Scholar
• Guohui H, Mao M, Ghosal S. Ion transport through a graphene nanopore. Nanotechnology. 2012;23:395501.
   PubMedGoogle Scholar
• Qiao R, Aluru NR. Ion concentrations and velocity profiles in nanochannel electroosmotic flows. J Chem Phys. 2003;118:4692–4701.
   Web of Science ®Google Scholar
• Qiao R, Aluru NR. Atypical dependence of electroosmotic transport on surface charge in a single-wall carbon nanotube. Nano Lett. 2003;3:1013–1017.
   Web of Science ®Google Scholar
• Freund JB. Electro-osmosis in a nanometer-scale channel studied by atomistic simulation. J Chem Phys. 2002;116:2194–2200.
   Web of Science ®Google Scholar
• Comer JR, Wells DB, Aksimentiev A. Modeling nanopores for sequencing dna. In: DNA nanotechnology. Springer; 2011. p. 317–358.
   Google Scholar
• Shahmardi A, Tammisola O, Chinappi M, et al. Effects of surface nanostructure and wettability on pool boiling: a molecular dynamics study. Int J Ther Sci. 2021;167:106980.
   Web of Science ®Google Scholar
• Marrink SJ, Jelger Risselada H, Serge Yefimov DPT, et al. The martini force field: coarse grained model for biomolecular simulations. J Phys Chem A. 2007;111:7812–7824.
   PubMed Web of Science ®Google Scholar
• Clementi C. Coarse-grained models of protein folding: toy models or predictive tools? Curr Opin Struct Biol. 2008;18:10–15.
   PubMed Web of Science ®Google Scholar
• Maffeo C, Ngo TTM, Taekjip H, et al. A coarse-grained model of unstructured single-stranded dna derived from atomistic simulation and single-molecule experiment. J Chem Theory Comput. 2014;10:2891–2896.
   PubMedGoogle Scholar
• Tuckerman M. Statistical mechanics: theory and molecular simulation. Oxford University Press; 2010.
   Google Scholar
• Allen MP, Tildesley DJ. Computer simulation of liquids. Vol. 385. New York: Oxford; 1989.
   Google Scholar
• Frenkel D, Smit B. Understanding molecular simulation: from algorithms to applications. Vol. 1. Elsevier; 2001.
   Google Scholar
• McPherson A, Gavira JA. Introduction to protein crystallization. Acta Crystallogr Sect F Struct Biol Commun. 2014;70:2–20.
   PubMedGoogle Scholar
• Thonghin N, Kargas V, Clews J, et al. Cryo-electron microscopy of membrane proteins. Methods. 2018;147:176–186.
   PubMedGoogle Scholar
• Lipfert J, Doniach S. Small-angle x-ray scattering from rna, proteins, and protein complexes. Annu Rev Biophys Biomol Struct. 2007;36:307–327.
   PubMedGoogle Scholar
• Sørensen TL-M, John Hjorth-Jensen S, Oksanen E, et al. Membrane-protein crystals for neutron diffraction. Acta Crystallogr Sect D Struct Biol. 2018;74:1208–1218.
   Google Scholar
• Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28:235–242.
   PubMed Web of Science ®Google Scholar
• Lomize MA, Pogozheva ID, Joo H, et al. Opm database and ppm web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 2012;40:D370–D376.
   PubMed Web of Science ®Google Scholar
• Stansfeld PJ, Goose JE, Caffrey M, et al. Memprotmd: automated insertion of membrane protein structures into explicit lipid membranes. Structure. 2015;23:1350–1361.
   PubMed Web of Science ®Google Scholar
• Song L, Hobaugh MR, Shustak C, et al. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science. 1996;274:1859–1865.
   PubMed Web of Science ®Google Scholar
• Tanaka K, Caaveiro JMM, Morante K, et al. Structural basis for self-assembly of a cytolytic pore lined by protein and lipid. Nat Commun. 2015;6:6337.
   PubMedGoogle Scholar
• Faller M, Niederweis M, Schulz GE. The structure of a mycobacterial outer-membrane channel. Science. 2004;303:1189–1192.
