Individual DNA Base Identification at the Transport Through Graphene Nanopore

2013 ◽  
Author(s):  
Kazuya Takeuchi ◽  
Tatiana Zolotoukhina
Keyword(s):  
Single Layer ◽  
Potential Interaction ◽  
Time Dependent ◽  
Single Layer Graphene ◽  
Stochastic Motion ◽  
Contact Mode ◽  
Additional Information ◽  
Dna Base ◽  
Force Signal ◽  
Graphene Nanopore

Use of solid film nanopore in which DNA is threaded through for efficient DNA sequencing devices has various practical issues concerned with nucleobase motion that should be controlled. Translocation rate and different orientation of nucleobases, stochastic motion of single-strand DNA through a nanopore introduce definite amount of noise into the signal defining interaction of nucleobase and nanopore. We propose to consider the single layer graphene nanopore as a two-way interaction scanning device. The interaction forces between pore and base are structure dependent, even within orientation and noise average over a base, and can be evaluated. The appropriate translocation rate of the base molecule provide a time-dependent function of interaction change inside of interaction interval of each individual base with graphene nanopore. In such case transient characteristics of the individual bases can be used for identification of the bases. The forces between bases and graphene nanopore of 1.5nm diameter are calculated as interaction characteristics of bases. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases and graphene are of the MM2/MM3 type although the possibility of the Van der Waals interaction only can also be considered. The noise of the force signal due to orientation of the bases in the pore is evaluated and base-dependent interaction recognition is considered relative to the magnitude of the AFM signal in the non-contact mode. The time-dependent in-plane for graphene transient force signal resolution for different bases is probed. Possibility of base identification by combination of transient in-plane force taken as orientation averaged signal is studied. Obtained results can simultaneously give additional information for the electronic transport calculations with possible transient base orientations relative to the edge of pore in graphene.

MD Evaluation of the IR Spectra of DNA Bases in the Process of Transport Through Graphene Nanopore

2015 ◽  
Author(s):  
Takumu Kitani ◽  
Tatiana Zolotoukhina
Keyword(s):  
Spatial Resolution ◽  
Single Molecule ◽  
Organic Molecules ◽  
Quantitative Information ◽  
Potential Interaction ◽  
Spectral Signature ◽  
Small Organic Molecules ◽  
Additional Information ◽  
The Individual ◽  
Graphene Nanopore

Development of the 1D and 2D IR spectroscopy of small organic molecules and clusters opens yet another way of possible identification of small organic molecules in the state of motion in the graphene nanopore scanning device. With the advantage of obtaining qualitative and at least semi-quantitative information of specimens real-time and non-invasively, vibrational spectroscopy techniques, infrared (IR) and Raman have become more and more important in the analysis of biomolecular samples. At present, the sensitivity and spatial resolution of these techniques stands at the challenge of the detection and analysis of biosamples at very low concentration (single molecule) and high spatial resolution (nanometer/sub-nanometer scale). Spectral analysis requires theoretical assignment of vibrational modes to each biomolecule. We considered vibrational spectra of DNA nucleobase at the time when they are translocated through the graphene nanopore. The Fourier transform of the density of states (DOS) of each base was calculated and the spectra of the base molecules and C atoms of graphene pore edge were obtained. Translocation rate was fixed to have maximum interaction of the base with 1.5 nm pore and single orientation of nucleobases was evaluated relative to molecular plane. Whether interaction of nucleobase and nanopore is able to enhance the signal is still remains unanswered. But we have shown that the spectra of each nucleobase are different and can be considered the fingerprint of the particular molecule. The interaction forces between pore and base are structure dependent and time-limited by translocation time. In such case, transient correlation functions were utilized for the DOSes of the individual bases and forces on each atom of the particular base were sorted by intensity. The spectra of individual atoms in the bases as well as of whole molecule were compared and frequencies of most intense peaks were related to particular atoms. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases can simultaneously give additional information for the electronic transport calculations with possible tra and graphene are of the MM2/MM3 part of the Van der Waals interaction only has been considered. Possibility of base identification by spectral signature is confirmed. Calculated spectra are compared with results of the existing IR measurements for nucleobases.

Sub 10nm Nanopore Sculpturing with Focused Electron Beam on Single Layer Graphene Oxide Film

2013 ◽  
Vol 631-632 ◽  
pp. 154-159
Author(s):  
Zhong Xian Li ◽  
Xiu Lan Cheng ◽  
Zhi Min Wang
Keyword(s):  
Graphene Oxide ◽  
Electron Beam ◽  
Oxide Film ◽  
Dna Sequencing ◽  
Single Layer ◽  
Single Layer Graphene ◽  
Sequencing Technology ◽  
Base Pairs ◽  
Spot Number ◽  
Graphene Nanopore

DNA sequencing by nanopore is a technique to detect DNA sequence by making the DNA strain passing through the nanopore material and measureing some characteristic parameters to determine the order of the four kinds of base-pairs. Graphene nanopore research becomes a hotspot for the DNA sequencing technology. In this paper, a kind of novel nanopore on graphene oxide is sculptured with FEB(Focused Electron Beam) to overcome the problem about the high noise for graphene nanopore. By tuning FEB parameters, e.g. the accelerating voltage, the spot number, the exposure time and the amplification factor, sub 10nm nanopores on single layer GO(Graphene Oxide) film will be achieved. At the same time, some challenges are discussed: difficult to get stable size, hard to take TEM pictures and hard to get relatively smaller size.

