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Ma C, Zheng F, Xu W, Liu W, Xu C, Chen Y, Sha J. Surface Roughness Effects on Confined Nanoscale Transport of Ions and Biomolecules. SMALL METHODS 2023:e2301485. [PMID: 38150654 DOI: 10.1002/smtd.202301485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Biological channels, especially membrane proteins, play a crucial role in metabolism, facilitating the transport of nutrients and other materials across cell membranes in a bio-electrolyte environment. Artificial nanopores are employed to study ion and biomolecule transport behavior inside. While the non-specific interaction between the nanopore surface and transport targets has garnered significant attention, the impact of surface roughness is overlooked. In this study, Nanopores with different levels of inner surface roughness is created by adjusting the FIB (Focus Ion Beam) fabrication parameters. Experiments and molecular dynamics (MD) simulations are employed to demonstrate that greater roughness results from larger FIB beam currents and shorter processing times. Lower roughness increases the capture rate of biomolecules, while greater roughness enhances the normalized blockade current (ΔI/I0 ). The phenomenon of rougher nanopores are attributed to a barrier-dominated capture mechanism and more likely to induce DNA folding. This transport barrier exists in rough nanopores by utilizing steer molecular dynamics (SMD) simulations to investigate the force profile of a dA10 DNA molecule during translocation is demonstrated. This work illustrates how surface roughness influences the ionic current features and the translocation of biomolecules, paving a new way for tunning the molecule transport in nanopores.
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Affiliation(s)
- Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Fei Zheng
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Changhui Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
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Ghahremanian S, Abbassi A, Mansoori Z, Toghraie D. Effect of copper nanoparticles on thermal behavior of two-phase argon-copper nanofluid flow in rough nanochannels with focusing on the interface properties and heat transfer using molecular dynamics simulation. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhou Y, Luo G, Hu Y, Wu D, Yao Z. Interaction properties between molten metal and quartz by molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ghahremanian S, Abbassi A, Mansoori Z, Toghraie D. Effect of nanostructured surface configuration on the interface properties and heat transfer of condensation process of argon inside nanochannels using molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Molecular Dynamics Simulation of the Influence of Nanoscale Structure on Water Wetting and Condensation. MICROMACHINES 2019; 10:mi10090587. [PMID: 31480496 PMCID: PMC6780133 DOI: 10.3390/mi10090587] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Recent advances in the microfabrication technology have made it possible to control surface properties at micro- and nanoscale levels. Functional surfaces drastically change wettability and condensation processes that are essential for controlling of heat transfer. However, the direct observation of condensation on micro- and nanostructure surfaces is difficult, and further understanding of the effects of the microstructure on the phase change is required. In this research, the contact angle of droplets with a wall surface and the initial condensation process were analyzed using a molecular dynamics simulation to investigate the impact of nanoscale structures and their adhesion force on condensation. The results demonstrated the dependence of the contact angle of the droplets and condensation dynamics on the wall structure and attractive force of the wall surface. Condensed water droplets were adsorbed into the nanostructures and formed a water film in case of a hydrophilic surface.
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