   PubMed Web of Science ®Google Scholar
• Biasini M, Bienert S, Waterhouse A, et al. Swiss-model: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014;42:W252–W258.
   PubMed Web of Science ®Google Scholar
• Webb B, Sali A. Comparative protein structure modeling using modeller. Curr Protoc Bioinf. 2016;54:5–6.
   PubMedGoogle Scholar
• Goyal P, Krasteva PV, Van Gerven N, et al. Structural and mechanistic insights into the bacterial amyloid secretion channel csgg. Nature. 2014;516:250.
   PubMed Web of Science ®Google Scholar
• Iacovache I, De Carlo S, Cirauqui N, et al. Cryo-em structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Nat Commun. 2016;7:12062.
   PubMed Web of Science ®Google Scholar
• Cao C, Cirauqui N, Jose Marcaida M, et al. Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores. Nat Commun. 2019;10:1–11.
   PubMedGoogle Scholar
• Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating p k prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 2012;40:W537–W541.
   PubMed Web of Science ®Google Scholar
• Olsson MHM, Søndergaard CR, Rostkowski M, et al. Propka3: consistent treatment of internal and surface residues in empirical p k a predictions. J Chem Theory Comput. 2011;7:525–537.
   PubMed Web of Science ®Google Scholar
• Huang J, Rauscher S, Nawrocki G, et al. Charmm36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017;14:71–73.
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118:11225–11236.
   Web of Science ®Google Scholar
• Hammond K, Cipcigan F, Al Nahas K, et al. Switching cytolytic nanopores into antimicrobial fractal ruptures by a single side chain mutation. ACS Nano. 2021.
   PubMedGoogle Scholar
• Bauer CK, Calligari P, Clementina Radio F, et al. Mutations in kcnk4 that affect gating cause a recognizable neurodevelopmental syndrome. Am J Hum Genet. 2018;103:621–630.
   PubMed Web of Science ®Google Scholar
• Di Muccio G, Eugenio Rossini A, Di Marino D, et al. Insights into protein sequencing with an α-hemolysin nanopore by atomistic simulations. Sci Rep. 2019;9:6440.
   PubMedGoogle Scholar
• Ming M, Tocci G, Michaelides A, et al. Fast diffusion of water nanodroplets on graphene. Nat Mater. 2016;15:66–71.
   PubMedGoogle Scholar
• Beckstein O, Biggin PC, Sansom MSP. A hydrophobic gating mechanism for nanopores. J Phys Chem A. 2001;105:12902–12905.
   Web of Science ®Google Scholar
• Giacomello A, Roth R. Bubble formation in nanopores: a matter of hydrophobicity, geometry, and size. Adv Phys X. 2020;5:1817780.
   Web of Science ®Google Scholar
• Tinti A, Giacomello A, Grosu Y, et al. Intrusion and extrusion of water in hydrophobic nanopores. Proc Nat Acad Sci. 2017;114:E10266–E10273.
   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.
   PubMed Web of Science ®Google Scholar
• Hess B, Kutzner C, Van Der Spoel D, et al. Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.
   PubMed Web of Science ®Google Scholar
• Plimpton S. Fast parallel algorithms for short-range molecular dynamics. J Comput Phys. 1995;117:1–19.
   Web of Science ®Google Scholar
• Marchio S, Meloni S, Giacomello A, et al. Wetting and recovery of nano-patterned surfaces beyond the classical picture. Nanoscale. 2019;11:21458–21470.
   PubMed Web of Science ®Google Scholar
• Gentili D, Guido Bolognesi AG, Chinappi M, et al. Pressure effects on water slippage over silane-coated rough surfaces: pillars and holes. Microfluid Nanofluid. 2014;16:1009–1018.
   Google Scholar
• Widom B. Some topics in the theory of fluids. J Chem Phys. 1963;39:2808–2812.
   Web of Science ®Google Scholar
• Sega M, Sbragaglia M, Biferale L, et al. The importance of chemical potential in the determination of water slip in nanochannels. Eur Phys J E. 2015;38:1–7.
   PubMedGoogle Scholar
• Bezrukov SM, Berezhkovskii AM, Pustovoit MA, et al. Particle number fluctuations in a membrane channel. J Chem Phys. 2000;113:8206–8211.
