51
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Tong X, Novak BR, Kavousi S, Moldovan D. Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics. J Phys Chem B 2021; 125:1259-1270. [PMID: 33481603 DOI: 10.1021/acs.jpcb.0c07797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonequilibrium molecular dynamics (MD) simulations were used to study the effect of three chemical surface groups on the separation of DNA mononucleotide velocity (or time-of-flight) distributions as they pass through nanoslits. We used nanoslits functionalize with self-assembled monolayers (SAMs) since they have relatively smooth surfaces. The SAM molecules were terminated with either a methyl, methylformyl, or phenoxy group, and the nucleotides were driven electrophoretically with an electric field intensity of 0.1 V/nm in slits about 3 nm wide. Although these large driving forces are physically difficult to achieve experimentally, the simulations are still of great value as they provide molecular level insight into nucleotide translocation events and allow comparison of different surfaces. Nucleotides adsorbed and desorbed from the slit surface multiple times during the simulations. The required slit length for 99% accuracy in identifying the deoxynucleotide monophosphates (dNMPs), based on the separation of the distributions of time of flight, was used to compare the surfaces with shorter lengths indicating more efficient separation. The lengths were 6.5 μm for phenoxy-terminated SAMs, 270 μm for methylformyl-terminated SAMs, and 2400 μm for methyl-terminated SAMs. Our study showed that a slit with a section with methyl termination and the second section with methylformyl termination lead to a required length of 120 μm, which was significantly lower than for only a methylformyl- or methyl-terminated surface.
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Affiliation(s)
- Xinjie Tong
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Brian R Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sepideh Kavousi
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Dorel Moldovan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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52
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Alizadeh A, Hsu WL, Wang M, Daiguji H. Electroosmotic flow: From microfluidics to nanofluidics. Electrophoresis 2021; 42:834-868. [PMID: 33382088 PMCID: PMC8247933 DOI: 10.1002/elps.202000313] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 01/06/2023]
Abstract
Electroosmotic flow (EOF), a consequence of an imposed electric field onto an electrolyte solution in the tangential direction of a charged surface, has emerged as an important phenomenon in electrokinetic transport at the micro/nanoscale. Because of their ability to efficiently pump liquids in miniaturized systems without incorporating any mechanical parts, electroosmotic methods for fluid pumping have been adopted in versatile applications—from biotechnology to environmental science. To understand the electrokinetic pumping mechanism, it is crucial to identify the role of an ionically polarized layer, the so‐called electrical double layer (EDL), which forms in the vicinity of a charged solid–liquid interface, as well as the characteristic length scale of the conducting media. Therefore, in this tutorial review, we summarize the development of electrical double layer models from a historical point of view to elucidate the interplay and configuration of water molecules and ions in the vicinity of a solid–liquid interface. Moreover, we discuss the physicochemical phenomena owing to the interaction of electrical double layer when the characteristic length of the conducting media is decreased from the microscale to the nanoscale. Finally, we highlight the pioneering studies and the most recent works on electro osmotic flow devoted to both theoretical and experimental aspects.
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Affiliation(s)
- Amer Alizadeh
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
| | - Wei-Lun Hsu
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
| | - Moran Wang
- Department of Engineering Mechanics, Tsinghua University, Beijing, P. R. China
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
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53
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Zhao D, Chen H, Wang Y, Li B, Duan C, Li Z, Li L. Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-020-2004-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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54
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Xie Z, Li Z, Li J, Kou J, Yao J, Fan J. Electric field-induced gas dissolving in aqueous solutions. J Chem Phys 2021; 154:024705. [PMID: 33445907 DOI: 10.1063/5.0037387] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gas dissolution or accumulation regulating in an aqueous environment is important but difficult in various fields. Here, we performed all-atom molecular dynamics simulations to study the dissolution/accumulation of gas molecules in aqueous solutions. It was found that the distribution of gas molecules at the solid-water interface is regulated by the direction of the external electric field. Gas molecules attach and accumulate to the interface with an electric field parallel to the interface, while the gas molecules depart and dissolve into the aqueous solutions with a vertical electric field. The above phenomena can be attributed to the redistribution of water molecules as a result of the change of hydrogen bonds of water molecules at the interface as affected by the electric field. This finding reveals a new mechanism of regulating gas accumulation and dissolution in aqueous solutions and can have tremendous applications in the synthesis of drugs, the design of microfluidic device, and the extraction of natural gas.
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Affiliation(s)
- Zhang Xie
- Institute of Condensed Matter Physics, Zhejiang Normal University, Jinhua 321004, China
| | - Zheng Li
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310058, China
| | - Jianlong Kou
- Institute of Condensed Matter Physics, Zhejiang Normal University, Jinhua 321004, China
| | - Jun Yao
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jintu Fan
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, New York 14853-4401, USA
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55
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Borthakur P, Boruah PK, Das P, Das MR. CuS nanoparticles decorated MoS 2 sheets as an efficient nanozyme for selective detection and photocatalytic degradation of hydroquinone in water. NEW J CHEM 2021. [DOI: 10.1039/d1nj00856k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cost effective and efficient CuS–MoS2 nanocomposite with enhanced peroxidase enzyme mimetics and photocatalytic activity was synthesized by simple hydrothermal method and successfully utilized for sensing and detection of toxic hydroquinone molecules in aqueous medium.
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Affiliation(s)
- Priyakshree Borthakur
- Materials Sciences and Technology Division
- CSIR-North East Institute of Science and Technology
- Jorhat 785006
- India
- Academy of Scientific and Innovative Research
| | - Purna K. Boruah
- Materials Sciences and Technology Division
- CSIR-North East Institute of Science and Technology
- Jorhat 785006
- India
- Academy of Scientific and Innovative Research
| | - Punamshree Das
- Materials Sciences and Technology Division
- CSIR-North East Institute of Science and Technology
- Jorhat 785006
- India
- Academy of Scientific and Innovative Research
| | - Manash R. Das
- Materials Sciences and Technology Division
- CSIR-North East Institute of Science and Technology
- Jorhat 785006
- India
- Academy of Scientific and Innovative Research
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56
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Sen P, Gupta M. Single nucleotide detection using bilayer MoS2 nanopores with high efficiency. RSC Adv 2021; 11:6114-6123. [PMID: 35423134 PMCID: PMC8694823 DOI: 10.1039/d0ra10222a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/14/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide detection is important for early detection of diseases and for DNA sequencing. Monolayer (ML) MoS2 nanopores have been used to identify and distinguish single nucleotides with good signal-to-noise ratio in the recent past. Here, we use a bilayer (BL) MoS2 nanopore (∼1.3 nm thick) to detect distinct single nucleotides with high spatial resolution and longer dwell time. In this study, the performance of similar sized (<3 nm) ML and BL MoS2 nanopores for detection of a single nucleotide has been compared. Both single nucleotide and single stranded DNA translocations through them are studied. For single nucleotide detection, we observe that BL MoS2 nanopores demonstrate twice the dwell time as compared to ML MoS2 nanopores with 95% confidence. Single nucleotide detection rate for BL MoS2 nanopores (50–60 nucleotides per s) is five-fold higher as compared to ML MoS2 nanopores (10–15 nucleotides per s) in 10 pM analyte concentration. For single stranded DNA, we observe 89% (for 60 DNA molecules detected) single nucleotide detection efficiency with BL MoS2 nanopores as compared to 85% for ML MoS2. The DNA sequencing efficiency through BL MoS2 nanopores is also found to be 8–10% better than through ML MoS2 nanopores, irrespective of DNA sequencing orientation. Thus, owing to improved analyte/nanopore charge interaction BL MoS2 nanopores can be used for single nucleotide detection with high resolution due to longer dwell time, detection rate and efficiency. This study demonstrates the improved ability of BL MoS2 nanopores in sequencing DNA with 8–10% higher efficiency, two-times temporally resolved single-nucleotide current signatures and five-times higher detection rate, compared to ML MoS2 nanopores. Bilayer MoS2 nanopores are suitable for fast and high-efficiency single nucleotide detection and DNA sequencing due to fast analyte capture and improved dwell time.![]()
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Affiliation(s)
- Payel Sen
- Department of Chemical and Materials Engineering
- University of Alberta
- Edmonton
- Canada
| | - Manisha Gupta
- Department of Electrical and Computer Engineering
- University of Alberta
- Edmonton
- Canada
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57
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Perez A, Amorim RG, Villegas CEP, Rocha AR. Nanogap-based all-electronic DNA sequencing devices using MoS 2 monolayers. Phys Chem Chem Phys 2020; 22:27053-27059. [PMID: 33215614 DOI: 10.1039/d0cp04138f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The realization of nanopores in atom-thick materials may pave the way towards electrical detection of single biomolecules in a stable and scalable manner. In this work, we theoretically study the potential of different phases of MoS2 nanogaps to act as all-electronic DNA sequencing devices. We carry out simulations based on density functional theory and the non-equilibrium Green's function formalism to investigate the electronic transport across the device. Our results suggest that the 1T'-MoS2 nanogap structure is energetically more favorable than its 2H counterpart. At zero bias, the changes in the conductance of the 1T'-MoS2 device can be well distinguished, making possible the selectivity of the DNA nucleobases. Although the conductance fluctuates around the resonances, the overall results suggest that it is possible to distinguish the four DNA bases for energies close to the Fermi level.