Comparative study of electron transfer on various graphene-metallic contacts

2019 ◽  
Vol 33 (31) ◽  
pp. 1950384
Author(s):  
Di Lu ◽  
Yu-E Yang ◽  
Weichun Zhang ◽  
Caixia Wang ◽  
Jining Fang ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Single Layer ◽  
Annealing Treatment ◽  
Single Layer Graphene ◽  
Strain Effect ◽  
Graphene Surface ◽  
Layer Graphene ◽  
Metallic Contacts ◽  
Nonuniform Strain ◽  
Main Factor

We have investigated Raman spectra of the G and 2D lines of a single-layer graphene (SLG) with metallic contacts. The shift of the G and 2D lines is correlated to two different factors. Before performing annealing treatment or annealing under low temperature, the electron transfer on graphene surface is dominated by nonuniform strain effect. As the annealing treatment is enhanced, however, a suitable annealing treatment can eliminate the nonuniform strain effect where the relative work function (WF) between graphene and metal becomes a main factor to determine electronic transfer. Moreover, it is confirmed that the optimized annealing treatment can also decrease effectively the structural defect and induced disorder in graphene due to metallic contacts.

scholarly journals Millisecond lattice gasification for high-density CO2- and O2-sieving nanopores in single-layer graphene

2021 ◽  
Vol 7 (9) ◽  
pp. eabf0116
Author(s):  
Shiqi Huang ◽  
Shaoxian Li ◽  
Luis Francisco Villalobos ◽  
Mostapha Dakhchoune ◽  
Marina Micari ◽  
...  
Keyword(s):  
Single Layer ◽  
High Density ◽  
Single Layer Graphene ◽  
Pore Density ◽  
Vacancy Defects ◽  
Carbon Gasification ◽  
Layer Graphene ◽  
Gas Molecules ◽  
Good Agreement

Etching single-layer graphene to incorporate a high pore density with sub-angstrom precision in molecular differentiation is critical to realize the promising high-flux separation of similar-sized gas molecules, e.g., CO2 from N2. However, rapid etching kinetics needed to achieve the high pore density is challenging to control for such precision. Here, we report a millisecond carbon gasification chemistry incorporating high density (>1012 cm−2) of functional oxygen clusters that then evolve in CO2-sieving vacancy defects under controlled and predictable gasification conditions. A statistical distribution of nanopore lattice isomers is observed, in good agreement with the theoretical solution to the isomer cataloging problem. The gasification technique is scalable, and a centimeter-scale membrane is demonstrated. Last, molecular cutoff could be adjusted by 0.1 Å by in situ expansion of the vacancy defects in an O2 atmosphere. Large CO2 and O2 permeances (>10,000 and 1000 GPU, respectively) are demonstrated accompanying attractive CO2/N2 and O2/N2 selectivities.

scholarly journals Enhanced ultraviolet absorption in graphene by aluminum and magnesium hole-arrays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xueling Cheng ◽  
Yunshan Wang
Keyword(s):  
Numerical Study ◽  
Uv Spectroscopy ◽  
Single Layer ◽  
Hybrid Structure ◽  
Uv Absorption ◽  
Single Layer Graphene ◽  
Visible Range ◽  
Uv Spectrum ◽  
Hole Arrays ◽  
Uv Range

AbstractOptoelectronic devices in the UV range have many applications including deep-UV communications, UV photodetectors, UV spectroscopy, etc. Graphene has unique exciton resonances, that have demonstrated large photosensitivity across the UV spectrum. Enhancing UV absorption in graphene has the potential to boost the performance of the various opto-electronic devices. Here we report numerical study of UV absorption in graphene on aluminum and magnesium hole-arrays. The absorption in a single-layer graphene on aluminum and magnesium hole-arrays reached a maximum value of 28% and 30% respectively, and the absorption peak is tunable from the UV to the visible range. The proposed graphene hybrid structure does not require graphene to be sandwiched between different material layers and thus is easy to fabricate and allows graphene to interact with its surroundings.

Mass spectrometry imaging of untreated wet cell membranes in solution using single-layer graphene

2021 ◽  
Vol 18 (3) ◽  
pp. 316-320 ◽  
Author(s):  
Heejin Lim ◽  
Sun Young Lee ◽  
Yereum Park ◽  
Hyeonggyu Jin ◽  
Daeha Seo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Cell Membranes ◽  
Single Layer ◽  
Single Layer Graphene ◽  
Layer Graphene
Sign in / Sign up

Export Citation Format

Share Document