   Google Scholar
• Janeček J, Netz RR. Interfacial water at hydrophobic and hydrophilic surfaces: depletion versus adsorption. Langmuir. 2007;23:8417–8429.
   PubMedGoogle Scholar
• Yoshida H, Marbach S, Bocquet L. Osmotic and diffusio-osmotic flow generation at high solute concentration. ii. molecular dynamics simulations. J Chem Phys. 2017;146:194702.
   PubMedGoogle Scholar
• Ramrez-Hinestrosa S, Yoshida H, Bocquet L, et al. Studying polymer diffusiophoresis with non-equilibrium molecular dynamics. J Chem Phys. 2020;152:164901.
   PubMedGoogle Scholar
• Thompson AP. Nonequilibrium molecular dynamics simulation of electro-osmotic flow in a charged nanopore. J Chem Phys. 2003;119:7503–7511.
   Web of Science ®Google Scholar
• Chinappi M, De Angelis E, Melchionna S, et al. Molecular dynamics simulation of ratchet motion in an asymmetric nanochannel. Phys Rev Lett. 2006;97:144509.
   PubMedGoogle Scholar
• Yoshida H, Mizuno H, Kinjo T, et al. Molecular dynamics simulation of electrokinetic flow of an aqueous electrolyte solution in nanochannels. J Chem Phys. 2014;140:214701.
   PubMedGoogle Scholar
• Español P, de la Torre JA, Duque-Zumajo D. Solution to the plateau problem in the green-kubo formula. Phys Rev E. 2019;99:022126.
   PubMedGoogle Scholar
• Angel González M, Abascal JLF. The shear viscosity of rigid water models. J Chem Phys. 2010;132:096101.
   PubMedGoogle Scholar
• Abascal JLF, Vega C. A general purpose model for the condensed phases of water: tip4p/2005. J Chem Phys. 2005;123:234505.
   PubMed Web of Science ®Google Scholar
• Döpke MF, Moultos OA, Hartkamp R. On the transferability of ion parameters to the tip4p/2005 water model using molecular dynamics simulations. J Chem Phys. 2020;152:024501.
   PubMed Web of Science ®Google Scholar
• Yoo J, Aksimentiev A. Improved parametrization of li+, na+, k+, and mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems. J Phys Chem Lett. 2011;3:45–50.
   Google Scholar
• Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh ewald method. J Chem Phys. 1995;103:8577–8593.
   Web of Science ®Google Scholar
• Gumbart J, Khalili-Araghi F, Sotomayor M, et al. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochimi Biophys Acta (BBA) Biomembr. 2012;1818:294–302.
   PubMed Web of Science ®Google Scholar
• Yoo J, Aksimentiev A. Molecular dynamics of membrane-spanning dna channels: conductance mechanism, electro-osmotic transport, and mechanical gating. J Phys Chem Lett. 2015;6:4680–4687.
   PubMedGoogle Scholar
• Wells DB, Abramkina V, Aksimentiev A. Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics. J Chem Phys. 2007;127:09B619.
   Web of Science ®Google Scholar
• Mathé J, Aksimentiev A, Nelson DR, et al. Orientation discrimination of single-stranded dna inside the α-hemolysin membrane channel. Proc Natl Acad Sci U S A. 2005;102:12377–12382.
   PubMedGoogle Scholar
• Martin HSC, Jha S, Howorka S, et al. Determination of free energy profiles for the translocation of polynucleotides through α-hemolysin nanopores using non-equilibrium molecular dynamics simulations. J Chem Theory Comput. 2009;5:2135–2148.
   PubMed Web of Science ®Google Scholar
• Li C-Y, Hemmig EA, Kong J, et al. Ionic conductivity, structural deformation, and programmable anisotropy of dna origami in electric field. ACS Nano. 2015;9:1420–1433.
   PubMedGoogle Scholar
• Langecker M, Arnaut V, Martin TG, et al. Synthetic lipid membrane channels formed by designed dna nanostructures. Science. 2012;338:932–936.