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Affiliation(s)
- A Perez
- Instituto de Física Teórica, Universidade Estadual Paulista (UNESP), Rua Dr Bento T. Ferraz, 271, São Paulo, SP 01140-070, Brazil.
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58
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Ryu GH, Chan RJ. Sequential conversion from line defects to atomic clusters in monolayer WS 2. Appl Microsc 2020; 50:27. [PMID: 33580451 PMCID: PMC7818298 DOI: 10.1186/s42649-020-00047-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 11/12/2020] [Indexed: 11/10/2022] Open
Abstract
Transition metal dichalcogenides (TMD), which is composed of a transition metal atom and chalcogen ion atoms, usually form vacancies based on the knock-on threshold of each atom. In particular, when electron beam is irradiated on a monolayer TMD such as MoS2 and WS2, S vacancies are formed preferentially, and they are aligned linearly to constitute line defects. And then, a hole is formed at the point where the successively formed line defects collide, and metal clusters are also formed at the edge of the hole. This study reports a process in which the line defects formed in a monolayer WS2 sheet expends into holes. Here, the process in which the W cluster, which always occurs at the edge of the formed hole, goes through a uniform intermediate phase is explained based on the line defects and the formation behavior of the hole. Further investigation confirms the atomic structure of the intermediate phase using annular dark field scanning transition electron microscopy (ADF-STEM) and image simulation.
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Affiliation(s)
- Gyeong Hee Ryu
- School of Materials Science and Engineering, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Ren-Jie Chan
- Department of Materials, University of Oxford, 16 Parks Road, Oxford, OX1 3PH, UK
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59
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Wang Z, Hsu WL, Tsuchiya S, Paul S, Alizadeh A, Daiguji H. Joule Heating Effects on Transport-Induced-Charge Phenomena in an Ultrathin Nanopore. MICROMACHINES 2020; 11:E1041. [PMID: 33256113 PMCID: PMC7761093 DOI: 10.3390/mi11121041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 01/14/2023]
Abstract
Transport-induced-charge (TIC) phenomena, in which the concentration imbalance between cations and anions occurs when more than two chemical potential gradients coexist within an ultrathin dimension, entail numerous nanofluidic systems. Evidence has indicated that the presence of TIC produces a nonlinear response of electroosmotic flow to the applied voltage, resulting in complex fluid behavior. In this study, we theoretically investigate thermal effects due to Joule heating on TIC phenomena in an ultrathin nanopore by computational fluid dynamics simulation. Our modeling results show that the rise of local temperature inside the nanopore significantly enhances TIC effects and thus has a significant influence on electroosmotic behavior. A local maximum of the solution conductivity occurs near the entrance of the nanopore at the high salt concentration end, resulting in a reversal of TIC across the nanopore. The Joule heating effects increase the reversal of TIC with the synergy of the negatively charged nanopore, and they also enhance the electroosmotic flow regardless of whether the nanopore is charged. These theoretical observations will improve our knowledge of nonclassical electrokinetic phenomena for flow control in nanopore systems.
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Affiliation(s)
| | - Wei-Lun Hsu
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan; (Z.W.); (S.T.); (S.P.); (A.A.)
| | | | | | | | - Hirofumi Daiguji
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan; (Z.W.); (S.T.); (S.P.); (A.A.)
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60
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Gorkan T, Kadioglu Y, Aktürk E, Ciraci S. Interactions of selected organic molecules with a blue phosphorene monolayer: self-assembly, solvent effect, enhanced binding and fixation through coadsorbed gold clusters. Phys Chem Chem Phys 2020; 22:26552-26561. [PMID: 33200766 DOI: 10.1039/d0cp04886k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this paper we investigate the interaction between a pristine blue phosphorene monolayer and selected organic molecules like amino acids and nucleic acid bases. These molecules are bound to the substrate by a weak van der Waals interaction leading to their physisorption. When isolated, they tend to orient themselves parallel to the surface and are located in flat minima with very low libration frequencies; thus the electronic structures of the substrate and physisorbed molecules are not affected except for relative shifts. Even though the regular self-assembly of these molecules on the pristine blue phosphorene cannot be realized under this weak interaction, only their irregular coating of the substrate can occur due to increased intermolecular coupling. In a solvent like water, the weak binding energy is further decreased. Gold adatoms and gold clusters can form strong chemical bonds with pristine blue phosphorene and modify its electronic and magnetic state depending on the coverage. While full coverage of a blue phosphorene monolayer by gold adatoms leads to instabilities followed by clustering, relatively lower coverage can attribute very interesting magnetic and electronic states, like a spin gapless semiconductor. When bound to the gold clusters already adsorbed on the blue phosphorene monolayer, amino acid and nucleic acid base molecules form relatively strong chemical bonds and hence can be fixed to the surface; they are reoriented to gain self-assembly character and the whole system acquires new functionalities.
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Affiliation(s)
- T Gorkan
- Department of Physics, Adnan Menderes University, 09100 Aydın, Turkey.
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61
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Zou A, Xiu P, Ou X, Zhou R. Spontaneous Translocation of Single-Stranded DNA in Graphene-MoS 2 Heterostructure Nanopores: Shape Effect. J Phys Chem B 2020; 124:9490-9496. [PMID: 33064482 DOI: 10.1021/acs.jpcb.0c06934] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The appropriate translocation speed of a single-stranded DNA (ssDNA) through a solid-state nanopore is crucial for DNA sequencing technologies. By studying the geometry effect of graphene-MoS2 hetero-nanopores with molecular dynamics simulations, we have found that the shape of these nanopores (circular, square, or triangular, with similar size) may have a significant effect on the spontaneous translocation of ssDNA, with the triangular nanopore showing the slowest translocation and the circular one the fastest. Further analyses reveal that such differences in the spontaneous ssDNA translocation arise from different electrostatic attractions between the positively charged Mo atoms exposed in the pore and the negatively charged phosphate groups (PO4-) in nucleotides; the "sharpness" and the total number of the exposed Mo atoms of the nanopores are responsible for different electrostatic attractions between ssDNA and the nanopore. Our findings suggest that graphene-MoS2 heterostructure nanopores with lower symmetries (i.e., having sharper corners) are capable of slowing down the ssDNA translocation, which might help better facilitate the nucleotide sensing and DNA sequencing. The conclusion from these findings might also extend to other solid-state nanopores in designing appropriate shapes for better controlling of the translocation speed.
