A biosensing expedition of nanopore: A review

Nehra, Anuj; Ahlawat, Sweeti; Singh, Krishna Pal

doi:10.1016/j.snb.2018.12.143

Cited by 38 publications

(22 citation statements)

References 201 publications

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“…Regarding interaction between nanopores and filler materials, numerical modeling is mostly used. Even though accurate observation is employed on nanopores, there are too many requirements on the specimen itself (Lee et al, 2018;Gu et al, 2019;Hou et al, 2019;Nehra et al, 2019). WC-Si 3 N 4 bulks after ball milling and sintering are too crude to meet the requirements.…”

Section: Resultsmentioning

confidence: 99%

Mechanical Properties of WC-Si3N4 Composites With Ultrafine Porous Boron Nitride Nanofiber Additive

Cao

et al. 2021

Front. Mater.

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WC-10 wt.% Si3N4 composites toughened with ultrafine porous boron nitride nanofiber (0, 0.01, 0.05, 0.1, and 0.15 wt.%) were prepared for the first time by spark plasma sintering. Compared with the WC-Si3N4 composite sintered in the same condition, the obtained WC-10 wt.% Si3N4 composites with ultrafine porous boron nitride were found to possess better hardness and fracture toughness. In addition, the Si3N4 phase in the UPBNNF toughened composites did not exhibit traditional catastrophic fracture as indicated in most investigations. In this study, the phenomena are discussed, and a probable mechanism is elucidated. It is deduced that the approach could be extended to materials with a feature of internal liquid phase during the sintering process and could improve hardness and fracture toughness.

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Section: Resultsmentioning

confidence: 99%

Mechanical Properties of WC-Si3N4 Composites With Ultrafine Porous Boron Nitride Nanofiber Additive

Cao

et al. 2021

Front. Mater.

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“…Cs-TEM has been used to drill the nanopore with a size <2 nm due to the smaller beam size as compared with that without the spherical aberration correction properties. Moreover, TEM is the major tool to drill nanopore in the atomic thickness two-dimensional (2D) materials (graphene, boron nitride (BN), MoS 2 , and MXenes) suspended on the SiN x membranes (Figures 1A,B; Garaj et al, 2010;Petrone et al, 2012;Liu et al, 2014;Nehra et al, 2019).…”

Section: Fabrication Characterization and Modification Of Nanoporesmentioning

confidence: 99%

Single-Entity Detection With TEM-Fabricated Nanopores

Saqib

Hao

2021

Front. Chem.

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Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

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“…With this partition sum, the free energy is easily calculated. The center of mass calculation for the planar geometry involves employing Equations (21) and (23) in Equations (16) and (17). This calculation is described in the Appendix and here we outline the main results.…”

Section: Theory For a Planar Geometrymentioning

confidence: 99%

“…In addition to fundamental biological processes, in recent years there has also been a significant increase in nanopore-based biotechnologies, which use protein or synthetic pores to manipulate and detect biological macromolecules (12)(13)(14)(15)(16)(17)(18)(19)(20). Most prominently this has been employed for DNA sequencing, which has led to the formation of several companies selling next generation sequencing devices (13,(18)(19)(20).…”

Section: Introductionmentioning

confidence: 99%

“…Most prominently this has been employed for DNA sequencing, which has led to the formation of several companies selling next generation sequencing devices (13,(18)(19)(20). Furthermore, adaptations of these devices to study RNA and protein structures is currently being explored (15,17,21). These biotechnologies in genomics and proteomics are an important aspect to advance personalized medicine.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

Dell¹,

Muthukumar²

2019

Preprint

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Many fundamental biological processes involve moving macromolecules across membranes, through nanopores, in a process called translocation. Such motion is necessary for gene expression and regulation, tissue formation, and viral infection. Furthermore, in recent years nanopore technologies have been developed for single molecule detection of biological and synthetic macromolecules, which have been most notably employed in next generation DNA sequencing devices. Many successful theories have been established, which calculate the entropic barrier required to elongate a chain during translocation. However, these theories are at the level of the translocation coordinate (number of forward steps) and thus lack a clear connection to experiments and simulations. Furthermore, the proper diffusion coefficient for such a coordinate is unclear. In order to address these issues, we propose a center of mass (CM) theory for translocation. We start with the entropic barrier approach and show that the translocation coordinate is equivalent to the center of mass of the chain, providing a direct interpretation of previous theoretical studies. We thus recognize that the appropriate dynamics is given by CM diffusion, and calculate the appropriate diffusion constant (Rouse or Zimm) as the chain translocates. We illustrate our theoretical approach with a planar nanopore geometry and calculate some characteristic dynamical predictions. Our main result is the connection between the translocation coordinate and the chain CM, however, we also find that the translocation time is sped up by 1-2 orders of magnitude if hydrodynamic interactions are present. Our approach can be extended to include the details included in previous translocation theories. Most importantly this work provides a direct connection between theoretical approaches and experiments or simulations. SIGNIFICANCE Macromolecule motion through nanopores is critical for many biological processes, and has been recently employed for nucleic acid sequencing. Despite this, direct theoretical understandings of translocation are difficult to evaluate due to the introduction of the translocation coordinate. In this manuscript, we propose a theory for translocation written at the center of mass level of the polymer chain. This theoretical approach is more easily compared to experimental and simulation results, and additionally allows one to accurately account for hydrodynamic interactions on the macromolecule dynamics.

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A biosensing expedition of nanopore: A review

Cited by 38 publications

References 201 publications

Mechanical Properties of WC-Si3N4 Composites With Ultrafine Porous Boron Nitride Nanofiber Additive

Mechanical Properties of WC-Si3N4 Composites With Ultrafine Porous Boron Nitride Nanofiber Additive

Single-Entity Detection With TEM-Fabricated Nanopores

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

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