   PubMed Web of Science ®Google Scholar
• Burns JR, Stulz E, Howorka S. Self-assembled dna nanopores that span lipid bilayers. Nano Lett. 2013;13:2351–2356.
   PubMedGoogle Scholar
• Douglas SM, Marblestone AH, Teerapittayanon S, et al. Rapid prototyping of 3d dna-origami shapes with cadnano. Nucleic Acids Res. 2009;37:5001–5006.
   PubMed Web of Science ®Google Scholar
• Burns JR, Göpfrich K, Wood JW, et al. Lipid-bilayer-spanning dna nanopores with a bifunctional porphyrin anchor. Angew Chem. 2013;125:12291–12294.
   Google Scholar
• Howorka S. Rationally engineering natural protein assemblies in nanobiotechnology. Curr Opin Biotechnol. 2011;22:485–491.
   PubMedGoogle Scholar
• Rotenberg B, Pagonabarraga I. Electrokinetics: insights from simulation on the microscopic scale. Mol Phys. 2013;111:827–842.
   Web of Science ®Google Scholar
• Hoogerbrugge PJ, Koelman JMVA. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. EPL Europhys Lett. 1992;19:155.
   Web of Science ®Google Scholar
• Espanol P, Warren P. Statistical mechanics of dissipative particle dynamics. EPL Europhys Lett. 1995;30:191.
   Web of Science ®Google Scholar
• Español P, Warren PB. Perspective: dissipative particle dynamics. J Chem Phys. 2017;146:150901.
   PubMed Web of Science ®Google Scholar
• Pagonabarraga I, Frenkel D. Dissipative particle dynamics for interacting systems. J Chem Phys. 2001;115:5015–5026.
   Web of Science ®Google Scholar
• Warren PB. Hydrodynamic bubble coarsening in off-critical vapor-liquid phase separation. Phys Rev Lett. 2001;87:225702.
   PubMedGoogle Scholar
• Trofimov SY, Nies ELF, Michels MAJ. Thermodynamic consistency in dissipative particle dynamics simulations of strongly nonideal liquids and liquid mixtures. J Chem Phys. 2002;117:9383–9394.
   Web of Science ®Google Scholar
• Bonet Avalos J, Mackie AD. Dissipative particle dynamics with energy conservation. EPL Europhys Lett. 1997;40:141.
   Google Scholar
• Espanol P. Dissipative particle dynamics with energy conservation. EPL Europhys Lett. 1997;40:631.
   Google Scholar
• Tong Z, Liu H, Liu Y, et al. A study on the dynamic behavior of macromolecular suspension flow in micro-channel under thermal gradient using energy-conserving dissipative particle dynamics simulation. Microfluid Nanofluid. 2020;24:1–11.
   Google Scholar
• Boek ES, Coveney PV, Lekkerkerker HNW, et al. Simulating the rheology of dense colloidal suspensions using dissipative particle dynamics. Phys Rev E. 1997;55:3124.
   Web of Science ®Google Scholar
• Keaveny EE, Pivkin IV, Maxey M, et al. A comparative study between dissipative particle dynamics and molecular dynamics for simple-and complex-geometry flows. J Chem Phys. 2005;123:104107.
   PubMed Web of Science ®Google Scholar
• Tiwari A, Reddy H, Mukhopadhyay S, et al. Simulations of liquid nanocylinder breakup with dissipative particle dynamics. Phys Rev E. 2008;78:016305.
   Google Scholar
• Zhigang L, Drazer G. Hydrodynamic interactions in dissipative particle dynamics. Phys Fluids. 2008;20:103601.
   Google Scholar
• Filipovic N, Kojic M, Ferrari M. Dissipative particle dynamics simulation of circular and elliptical particles motion in 2d laminar shear flow. Microfluid Nanofluid. 2011;10:1127–1134.
   Google Scholar
• Gubbiotti A, Chinappi M, Massimo Casciola C. Confinement effects on the dynamics of a rigid particle in a nanochannel. Phys Rev E. 2019;100:053307.
   PubMedGoogle Scholar
• Lsal M, Limpouchová Z, Procházka K. The self-assembly of copolymers with one hydrophobic and one polyelectrolyte block in aqueous media: a dissipative particle dynamics study. Phys Chem Chem Phys. 2016;18:16127–16136.