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Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Institute of Quantitative Biology, and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Peng Xiu
- Department of Engineering Mechanics, Institute of Quantitative Biology, and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Department of Engineering Mechanics, Institute of Quantitative Biology, and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Department of Engineering Mechanics, Institute of Quantitative Biology, and Department of Physics, Zhejiang University, Hangzhou 310027, China.,Department of Chemistry, Columbia University, New York, New York 10027, United States
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62
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Alshehri MH, Duraihem FZ, Aba Oud MA. Instability and translocation through nanopores of DNA interacting with single-layer materials. RSC Adv 2020; 10:36962-36970. [PMID: 35521264 PMCID: PMC9057072 DOI: 10.1039/d0ra06359b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, we use classical applied mathematical modelling to employ the 6-12 Lennard-Jones potential function along with the continuous approximation to investigate the interaction energies between a double-stranded deoxyribonucleic acid (dsDNA) molecule and two-dimensional nanomaterials, namely graphene (GRA), hexagonal boron nitride (h-BN), molybdenum disulphide (MoS2), and tungsten disulphide (WS2). Assuming that the dsDNA molecule has a perpendicular distance Δ above the nano-sheet surface, we calculated the molecular interaction energy and determined the relation between the location of the minimum energy and Δ. We also investigated the interaction of a dsDNA molecule with the surface of each nano-sheet in the presence of a circular hole simulating a nanopore. The radius of the nanopore that results in the minimum energy was determined. Our results show that the adsorption energies of the dsDNA molecule with GRA, h-BN, MoS2, and WS2 nano-sheets corresponding to the perpendicular distance Δ = 20 Å are approximately 70, 82, 28, and 26 (kcal mol-1), respectively, and we observed that the dsDNA molecule moves through nanopores of radii greater than 12.2 Å.
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Affiliation(s)
- Mansoor H Alshehri
- Department of Mathematics, College of Science, King Saud University Riyadh-11451 Saudi Arabia
| | - Faisal Z Duraihem
- Department of Mathematics, College of Science, King Saud University Riyadh-11451 Saudi Arabia
| | - Mohammed A Aba Oud
- Department of Mathematics and Statistics, Al Imam Mohammad Ibn Saud Islamic University (IMSIU) Riyadh Kingdom of Saudi Arabia
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63
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Kumawat RL, Pathak B. Functionalized carbon nanotube electrodes for controlled DNA sequencing. NANOSCALE ADVANCES 2020; 2:4041-4050. [PMID: 36132799 PMCID: PMC9417824 DOI: 10.1039/d0na00241k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/14/2020] [Indexed: 06/14/2023]
Abstract
In the last decade, solid-state nanopores/nanogaps have attracted significant attention in the rapid detection of DNA nucleotides. However, reducing the noise through controlled translocation of the DNA nucleobases is a central issue for the development of nanogap/nanopore-based DNA sequencing to achieve single-nucleobase resolution. Furthermore, the high reactivity of the graphene pores/gaps causes clogging of the pore/gap, leading to the blockage of the pores/gaps, sticking, and irreversible pore closure. To address the prospective of functionalization of the carbon nanostructure and for accomplishing this objective, herein, we have studied the performance of functionalized closed-end cap armchair carbon nanotube (CNT) nanogap-embedded electrodes, which can improve the coupling through non-bonding electrons and may provide the possibility of N/O-H⋯π interactions with the nucleotides, as single-stranded DNA is transmigrated across the electrode. We have investigated the effect of functionalizing the closed-end cap CNT (6,6) electrodes with purine (adenine, guanine) and pyrimidine (thymine, cytosine) molecules. Weak hydrogen bonds formed between the probe molecule and the target DNA nucleobase enhance the electronic coupling and temporarily stabilize the translocating nucleobase against the orientational fluctuations, which may reduce noise in the current signal during experimental measurements. The findings of our density functional theory and non-equilibrium Green's function-based study indicate that this modeled setup could allow DNA nucleotide sequencing with a better and reliable yield, giving current traces that differ by at least 1 order of current magnitude for all the four target nucleotides. Thus, we feel that the functionalized armchair CNT (6,6) nanogap-embedded electrodes may be utilized for controlled DNA sequencing.
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Affiliation(s)
- Rameshwar L Kumawat
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
| | - Biswarup Pathak
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
- Discipline of Chemistry, School of Basic Sciences, Indian Institute of Technology (IIT) Indore Indore Madhya Pradesh 453552 India
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64
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Shankla M, Aksimentiev A. Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS 2 Nanopore. ACS APPLIED MATERIALS & INTERFACES 2020; 12:26624-26634. [PMID: 32393017 PMCID: PMC7292782 DOI: 10.1021/acsami.0c04523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.
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Affiliation(s)
- Manish Shankla
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
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65
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Sapkota B, Liang W, VahidMohammadi A, Karnik R, Noy A, Wanunu M. High permeability sub-nanometre sieve composite MoS 2 membranes. Nat Commun 2020; 11:2747. [PMID: 32488183 PMCID: PMC7265532 DOI: 10.1038/s41467-020-16577-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 11/24/2022] Open
Abstract
Two-dimensional membranes have gained enormous interest due to their potential to deliver precision filtration of species with performance that can challenge current desalination membrane platforms. Molybdenum disulfide (MoS2) laminar membranes have recently demonstrated superior stability in aqueous environment to their extensively-studied analogs graphene-based membranes; however, challenges such as low ion rejection for high salinity water, low water flux, and low stability over time delay their potential adoption as a viable technology. Here, we report composite laminate multilayer MoS2 membranes with stacked heterodimensional one- to two-layer-thick porous nanosheets and nanodisks. These membranes have a multimodal porous network structure with tunable surface charge, pore size, and interlayer spacing. In forward osmosis, our membranes reject more than 99% of salts at high salinities and, in reverse osmosis, small-molecule organic dyes and salts are efficiently filtered. Finally, our membranes stably operate for over a month, implying their potential for use in commercial water purification applications.
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Affiliation(s)
- Bedanga Sapkota
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Wentao Liang
- Kostas Advanced Nanocharacterization Facility (KANCF), Northeastern University, Burlington, MA, 01803, USA
| | | | - Rohit Karnik
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.
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66
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Chen X, Liu C, Mao S. Environmental Analysis with 2D Transition-Metal Dichalcogenide-Based Field-Effect Transistors. NANO-MICRO LETTERS 2020; 12:95. [PMID: 34138098 PMCID: PMC7770660 DOI: 10.1007/s40820-020-00438-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/23/2020] [Indexed: 05/27/2023]
Abstract
Field-effect transistors (FETs) present highly sensitive, rapid, and in situ detection capability in chemical and biological analysis. Recently, two-dimensional (2D) transition-metal dichalcogenides (TMDCs) attract significant attention as FET channel due to their unique structures and outstanding properties. With the booming of studies on TMDC FETs, we aim to give a timely review on TMDC-based FET sensors for environmental analysis in different media. First, theoretical basics on TMDC and FET sensor are introduced. Then, recent advances of TMDC FET sensor for pollutant detection in gaseous and aqueous media are, respectively, discussed. At last, future perspectives and challenges in practical application and commercialization are given for TMDC FET sensors. This article provides an overview on TMDC sensors for a wide variety of analytes with an emphasize on the increasing demand of advanced sensing technologies in environmental analysis.
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Affiliation(s)
- Xiaoyan Chen
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, USA
| | - Chengbin Liu
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China
| | - Shun Mao
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China.
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67
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Zhou X, Sun H, Bai X. Two-Dimensional Transition Metal Dichalcogenides: Synthesis, Biomedical Applications and Biosafety Evaluation. Front Bioeng Biotechnol 2020; 8:236. [PMID: 32318550 PMCID: PMC7154136 DOI: 10.3389/fbioe.2020.00236] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/06/2020] [Indexed: 11/29/2022] Open
Abstract
Recently, two-dimensional transition metal dichalcogenides (2D TMDCs) have drawn certain attentions in many fields. The unique and diversified electronic structure and ultrathin sheet structure of 2D TMDCs offer opportunities for moving ahead of other 2D nanomaterials such as graphene and expanding the wide application of inorganic 2D nanomaterials in many fields. For a better understanding of 2D TMDCs, one needs to know methods for their synthesis and modification, as well as their potential applications and possible biological toxicity. Herein, we summarized the recent research progress of 2D TMDCs with particular focus on their biomedical applications and potential health risks. Firstly, two kinds of synthesis methods of 2D TMDCs, top-down and bottom-up, and methods for their surface functionalization are reviewed. Secondly, the applications of 2D TMDCs in the field of biomedicine, including drug loading, photothermal therapy, biological imaging and biosensor were summarized. After that, we presented the existing researches on biosafety evaluation of 2D TMDCs. At last, we discussed major research gap in current researches and challenges and coping strategies in future studies.
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Affiliation(s)
- Xiaofei Zhou
- Faculty of Science and Technology, Bohai Campus, Hebei Agricultural University, Cangzhou, China
| | - Hainan Sun
- Shandong Vocational College of Light Industry, Zibo, China
| | - Xue Bai
- School of Public Health, Shandong University, Jinan, China
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68
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Adir O, Poley M, Chen G, Froim S, Krinsky N, Shklover J, Shainsky-Roitman J, Lammers T, Schroeder A. Integrating Artificial Intelligence and Nanotechnology for Precision Cancer Medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901989. [PMID: 31286573 PMCID: PMC7124889 DOI: 10.1002/adma.201901989] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/17/2019] [Indexed: 05/13/2023]
Abstract
Artificial intelligence (AI) and nanotechnology are two fields that are instrumental in realizing the goal of precision medicine-tailoring the best treatment for each cancer patient. Recent conversion between these two fields is enabling better patient data acquisition and improved design of nanomaterials for precision cancer medicine. Diagnostic nanomaterials are used to assemble a patient-specific disease profile, which is then leveraged, through a set of therapeutic nanotechnologies, to improve the treatment outcome. However, high intratumor and interpatient heterogeneities make the rational design of diagnostic and therapeutic platforms, and analysis of their output, extremely difficult. Integration of AI approaches can bridge this gap, using pattern analysis and classification algorithms for improved diagnostic and therapeutic accuracy. Nanomedicine design also benefits from the application of AI, by optimizing material properties according to predicted interactions with the target drug, biological fluids, immune system, vasculature, and cell membranes, all affecting therapeutic efficacy. Here, fundamental concepts in AI are described and the contributions and promise of nanotechnology coupled with AI to the future of precision cancer medicine are reviewed.
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Affiliation(s)
- Omer Adir
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Maria Poley
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gal Chen
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sahar Froim
- Department of Physical Electronics, School of Electrical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Nitzan Krinsky
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Jeny Shklover
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Janna Shainsky-Roitman
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Twan Lammers
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen, 52074, Germany
| | - Avi Schroeder
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
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69
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He W, Huang Y, Wu J. Enzyme-Free Glucose Biosensors Based on MoS 2 Nanocomposites. NANOSCALE RESEARCH LETTERS 2020; 15:60. [PMID: 32166428 PMCID: PMC7067927 DOI: 10.1186/s11671-020-3285-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/18/2020] [Indexed: 05/07/2023]
Abstract
High-performance glucose biosensors are highly desired for healthcare. To meet these demands, glucose biosensors, particularly enzyme-free glucose biosensors, have received much attention. Two-dimensional materials, e.g., graphene, with high surface area, excellent electrical properties, and good biocompatibility, have been the main focus of biosensor research in the last decade. This review presents the recent progress made in enzyme-free glucose biosensors based on MoS2 nanocomposites. Two different techniques for glucose detections are introduced, with an emphasis on electrochemical glucose biosensors. Challenges and future perspectives of MoS2 nanocomposite glucose biosensors are also discussed.
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Affiliation(s)
- Weijie He
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Yixuan Huang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Jiang Wu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China.
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70
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Taniguchi M. Analysis Method of the Ion Current-Time Waveform Obtained from Low Aspect Ratio Solid-state Nanopores. ANAL SCI 2020; 36:161-165. [PMID: 31813895 DOI: 10.2116/analsci.19r009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Low aspect ratio nanopores are expected to be applied to the detection of viruses and bacteria because of their high spatial resolution. Multiphysics simulations have revealed that the ion current-time waveform obtained from low aspect ratio nanopores contains information on not only the volume of viruses and bacteria, but also the structure, surface charge, and flow dynamics. Analysis using machine learning extracts information about these analytes from the ion current-time waveform. The combination of low aspect ratio nanopores, multiphysics simulation, and machine learning has made it possible to distinguish different types of viruses and bacteria with high accuracy.
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71
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Heiranian M, Aluru NR. Nanofluidic Transport Theory with Enhancement Factors Approaching One. ACS NANO 2020; 14:272-281. [PMID: 31854970 DOI: 10.1021/acsnano.9b04328] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High performance water transport in nanopores has drawn a great deal of attention in a variety of applications, such as water desalination, power generation, and biosensing. High water transport enhancement factors in carbon-based nanopores have been reported over the classical Hagen-Poiseuille (HP) equation which does not account for the physics of transport at molecular scale. Instead, comparing the experimentally measured transport rates to that of a theory, that accounts for the microscopic physics of transport, would result in enhancement factors approaching unity. Such a theory is currently missing. Here, molecular corrections are introduced into the HP equation by considering the variation of key hydrodynamical properties (viscosity and friction) with thickness and diameter of pores in ultrathin graphene and finite-length carbon nanotubes (CNTs) using Green-Kubo relations and molecular dynamics (MD) simulations. The corrected HP (CHP) theory successfully predicts the permeation rates from nonequilibrium MD pressure driven flows. The previously reported enhancement factors over no-slip HP (of the order of 1000) approach unity when the permeations are normalized by the CHP flow rates. The results of our study will help better understand nanoscale flows in carbon-based pores and tubes.
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Affiliation(s)
- Mohammad Heiranian
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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72
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Recent Advances in Two-dimensional Materials for Electrochemical Energy Storage and Conversion. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-9068-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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73
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Sadeghi M, Jahanshahi M, Javadian H. Highly sensitive biosensor for detection of DNA nucleobases: Enhanced electrochemical sensing based on polyaniline/single-layer MoS2 nanosheets nanocomposite modified carbon paste electrode. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104315] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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74
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Rani S, Ray SJ. Two-dimensional C3N based sub-10 nanometer biosensor. Phys Chem Chem Phys 2020; 22:11452-11459. [DOI: 10.1039/d0cp00546k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The current observation demonstrates the usefulness of the two-dimensional C3N system as a next generation bio-sensor for the sequencing of various nucleobases, offering new leads for future developments in bioelectronics, superior sensing architectures and sustainable designs.
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Affiliation(s)
- S. Rani
- Department of Physics
- Indian Institute of Technology Patna
- Bihta
- India
| | - S. J. Ray
- Department of Physics
- Indian Institute of Technology Patna
- Bihta
- India
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75
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Graf M, Lihter M, Altus D, Marion S, Radenovic A. Transverse Detection of DNA Using a MoS 2 Nanopore. NANO LETTERS 2019; 19:9075-9083. [PMID: 31710497 DOI: 10.1021/acs.nanolett.9b04180] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Classical nanopore sensing relies on the measurement of the ion current passing through a nanopore. Whenever a molecule electrophoretically translocates through the narrow constriction, it modulates the ion current. Although this approach allows one to measure single molecules, the access resistance limits the spatial resolution. This physical limitation could potentially be overcome by an alternative sensing scheme taking advantage of the current across the membrane material itself. Such an electronic readout would also allow better temporal resolution than the ionic current. In this work, we present the fabrication of an electrically contacted molybdenum disulfide (MoS2) nanoribbon integrated with a nanopore. DNA molecules are sensed by correlated signals from the ionic current through the nanopore and the transverse current through the nanoribbon. The resulting signal suggests a field-effect sensing scheme where the charge of the molecule is directly sensed by the nanoribbon. We discuss different sensing schemes such as local potential sensing and direct charge sensing. Furthermore, we show that the fabrication of freestanding MoS2 ribbons with metal contacts is reliable and discuss the challenges that arise in the fabrication and usage of these devices.