   PubMedGoogle Scholar
• Smiatek J, Schmid F. Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels. Comput Phys Commun. 2011;182:1941–1944.
   Web of Science ®Google Scholar
• Warren PB, Vlasov A. Screening properties of four mesoscale smoothed charge models, with application to dissipative particle dynamics. J Chem Phys. 2014;140:084904.
   PubMed Web of Science ®Google Scholar
• Peter EK, Pivkin IV. A polarizable coarse-grained water model for dissipative particle dynamics. J Chem Phys. 2014;141:10B613_1.
   Google Scholar
• Peter EK, Lykov K, Pivkin IV. A polarizable coarse-grained protein model for dissipative particle dynamics. Phys Chem Chem Phys. 2015;17:24452–24461.
   PubMed Web of Science ®Google Scholar
• Deng M, Zhen L. Borodin O, et al. cdpd: a new dissipative particle dynamics method for modeling electrokinetic phenomena at the mesoscale. J Chem Phys. 2016;145:144109.
   PubMed Web of Science ®Google Scholar
• Gubbiotti A, Chinappi M, Massimo Casciola C. Eh-dpd: a dissipative particle dynamics approach to electro-hydrodynamics. arXiv preprint arxiv:2201 06292. 2022.
   Google Scholar
• Zhen L, Yazdani A, Tartakovsky A, et al. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. J Chem Phys. 2015;143:014101.
   PubMedGoogle Scholar
• Han Y, Jin J, Voth GA. Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining. J Chem Phys. 2021;154:084122.
   PubMedGoogle Scholar
• Groot RD, Warren PB. Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J Chem Phys. 1997;107:4423–4435.
   Web of Science ®Google Scholar
• Boromand A, Jamali S, Maia JM. Viscosity measurement techniques in dissipative particle dynamics. Comput Phys Commun. 2015;196:149–160.
   Web of Science ®Google Scholar
• Gompper G, Ihle T, Kroll DM, et al. Multi-particle collision dynamics: a particle-based mesoscale simulation approach to the hydrodynamics of complex fluids. Adv Comp Simulat Approach Soft Matt Sci. 2009;III:1–87.
   Google Scholar
• Ceratti DR, Obliger A, Jardat M, et al. Stochastic rotation dynamics simulation of electro-osmosis. Mol Phys. 2015;113:2476–2486.
   Web of Science ®Google Scholar
• Katkar HH, Muthukumar M. Role of non-equilibrium conformations on driven polymer translocation. J Chem Phys. 2018;148:024903.
   PubMedGoogle Scholar
• Aidun CK, Clausen JR. Lattice-boltzmann method for complex flows. Annu Rev Fluid Mech. 2010;42:439–472.
   Web of Science ®Google Scholar
• Melchionna S, Succi S. Electrorheology in nanopores via lattice boltzmann simulation. J Chem Phys. 2004;120:4492–4497.
   PubMed Web of Science ®Google Scholar
• Capuani F, Pagonabarraga I, Frenkel D. Discrete solution of the electrokinetic equations. J Chem Phys. 2004;121:973–986.
   PubMed Web of Science ®Google Scholar
• Obliger A, Duvail M, Jardat M, et al. Numerical homogenization of electrokinetic equations in porous media using lattice-boltzmann simulations. Phys Rev E. 2013;88:013019.
   Web of Science ®Google Scholar
• Asta AJ, Palaia I, Trizac E, et al. Lattice boltzmann electrokinetics simulation of nanocapacitors. J Chem Phys. 2019;151:114104.
   PubMedGoogle Scholar
• Ortiz De Zarate JM, Sengers JV. Hydrodynamic fluctuations in fluids and fluid mixtures. Elsevier; 2006.
   Google Scholar
• Péraud J-P, Nonaka A, Chaudhri A, et al. Low mach number fluctuating hydrodynamics for electrolytes. Phys Rev Fluids. 2016;1:074103.
   Web of Science ®Google Scholar
• Mecke K, Rauscher M. On thermal fluctuations in thin film flow. J Phys. 2005;17:S3515.