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Affiliation(s)
- Michael Graf
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Martina Lihter
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Damir Altus
- Institute of Physics , HR-10000 Zagreb , Croatia
| | - Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
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76
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L de Souza FA, Amorim RG, Scopel WL, Scheicher RH. Controlled current confinement in interfaced 2D nanosensor for electrical identification of DNA. Phys Chem Chem Phys 2019; 21:24884-24890. [PMID: 31584588 DOI: 10.1039/c9cp03950c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The controlled synthesis of hybrid two-dimensional (2D) materials and the development of atomically precise nanopore fabrication techniques have opened up entirely new possibilities for sensing applications via nanoelectronics. Here, we investigate the electronic transport properties of an in-plane hybrid graphene/h-BN device, containing a graphene nanopore, to assess its feasibility to act as a molecular sensor. The results from our calculations based on density functional theory and the non-equilibrium Green's function formalism reveal the capability to confine the electric current pathways to the two carbon wires lining either edge of the nanopore, thereby creating conditions in which the conductance is highly sensitive to any changes in the electrical potential inside the nanopore. We apply this setup to assess whether it is possible to electrically determine the base sequence in a DNA molecule. Indeed, the modulation of the device conductance reveals a characteristic fingerprint of each nucleotide, which manifests itself in a pronounced difference in the sensitivity of the four different nucleotides, thereby allowing electrical discrimination. These findings lead us to propose this device architecture as a promising nanobiosensor. While fabrication in the lab may represent a profound experimental challenge, it should nevertheless in principle be feasible with existing contemporary techniques of hybrid 2D material synthesis, in conjunction with approaches for highly controlled nanopore creation.
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Affiliation(s)
- Fábio A L de Souza
- Federal Institute of Education, Science and Technology of Espírito Santo, Ibatiba/ES, Brazil.
| | - Rodrigo G Amorim
- Departamento de Física, ICEx, Universidade Federal Fluminense - UFF, Volta Redonda/RJ, Brazil.
| | - Wanderlã L Scopel
- Departamento de Física, Universidade Federal do Espírito Santo-UFES, Vitória/ES, Brazil.
| | - Ralph H Scheicher
- Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Sweden.
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77
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Tan E, Li BL, Ariga K, Lim CT, Garaj S, Leong DT. Toxicity of Two-Dimensional Layered Materials and Their Heterostructures. Bioconjug Chem 2019; 30:2287-2299. [PMID: 31381854 DOI: 10.1021/acs.bioconjchem.9b00502] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Two-dimensional layered materials (2D LMs) are taking the scientific world by storm. Graphene epitomizes 2D LMs with many interesting properties and corresponding applications. Following the footsteps of graphene, many other types of 2D LMs such as transition metal dichalcogenides, black phosphorus, and graphitic-phase C3N4 nanosheets are emerging to be equally interesting as graphene and its derivatives. Some of these applications such as nanomedicine do have a high probability of human exposure. This review focuses on the biological and toxicity effects of 2D LMs and their associated mechanisms linking their chemistries to their biological end points. This review aims to help researchers to predict and mitigate any toxic effects. With understanding, redesign of newer and safer 2D LMs becomes possible.
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Affiliation(s)
- Eveline Tan
- Department of Chemical & Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
| | - Bang Lin Li
- Department of Chemical & Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore.,School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P. R. China
| | - Katsuhiko Ariga
- WPI-MANA , National Institute for Materials Science (NIMS) , 1-1 Namiki , Tsukuba , Ibaraki 305-0044 , Japan.,Department of Advanced Materials Science, Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8561 , Japan
| | - Chwee-Teck Lim
- Department of Physics , National University of Singapore , Singapore 117542 , Singapore.,Department of Biomedical Engineering , National University of Singapore , Singapore 117575 , Singapore.,Centre for Advanced 2D Materials , Graphene Research Centre , Singapore 117546 , Singapore.,NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore 117456 , Singapore.,Mechanobiology Institute , National University of Singapore , Singapore 117411 , Singapore
| | - Slaven Garaj
- Department of Physics , National University of Singapore , Singapore 117542 , Singapore.,Department of Biomedical Engineering , National University of Singapore , Singapore 117575 , Singapore.,Centre for Advanced 2D Materials , Graphene Research Centre , Singapore 117546 , Singapore
| | - David Tai Leong
- Department of Chemical & Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore.,NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore 117456 , Singapore
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78
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Li W, Zhan X, Song X, Si S, Chen R, Liu J, Wang Z, He J, Xiao X. A Review of Recent Applications of Ion Beam Techniques on Nanomaterial Surface Modification: Design of Nanostructures and Energy Harvesting. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901820. [PMID: 31166661 DOI: 10.1002/smll.201901820] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/13/2019] [Indexed: 05/23/2023]
Abstract
Nanomaterials have gained plenty of research interest because of their excellent performance, which is derived from their small size and special structure. In practical applications, to acquire nanomaterials with high performance, many methods have been used to modulate the structure and components of materials. To date, ion beam techniques have extensively been applied for modulating the performance of various nanomaterials. Energetic ion beams can modulate the surface morphology and chemical components of nanomaterials. In addition, ion beam techniques have also been used to fabricate nanomaterials, including 2D materials, nanoparticles, and nanowires. Compared with conventional methods, ion beam techniques, including ion implantation, ion irradiation, and focused ion beam, are all pure physical processes; these processes do not introduce any impurities into the target materials. In addition, ion beam techniques exhibit high controllability and repeatability. Here, recent progress in ion beam techniques for nanomaterial surface modification is systematically summarized and existing challenges and potential solutions are presented.
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Affiliation(s)
- Wenqing Li
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
| | - Xueying Zhan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Xianyin Song
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
| | - Shuyao Si
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
| | - Rui Chen
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
| | - Jing Liu
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
| | - Zhenxing Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Jun He
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Xiangheng Xiao
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application, Wuhan University, Wuhan, 430072, P. R. China
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79
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Putri AD, Murti BT, Kanchi S, Sabela MI, Bisetty K, Tiwari A, Inamuddin, Asiri AM. Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics. Sci Rep 2019; 9:7873. [PMID: 31133671 PMCID: PMC6536548 DOI: 10.1038/s41598-019-44378-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 05/13/2019] [Indexed: 01/04/2023] Open
Abstract
This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.
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Affiliation(s)
- Athika Darumas Putri
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
- Semarang College of Pharmaceutical Sciences, Jl. Letnand Jendral Sarwo Edi Wibowo, Semarang City, 50192, Indonesia
| | - Bayu Tri Murti
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
- Semarang College of Pharmaceutical Sciences, Jl. Letnand Jendral Sarwo Edi Wibowo, Semarang City, 50192, Indonesia
| | - Suvardhan Kanchi
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
| | - Myalowenkosi I Sabela
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
| | - Krishna Bisetty
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa.
| | - Ashutosh Tiwari
- Institute of Advanced Materials, UCS, Teknikringen 4A, Mjärdevi Science Park, SE-58330, Linköping, Sweden
- Vinoba Bhave Research Institute, Binda-Dhokri Road, Saidabad, Allahabad, 221508, India
| | - Inamuddin
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
- Centre of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Centre of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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80
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81
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Bae JH, Wang D, Hu K, Mirkin MV. Surface-Charge Effects on Voltammetry in Carbon Nanocavities. Anal Chem 2019; 91:5530-5536. [PMID: 30977642 DOI: 10.1021/acs.analchem.9b00426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ion transport controlled by electrostatic interactions is an important phenomenon in biological and artificial membranes, channels, and nanopores. Here, we employ carbon-coated nanopipets (CNPs) for studying permselective electrochemistry in a conductive nanopore. A significant accumulation (up to 2000-fold) of cationic redox species and anion depletion inside a CNP by diffuse-layer and surface-charge effects in a solution of low ionic strength were observed as well as the shift of the voltammetric midpeak potential. Finite-element simulations of electrostatic effects on CNP voltammograms show permselective ion transport in a single conducting nanopore and semiquantitatively explain our experimental data. The reported results are potentially useful for improving sensitivity and selectivity of CNP sensors for ionic analytes.