   Google Scholar
• Gallo M, Magaletti F, Massimo Casciola C. Fluctuating hydrodynamics as a tool to investigate nucleation of cavitation bubbles. Multiph Flow Theor Appl. 2018;347.
   Google Scholar
• François Detcheverry and Lydéric Bocquet. Thermal fluctuations in nanofluidic transport. Phys Rev Lett. 2012;109:024501.
   PubMedGoogle Scholar
• Balboa F, Bell JB, Delgado-Buscalioni R, et al. Staggered schemes for fluctuating hydrodynamics. Multiscale Model Simul. 2012;10:1369–1408.
   Google Scholar
• Sprinkle B, Balboa Usabiaga F, Patankar NA, et al. Large scale brownian dynamics of confined suspensions of rigid particles. J Chem Phys. 2017;147:244103.
   PubMedGoogle Scholar
• Atzberger PJ, Kramer PR, Peskin CS. A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales. J Comput Phys. 2007;224:1255–1292.
   Web of Science ®Google Scholar
• Atzberger PJ. Stochastic eulerian lagrangian methods for fluid–structure interactions with thermal fluctuations. J Comput Phys. 2011;230:2821–2837.
   Google Scholar
• Donev A, Garcia AL, Péraud J-P, et al. Fluctuating hydrodynamics and debye-hückel-onsager theory for electrolytes. Curr Opin Electrochem. 2019;13:1–10.
   Google Scholar
• Pagonabarraga I, Pérez-Madrid A, Rubi JM. Fluctuating hydrodynamics approach to chemical reactions. Phys A Stat Mech Appli. 1997;237:205–219.
   Google Scholar
• Dean DS. Langevin equation for the density of a system of interacting langevin processes. J Phys A. 1996;29:L613.
   Google Scholar
• Péraud J-P, Nonaka AJ, Bell JB, et al. Fluctuation-enhanced electric conductivity in electrolyte solutions. Proc Nat Acad Sci. 2017;114:10829–10833.
   PubMedGoogle Scholar
• Donev A, Nonaka AJ, Kim C, et al. Fluctuating hydrodynamics of electrolytes at electroneutral scales. Phys Rev Fluids. 2019;4:043701.
   Google Scholar
• Klymko K, Nonaka A, Bell JB, et al. Low mach number fluctuating hydrodynamics model for ionic liquids. Phys Rev Fluids. 2020;5:093701.
   Google Scholar
• Woon Kim Y, Netz RR. Electroosmosis at inhomogeneous charged surfaces. EPL Europhys Lett. 2005;72:837.
   Google Scholar
• Ladiges DR, Nonaka A, Klymko K, et al. Discrete ion stochastic continuum overdamped solvent algorithm for modeling electrolytes. Phys Rev Fluids. 2021;6:044309.
   Google Scholar
• Chen-Hung W, Fai TG, Atzberger PJ, et al. Simulation of osmotic swelling by the stochastic immersed boundary method. SIAM J Sci Comput. 2015;37:B660–B688.
   Google Scholar
• Mittal R, Iaccarino G. Immersed boundary methods. Annu Rev Fluid Mech. 2005;37:239–261.
   Web of Science ®Google Scholar
• Delong S, Balboa Usabiaga F, Delgado-Buscalioni R, et al. Brownian dynamics without green’s functions. J Chem Phys. 2014;140:134110.
   PubMedGoogle Scholar
• Fadlun EA, Verzicco R, Orlandi P, et al. Combined immersed-boundary finite-difference methods for three-dimensional complex flow simulations. J Comput Phys. 2000;161:35–60.
   Web of Science ®Google Scholar
• Lomholt S, Maxey MR. Force-coupling method for particulate two-phase flow: stokes flow. J Comput Phys. 2003;184:381–405.
   Google Scholar
• Delmotte B, Keaveny EE. Simulating brownian suspensions with fluctuating hydrodynamics. J Chem Phys. 2015;143:244109.
   PubMedGoogle Scholar
• Pep Espanol and Mariano Revenga. Smoothed dissipative particle dynamics. Phys Rev E. 2003;67:026705.