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Affiliation(s)
- Je Hyun Bae
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States
| | - Dengchao Wang
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States
| | - Keke Hu
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States.,The Graduate Center of CUNY , New York , New York 10016 , United States
| | - Michael V Mirkin
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States.,The Graduate Center of CUNY , New York , New York 10016 , United States
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82
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Mojtabavi M, VahidMohammadi A, Liang W, Beidaghi M, Wanunu M. Single-Molecule Sensing Using Nanopores in Two-Dimensional Transition Metal Carbide (MXene) Membranes. ACS NANO 2019; 13:3042-3053. [PMID: 30844249 DOI: 10.1021/acsnano.8b08017] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Label-free nanopore technology for sequencing biopolymers such as DNA and RNA could potentially replace existing methods if improvements in cost, speed, and accuracy are achieved. Solid-state nanopores have been developed over the past two decades as physically and chemically versatile sensors that mimic biological channels, through which transport and sequencing of biomolecules have already been demonstrated. Of particular interest is the use of two-dimensional (2D) materials as nanopore substrates, since these can in theory provide the highest resolution readout (<1 nm of a biopolymer segment) and opportunities for electronic multiplexed readout through their interesting electronic properties. In this work, we report on nanopores comprising atomically thin flakes of 2D transition metal carbides called MXenes. We demonstrate a high-yield (60%), contamination-free, and alignment-free transfer method that involves their self-assembly at a liquid-liquid interface to large-scale (mm-sized) films composed of sheets, followed by nanopore fabrication using focused electron beams. Our work demonstrates the feasibility of MXenes, a class of hydrophilic 2D materials with over 20 compositions known to date, as nanopore membranes for DNA translocation and single-molecule sensing applications.
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Affiliation(s)
- Mehrnaz Mojtabavi
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Armin VahidMohammadi
- Department of Materials Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Wentao Liang
- Kostas Advanced Nano-Characterization Facility , Northeastern University , Burlington Campus, 141 South Bedford Street , Burlington , Massachusetts 01803 , United States
| | - Majid Beidaghi
- Department of Materials Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Meni Wanunu
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
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83
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Affiliation(s)
- Amita Sihag
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
| | - Sairam S. Mallajosyula
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
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84
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Fabrication and practical applications of molybdenum disulfide nanopores. Nat Protoc 2019; 14:1130-1168. [PMID: 30903110 DOI: 10.1038/s41596-019-0131-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023]
Abstract
Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores' efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS2 nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS2 nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS2, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2-3 d), transfer of MoS2 and cleaning procedure (24 h), the creation of nanopores within MoS2 (30 min) and performing DNA translocations (2-3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.
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85
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Kozubek R, Tripathi M, Ghorbani-Asl M, Kretschmer S, Madauß L, Pollmann E, O'Brien M, McEvoy N, Ludacka U, Susi T, Duesberg GS, Wilhelm RA, Krasheninnikov AV, Kotakoski J, Schleberger M. Perforating Freestanding Molybdenum Disulfide Monolayers with Highly Charged Ions. J Phys Chem Lett 2019; 10:904-910. [PMID: 30646683 DOI: 10.1021/acs.jpclett.8b03666] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Porous single-layer molybdenum disulfide (MoS2) is a promising material for applications such as DNA sequencing and water desalination. In this work, we introduce irradiation with highly charged ions (HCIs) as a new technique to fabricate well-defined pores in MoS2. Surprisingly, we find a linear increase of the pore creation efficiency over a broad range of potential energies. Comparison to atomistic simulations reveals the critical role of energy deposition from the ion to the material through electronic excitation in the defect creation process and suggests an enrichment in molybdenum in the vicinity of the pore edges at least for ions with low potential energies. Analysis of the irradiated samples with atomic resolution scanning transmission electron microscopy reveals a clear dependence of the pore size on the potential energy of the projectiles, establishing irradiation with highly charged ions as an effective method to create pores with narrow size distributions and radii between ca. 0.3 and 3 nm.
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Affiliation(s)
- Roland Kozubek
- Fakultät für Physik and CENIDE , Universität Duisburg-Essen , D-47057 Duisburg , Germany
| | - Mukesh Tripathi
- Faculty of Physics , University Vienna , A-1090 Vienna , Austria
| | - Mahdi Ghorbani-Asl
- Institute of Ion Beam Physics and Materials Research , Helmholtz-Zentrum Dresden-Rossendorf , D-01328 Dresden , Germany
| | - Silvan Kretschmer
- Institute of Ion Beam Physics and Materials Research , Helmholtz-Zentrum Dresden-Rossendorf , D-01328 Dresden , Germany
| | - Lukas Madauß
- Fakultät für Physik and CENIDE , Universität Duisburg-Essen , D-47057 Duisburg , Germany
| | - Erik Pollmann
- Fakultät für Physik and CENIDE , Universität Duisburg-Essen , D-47057 Duisburg , Germany
| | - Maria O'Brien
- Advanced Materials and Bioengineering Research Centre (AMBER) and School of Chemistry , Trinity College Dublin , College Green, Dublin 2 , Ireland
| | - Niall McEvoy
- Advanced Materials and Bioengineering Research Centre (AMBER) and School of Chemistry , Trinity College Dublin , College Green, Dublin 2 , Ireland
| | - Ursula Ludacka
- Faculty of Physics , University Vienna , A-1090 Vienna , Austria
| | - Toma Susi
- Faculty of Physics , University Vienna , A-1090 Vienna , Austria
| | - Georg S Duesberg
- Institute of Physics, EIT 2, Faculty of Electrical Engineering and Information Technology , Universität der Bundeswehr München , D-85577 Neubiberg , Germany
| | - Richard A Wilhelm
- Institute of Ion Beam Physics and Materials Research , Helmholtz-Zentrum Dresden-Rossendorf , D-01328 Dresden , Germany
- Institute of Applied Physics , TU Wien , A-1040 Vienna , Austria
| | - Arkady V Krasheninnikov
- Institute of Ion Beam Physics and Materials Research , Helmholtz-Zentrum Dresden-Rossendorf , D-01328 Dresden , Germany
- Department of Applied Physics , Aalto University , P.O. Box 11100, FI-00076 Aalto , Finland
| | - Jani Kotakoski
- Faculty of Physics , University Vienna , A-1090 Vienna , Austria
| | - Marika Schleberger
- Fakultät für Physik and CENIDE , Universität Duisburg-Essen , D-47057 Duisburg , Germany
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86
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Swaminathan H, Balasurbamanian K. Design of “turn-ON and turn-OFF” fluorescence switching based photonic logic gates through multiple input-output models by MoS2 quantum dots. J Colloid Interface Sci 2019; 540:258-264. [DOI: 10.1016/j.jcis.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022]
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87
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Recent Progress on Irradiation-Induced Defect Engineering of Two-Dimensional 2H-MoS2 Few Layers. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9040678] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Atom-thick two-dimensional materials usually possess unique properties compared to their bulk counterparts. Their properties are significantly affected by defects, which could be uncontrollably introduced by irradiation. The effects of electromagnetic irradiation and particle irradiation on 2H MoS 2 two-dimensional nanolayers are reviewed in this paper, covering heavy ions, protons, electrons, gamma rays, X-rays, ultraviolet light, terahertz, and infrared irradiation. Various defects in MoS 2 layers were created by the defect engineering. Here we focus on their influence on the structural, electronic, catalytic, and magnetic performance of the 2D materials. Additionally, irradiation-induced doping is discussed and involved.
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88
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Yu YS, Lu X, Ding HM, Ma YQ. Computational investigation on DNA sequencing using functionalized graphene nanopores. Phys Chem Chem Phys 2019; 20:9063-9069. [PMID: 29446423 DOI: 10.1039/c7cp07462j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fast, low-cost and reliable DNA sequencing is one of the most desirable innovations in recent years, which can pave the way for high throughput, label-free and inexpensive personalized genome sequencing techniques. Although graphene-based nanopore devices hold great promise for next-generation DNA sequencing, it is still a challenging problem to detect different DNA sequences efficiently and accurately. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through the functionalized graphene nanopores is investigated by all-atom molecular dynamic simulations. Interestingly, it is found that the four types of bases could be identified by different ionic currents when they pass through the hydrogenated and hydroxylated pores. For the hydrogenated nanopore, the difference in the ionic current for the four bases is mainly attributed to the different electrostatic interactions between the base and the ion. For the hydroxylated nanopore, apart from the electrostatic interactions, the position of a nucleotide inside the nanopore and the dwell time of an ion around the nucleotide also play an important role in the ionic current. The present study could be helpful to better design a novel device for DNA sequencing in the future.