   Google Scholar
• Chapter 4 - electroosmotic flows in microchannels. In: Li D, editor. Interface science and technology. Electrokinetics in Microfluidics Vol. 2. Elsevier; 2004. p. 92–203.
   Google Scholar
• Chang C-C, Yang R-J. Electrokinetic mixing in microfluidic systems. Microfluid Nanofluidics. 2007;3:501–525.
   Web of Science ®Google Scholar
• Kusama S, Sato K, Matsui Y, et al. Transdermal electroosmotic flow generated by a porous microneedle array patch. Nat Commun. 2021;12:1–11.
   PubMedGoogle Scholar
• Ai Y, Yalcin SE, Diefeng G, et al. A low-voltage nano-porous electroosmotic pump. J Colloid Interface Sci. 2010;350:465–470.
   PubMedGoogle Scholar
• Xiaojian W, Ramiah Rajasekaran P, Martin CR. An alternating current electroosmotic pump based on conical nanopore membranes. Acs Nano. 2016;10:4637–4643.
   PubMedGoogle Scholar
• Xiaojian W, Experton J, Weihuang X, et al. Chemoresponsive nanofluidic pump that turns off in the presence of lead ion. Anal Chem. 2018;90:7715–7720.
   PubMedGoogle Scholar
• Hashemi Amrei SMH, Bukosky SC, Rader SP, et al. Oscillating electric fields in liquids create a long-range steady field. Phys Rev Lett. 2018;121:185504.
   PubMedGoogle Scholar
• Bukosky SC, Hashemi Amrei SMH, Rader SP, et al. Extreme levitation of colloidal particles in response to oscillatory electric fields. Langmuir. 2019;35:6971–6980.
   PubMedGoogle Scholar
• Bengtsson K, Robinson ND. A large-area, all-plastic, flexible electroosmotic pump. Microfluid Nanofluid. 2017;21:178.
   Google Scholar
• Jongkuk K, Kim D, Song Y, et al. Electroosmosis-driven hydrogel actuators using hydrophobic/hydrophilic layer-by-layer assembly-induced crack electrodes. ACS Nano. 2020;14:11906–11918.
   PubMedGoogle Scholar
• Wei S, Meng Y, Gensheng W, et al. A nanoparticle-dna assembled nanorobot powered by charge-tunable quad-nanopore system. ACS Nano. 2020;14:15349–15360.
   PubMedGoogle Scholar
• Humphrey W, Dalke A, Schulten K. Vmd: visual molecular dynamics. J Mol Graph. 1996;14:33–38.
   PubMed Web of Science ®Google Scholar
• Varongchayakul N, Huttner D, Grinstaff MW, et al. Sensing native protein solution structures using a solid-state nanopore: unraveling the states of vegf. Sci Rep. 2018;8:1017.
   PubMedGoogle Scholar
• Luo L, German SR, Lan W-J, et al. Resistive-pulse analysis of nanoparticles. Ann Rev Anal Chem. 2014;7:513–535.
   PubMedGoogle Scholar
• Di Ventra M, Taniguchi M. Decoding dna, rna and peptides with quantum tunnelling. Nat Nanotechnol. 2016;11:117–126.
   PubMedGoogle Scholar
• Ohayon S, Girsault A, Nasser M, et al. Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput Biol. 2019;15:e1007067.
   PubMedGoogle Scholar
• Spitaleri A, Garoli D, Schütte M, et al. Adaptive nanopores: a bioinspired label-free approach for protein sequencing and identification. Nano Res. 2021;14:328–333.
   Google Scholar
• Garoli D, Yamazaki H, Maccaferri N, et al. Plasmonic nanopores for single-molecule detection and manipulation: toward sequencing applications. Nano Lett. 2019;19:7553–7562.
   PubMedGoogle Scholar
• Tarun OB, Yu Eremchev M, Radenovic A, et al. Spatiotemporal imaging of water in operating voltage-gated ion channels reveals the slow motion of interfacial ions. Nano Lett. 2019;19:7608–7613.
   PubMedGoogle Scholar
• Huang G, Willems K, Bartelds M, et al. Electro-osmotic vortices promote the capture of folded proteins by plyab nanopores. Nano Lett. 2020;20:3819–3827.