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Affiliation(s)
- You-Sheng Yu
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
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89
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Kumawat RL, Garg P, Kumar S, Pathak B. Electronic Transport through DNA Nucleotides in Atomically Thin Phosphorene Electrodes for Rapid DNA Sequencing. ACS APPLIED MATERIALS & INTERFACES 2019; 11:219-225. [PMID: 30540178 DOI: 10.1021/acsami.8b17239] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rapid progresses in developing the fast, low-cost, and reliable methods for DNA sequencing are envisaged for development of personalized medicine. In this respect, nanotechnology has paved the role for the development of advanced DNA sequencing techniques including sequencing with solid-state nanopores or nanogaps. Herein, we have explored the application of a black phosphorene based nanogap-device for DNA sequencing. Using density-functional-theory based non-equilibrium Green's function approach, we have computed transverse transmission and current-voltage ( I- V) characteristics of all the four DNA nucleotides (deoxy adenosine monophosphate, deoxy guanidine monophosphate, deoxy thymidine monophosphate, and deoxy cytosine monophosphate) as functions of applied bias voltages. We deduce that it is in principle; possible to differentiate between all the four nucleotides by three sequencing runs at distinct applied bias voltages, i.e., at 0.2, 1.4, and 1.6 V, where individual identification of all the four nucleotides may be possible. Hence, we believe our study might be helpful for experimentalist towards the development of a phosphorene based nanodevice for DNA sequencing to diagnose critical diseases.
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90
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Detecting topological variations of DNA at single-molecule level. Nat Commun 2019; 10:3. [PMID: 30602774 PMCID: PMC6315031 DOI: 10.1038/s41467-018-07924-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/05/2018] [Indexed: 11/08/2022] Open
Abstract
In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electrophoretic forces, translocate through a narrow orifice, transient residings of edited segments inside the orifice modulate the ionic flow. Here we utilize two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating protrusion sites in ssDNA for generating a hybrid DNA complex. We integrate a discriminative noise analysis for ds and ss DNA topologies into the threshold detection, resulting in improved multi-level signal detection and consequent extraction of reliable information about topological variations. Moreover, the positional information of the barcode along the template sequence can be determined unambiguously. All methods may be further modified to detect nicks in DNA, and thereby detect DNA damage and repair sites.
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91
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Dettori R, Yang Q, Achenie LEK, Schwarz RD. A Temperature-, pH- and Voltage-Responsive Nanogate with a Remarkably High Factor of Change in Ion Currents due to ON/OFF Switching. Chemistry 2018; 24:18897-18902. [PMID: 30252993 DOI: 10.1002/chem.201804842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Indexed: 11/10/2022]
Abstract
In biological cells, nuclear pore complexes (NPCs) embedded in cell membranes are capable of controlling the flow of ions, for example, Na+ , K+ , and Ca2+ by responding to stimuli, for example, pH and voltage. Inspired by NPCs, researchers have been endeavoring to develop nanogates to achieve the control of ion transport, but the developed nanogates only have a low factor of change in ion currents due to ON/OFF switching. As such nanopores with high temperature and pH responsivities were developed in this work. According to the experimental results, at a voltage of 3 V, the change in ion currents due to pH change is up to a factor of 170, which is remarkably high compared to other nanogates reported. Quantum chemical (QC) calculation results show that a protonated cytosine molecule (C+ ) and an unprotonated cytosine molecule (C) form three pairs of hydrogen bonds and consequently a nucleobase pair, CC+ , leading to the binding of various strands, assembly of a strand net, and blockage of ion transport. The nanogate developed is capable of responding to temperature change. At a voltage of 3 V, the factor of change in ion currents in response to temperature variation is as high as 110. Further experiments were performed to investigate the influence of the NaCl concentrations and small opening diameters exerted on nanogate performance.
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Affiliation(s)
| | - Quan Yang
- Sandia National Laboratories, Livermore, CA, 94551-0969, USA.,Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Luke E K Achenie
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Roland D Schwarz
- Department of Material Science and Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
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92
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Ryu GH, France-Lanord A, Wen Y, Zhou S, Grossman JC, Warner JH. Atomic Structure and Dynamics of Self-Limiting Sub-Nanometer Pores in Monolayer WS 2. ACS NANO 2018; 12:11638-11647. [PMID: 30375855 DOI: 10.1021/acsnano.8b07051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We reveal a self-limiting mechanism during the formation of a specific type of circular nanopore in monolayer WS2 that limits its diameter to sub-nm. A single W atom vacancy (triangular nanopore) is transformed into the self-limiting nanopore (SLNP) through the atomic restructuring of S atoms around the area, reducing the number of dangling bonds at the nanopore edge by shifting them further in-plane with W-W bonding instead. Bond rotations in WS2 help accommodate the electron beam induced atomic loss and ensure the stability of the SLNP. The SLNP shows significant improvement in diameter stability during electron beam irradiation compared to other triangular nanopores in WS2 that typically continue to expand in diameter during atom loss. The atomic structure of these SLNPs is studied using aberration-corrected scanning transmission electron microscopy with an in situ heating holder, revealing that the SLNPs are mostly formed at a temperature of ∼500 °C, which is a balance between thermally activated S vacancy diffusion and sufficient S vacancy density to initiate local atomic reconstruction. At higher temperatures ( i. e., 1000 °C), S vacancies quickly migrate away into long line vacancies, resulting in low S vacancy density and rapidly expanding holes generated at the edges of the line vacancies. At room temperature, S vacancy migration is low and vacancy density is very high, which limits atomic reconstruction, and instead many small holes open up. These results provide insights into the factors that lead to uniform sized nanopores in the sub-nm range in transition-metal dichalcogenides.
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Affiliation(s)
- Gyeong Hee Ryu
- Department of Materials , University of Oxford , 16 Parks Road , Oxford OX1 3PH , United Kingdom
| | - Arthur France-Lanord
- Department of Materials Science and Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yi Wen
- Department of Materials , University of Oxford , 16 Parks Road , Oxford OX1 3PH , United Kingdom
| | - Si Zhou
- Department of Materials , University of Oxford , 16 Parks Road , Oxford OX1 3PH , United Kingdom
| | - Jeffrey C Grossman
- Department of Materials Science and Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jamie H Warner
- Department of Materials , University of Oxford , 16 Parks Road , Oxford OX1 3PH , United Kingdom
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93
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Si W, Zhang Y, Sha J, Chen Y. Controllable and reversible DNA translocation through a single-layer molybdenum disulfide nanopore. NANOSCALE 2018; 10:19450-19458. [PMID: 30311618 DOI: 10.1039/c8nr05830j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A challenge that remains to be solved in the high-throughput and low-cost nanopore DNA sequencing is that DNA translocates through the nanopore too quickly to be sequenced with enough accuracy. Here, we present a proof of principle study of slowing down DNA translocation across the molybdenum disulfide nanopore and even reversing its translocation direction by adjusting the proportion of molybdenum atoms to sulfur atoms at the nanopore boundary. When the proportion is smaller than 0.17, the electro-osmotic flow moves in the opposite direction to the electric force exerted on the DNA molecule and the more sulfur atoms at the nanopore boundary, the stronger the electro-osmotic flow is. For the nanopore with the proportion equal to 0.17, the electro-osmotic force exerted on DNA is smaller than the electrophoretic force, DNA can be captured and its translocation speed was found to be almost three times smaller than the speed through nanopores with the proportion larger than 0.27. However, for nanopores with the proportion smaller than 0.08, DNA would even be pushed away and prevented from entering the nanopore so that its translocation direction would be reversed. The theoretical study performed here provides a new means for controlling DNA transport dynamics in both translocation velocity and direction, which would facilitate better and cheaper nanopore DNA sequencing in the future.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 210096, China.
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94
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Houghtaling J, List J, Mayer M. Nanopore-Based, Rapid Characterization of Individual Amyloid Particles in Solution: Concepts, Challenges, and Prospects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802412. [PMID: 30225962 DOI: 10.1002/smll.201802412] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Aggregates of misfolded proteins are associated with several devastating neurodegenerative diseases. These so-called amyloids are therefore explored as biomarkers for the diagnosis of dementia and other disorders, as well as for monitoring disease progression and assessment of the efficacy of therapeutic interventions. Quantification and characterization of amyloids as biomarkers is particularly demanding because the same amyloid-forming protein can exist in different states of assembly, ranging from nanometer-sized monomers to micrometer-long fibrils that interchange dynamically both in vivo and in samples from body fluids ex vivo. Soluble oligomeric amyloid aggregates, in particular, are associated with neurotoxic effects, and their molecular organization, size, and shape appear to determine their toxicity. This concept article proposes that the emerging field of nanopore-based analytics on a single molecule and single aggregate level holds the potential to account for the heterogeneity of amyloid samples and to characterize these particles-rapidly, label-free, and in aqueous solution-with regard to their size, shape, and abundance. The article describes the concept of nanopore-based resistive pulse sensing, reviews previous work in amyloid analysis, and discusses limitations and challenges that will need to be overcome to realize the full potential of amyloid characterization on a single-particle level.
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Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
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95
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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96
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Palumbo A, Tourlomousis F, Chang RC, Yang EH. Influence of Transition Metal Dichalcogenide Surfaces on Cellular Morphology and Adhesion. ACS APPLIED BIO MATERIALS 2018; 1:1448-1457. [DOI: 10.1021/acsabm.8b00405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony Palumbo
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Filippos Tourlomousis
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
- The Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, United States
| | - Robert C. Chang
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Eui-Hyeok Yang
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
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97
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Schleberger M, Kotakoski J. 2D Material Science: Defect Engineering by Particle Irradiation. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1885. [PMID: 30279366 PMCID: PMC6212862 DOI: 10.3390/ma11101885] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/02/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
Two-dimensional (2D) materials are at the heart of many novel devices due to their unique and often superior properties. For simplicity, 2D materials are often assumed to exist in their text-book form, i.e., as an ideal solid with no imperfections. However, defects are ubiquitous in macroscopic samples and play an important ⁻ if not imperative ⁻ role for the performance of any device. Thus, many independent studies have targeted the artificial introduction of defects into 2D materials by particle irradiation. In our view it would be beneficial to develop general defect engineering strategies for 2D materials based on a thorough understanding of the defect creation mechanisms, which may significantly vary from the ones relevant for 3D materials. This paper reviews the state-of-the-art in defect engineering of 2D materials by electron and ion irradiation with a clear focus on defect creation on the atomic scale and by individual impacts. Whenever possible we compile reported experimental data alongside corresponding theoretical studies. We show that, on the one hand, defect engineering by particle irradiation covers a wide range of defect types that can be fabricated with great precision in the most commonly investigated 2D materials. On the other hand, gaining a complete understanding still remains a challenge, that can be met by combining advanced theoretical methods and improved experimental set-ups, both of which only now begin to emerge. In conjunction with novel 2D materials, this challenge promises attractive future opportunities for researchers in this field.
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Affiliation(s)
- Marika Schleberger
- Fakultät für Physik and Cenide, Universität Duisburg-Essen, Lotharstraße 1, 47057 Duisburg, Germany.
| | - Jani Kotakoski
- Fakultät für Physik, Universität Wien, Boltzmanngasse 5, 1090 Wien, Austria.
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98
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Garoli D, Mosconi D, Miele E, Maccaferri N, Ardini M, Giovannini G, Dipalo M, Agnoli S, De Angelis F. Hybrid plasmonic nanostructures based on controlled integration of MoS 2 flakes on metallic nanoholes. NANOSCALE 2018; 10:17105-17111. [PMID: 30179242 DOI: 10.1039/c8nr05026k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we propose an easy and robust strategy for the versatile preparation of hybrid plasmonic nanopores by means of controlled deposition of single flakes of MoS2 directly on top of metallic holes. The device is realized on silicon nitride membranes and can be further refined by TEM or FIB milling to achieve the passing of molecules or nanometric particles through a pore. Importantly, we show that the plasmonic enhancement provided by the nanohole is strongly accumulated in the 2D nanopore, thus representing an ideal system for single-molecule sensing and sequencing in a flow-through configuration. Here, we also demonstrate that the prepared 2D material can be decorated with metallic nanoparticles that can couple their resonance with the nanopore resonance to further enhance the electromagnetic field confinement at the nanoscale level. This method can be applied to any gold nanopore with a high level of reproducibility and parallelization; hence, it can pave the way to the next generation of solid-state nanopores with plasmonic functionalities. Moreover, the controlled/ordered integration of 2D materials on plasmonic nanostructures opens a pathway towards new investigation of the following: enhanced light emission; strong coupling from plasmonic hybrid structures; hot electron generation; and sensors in general based on 2D materials.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
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99
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Ma D, Yu J, Yin W, Zhang X, Mei L, Zu Y, An L, Gu Z. Synthesis of Surface-Modification-Oriented Nanosized Molybdenum Disulfide with High Peroxidase-Like Catalytic Activity for H2
O2
and Cholesterol Detection. Chemistry 2018; 24:15868-15878. [DOI: 10.1002/chem.201803040] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Dongqing Ma
- College of Science; College of Chemical Engineering, and Materials Science; Tianjin University of Science and Technology; Tianjin 300457 P. R. China
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Jie Yu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Wenyan Yin
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Xiao Zhang
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Linqiang Mei
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Yan Zu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Lijuan An
- College of Science; College of Chemical Engineering, and Materials Science; Tianjin University of Science and Technology; Tianjin 300457 P. R. China
| | - Zhanjun Gu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; Institute of High Energy Physics, Chinese Academy of Sciences; Beijing 100049 P. R. China
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100
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Yin K, Huang S, Chen X, Wang X, Kong J, Chen Y, Xue J. Generating Sub-nanometer Pores in Single-Layer MoS 2 by Heavy-Ion Bombardment for Gas Separation: A Theoretical Perspective. ACS APPLIED MATERIALS & INTERFACES 2018; 10:28909-28917. [PMID: 30062872 DOI: 10.1021/acsami.8b10569] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-layer molybdenum disulfide (MoS2) filters with nanometer-size pores have attracted great attention recently due to their promising performance for membrane separation. Generating nanopores in MoS2 controllably, however, is still a challenging task, which greatly limits the real application of MoS2 filters. In this work, the pore forming process in single-layer MoS2 by heavy-ion bombardment was investigated in detail using molecular dynamics simulations. We found that pores with sub-nanometer size (0.6-1.2 nm) can be created in the MoS2 sheet by single-ion bombardment, with a probability as high as 0.8 pores per incident ion. The size and shape of the nanopore can be tuned controllably by adjusting bombardment parameters. Furthermore, the performance of the MoS2 filter with these sub-nanometer-size pores for separation of He, Ne, H2, Ar, and Kr gases was evaluated by density functional theory-based first-principles calculations. The MoS2 filter was found to show much higher selectivity for separating H2/He and He/Ne than that reported for graphene and other membranes. Such high selectivity was attributed to the interaction between gases and the charged edge of pores in MoS2. Our results suggest the potential application of ion beam technology in single-layer MoS2 for membrane separation.
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Affiliation(s)
- Kedi Yin
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, CAPT, HEDPS, and IFSA Collaborative Innovation Center of MoE , Peking University , Beijing 100871 , China
- Guangzhou Key Laboratory for Surface Chemistry of Energy Materials, New Energy Research Institute, School of Environment and Energy , South China University of Technology , Guangzhou , Guangdong 510006 , China
| | - Shengxi Huang
- Department of Electrical Engineering and Computer Science , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Electrical Engineering , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Xiaofei Chen
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, CAPT, HEDPS, and IFSA Collaborative Innovation Center of MoE , Peking University , Beijing 100871 , China
| | - Xinwei Wang
- School of Advanced Materials, Shenzhen Graduate School , Peking University , Shenzhen 518055 , China
| | - Jing Kong
- Department of Electrical Engineering and Computer Science , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Yan Chen
- Guangzhou Key Laboratory for Surface Chemistry of Energy Materials, New Energy Research Institute, School of Environment and Energy , South China University of Technology , Guangzhou , Guangdong 510006 , China
| | - Jianming Xue
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, CAPT, HEDPS, and IFSA Collaborative Innovation Center of MoE , Peking University , Beijing 100871 , China
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