   PubMedGoogle Scholar
• Firnkes M, Pedone D, Knezevic J, et al. Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. Nano Lett. 2010;10:2162–2167.
   PubMed Web of Science ®Google Scholar
• Arima A, Tsutsui M, Hanun Harlisa I, et al. Selective detections of single-viruses using solid-state nanopores. Sci Rep. 2018;8:1–7.
   PubMedGoogle Scholar
• Bafna JA, Pangeni S, Winterhalter M, et al. Electroosmosis dominates electrophoresis of antibiotic transport across the outer membrane porin f. Biophys J. 2020;118:2844–2852.
   PubMed Web of Science ®Google Scholar
• Prathyusha Bhamidimarri S, Dahyabhai Prajapati J, van den Berg B, et al. Role of electroosmosis in the permeation of neutral molecules: cyma and cyclodextrin as an example. Biophys J. 2016;110:600–611.
   PubMedGoogle Scholar
• Dahyabhai Prajapati J, Kleinekathöfer U. Voltage-dependent transport of neutral solutes through nanopores: a molecular view. J Phys Chem A. 2020;124:10718–10731.
   Google Scholar
• Muthukumar M. Theory of capture rate in polymer translocation. J Chem Phys. 2010;132:05B605.
   Google Scholar
• Tsutsui M, Ryuzaki S, Yokota K, et al. Field effect control of translocation dynamics in surround-gate nanopores. Commun Mater. 2021;2:1–9.
   Google Scholar
• Zhang Y, Zhao J, Wei S, et al. Electroosmotic facilitated protein capture and transport through solid-state nanopores with diameter larger than length. Small Methods. 2020;4:1900893.
   Google Scholar
• Siria A, Bocquet M-L, Bocquet L. New avenues for the large-scale harvesting of blue energy. Nat Rev Chem. 2017;1:0091.
   Google Scholar
• Werber JR, Osuji CO, Elimelech M. Materials for next-generation desalination and water purification membranes. Nat Rev Mater. 2016;1:16018.
   Web of Science ®Google Scholar
• Yin Yip N, Brogioli D, Hamelers HVM, et al. Salinity gradients for sustainable energy: primer, progress, and prospects. Environ Sci Technol. 2016;50:12072–12094.
   PubMedGoogle Scholar
• Cohen-Tanugi D, Grossman JC. Water desalination across nanoporous graphene. Nano Lett. 2012;12:3602–3608.
   PubMed Web of Science ®Google Scholar
• Heiranian M, Barati Farimani A, Aluru NR. Water desalination with a single-layer mos 2 nanopore. Nat Commun. 2015;6:8616.
   PubMed Web of Science ®Google Scholar
• Tu Y-M, Song W, Ren T, et al. Rapid fabrication of precise high-throughput filters from membrane protein nanosheets. Nat Mater. 2020;19:347–354.
   PubMedGoogle Scholar
• She Q, Wang R, Fane AG, et al. Membrane fouling in osmotically driven membrane processes: a review. J Membr Sci. 2016;499:201–233.
   Web of Science ®Google Scholar
• Richard Bowen W, Sabuni HAM. Electroosmotic membrane backwashing. Ind Eng Chem Res. 1994;33:1245–1249.
   Google Scholar
• Nadh Jagannadh S, Muralidhara HS. Electrokinetics methods to control membrane fouling. Ind Eng Chem Res. 1996;35:1133–1140.
   Google Scholar
• Sheng Chan F, Keong Tan C, Ratnayake P, et al. Reduced-order modelling of concentration polarization with varying permeation: analysis of electro-osmosis in membranes. Desalination. 2020;495:114677.
   Google Scholar
• Marbach S, Bocquet L. Osmosis, from molecular insights to large-scale applications. Chem Soc Rev. 2019;48:3102–3144.
   PubMedGoogle Scholar
• Qiu Y, Siwy ZS, Wanunu M. Abnormal ionic-current rectification caused by reversed electroosmotic flow under viscosity gradients across thin nanopores. Anal Chem. 2018;91:996–1004.
   PubMedGoogle Scholar