Microscopic Detection Analysis of Single Molecules in MoS2 Membrane Nanopores

Asymmetric ion transport through "Janus" MoSSe sub-nanometer pores

We conduct all-atom molecular dynamics simulations to systematically investigate the underlying mechanisms governing ion transport through a sub-nanometer pore decorated with negative charges in a "Janus" MoSSe membrane. The charge imbalance between S and Se atoms on each side of the membrane induces different types of ion adsorption processes depending on the pore inner charge configuration, and the polarity of external biases, which leads to asymmetry in ionic I-V characteristics. Statistical analysis of the total translocation times including adsorption-desorption processes, and ion dwell times indicates that potassium ions predominantly remain adsorbed during their interaction with the membrane before undertaking a quick translocation through the pore. High applied biases suppress cation adsorption, which results in fast translocation with the current flow boosted by negative inner charges around the pore. We also show that in a membrane consisting of several "Janus" layers, the applied bias necessary to overcome the sub-nm pore barrier increases with the number of layers, providing control over the ionic current.

Ion Trapping and Thermionic Emission across Sub-nm Pores

Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers. Our analysis of the different types of energy involved in ion translocations indicates that electrostatics is the dominant factor controlling ion transfer across these sub-nm pores. A physical model based on the thermionic emission formalism to account for the free energy barriers to ion flow reproduces the I-V characteristics.

2D materials towards energy conversion processes in nanofluidics

Hierarchically assembled 2D material membranes are extremely promising platforms for energy conversion processes in nanofluidics. In this perspective, we discuss recent advances in the production of smart 2D material membranes that come close to mimicking biological energy conversion processes and how these efforts translate into the design of water purification systems, artificial photosynthesis, and solar energy conversion devices. As we depict here, 2D material membranes synergistically modulate the intrinsic active sites (nanopores), electron transport, mass transfer, and mechanical and chemical stability aiming at cost-effective and highly efficient smart membranes.

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.

Reservoir Physical Properties and Micropore Nanocharacteristics of Cores in the Shihezi Formation, Sudong District, Sulige Gas Field, Ordos Basin

Sulige gas field is a very complex large-scale gas field with low porosity, low permeability, low abundance, and strong heterogeneity. In this study, the nanopore structure of the reservoir in the study area was analyzed. The analysis of reservoir physical properties and core microscopic pore characteristics of Shihezi formation in Sudong District, Sulige gas field, Ordos Basin, was put forward. According to core observation, thin section identification, and grain size analysis, the lithology of gas reservoirs in Shan-1 member and He-8 member in the study area is mainly lithic sandstone, lithic quartz sandstone, and quartz sandstone. According to the analysis of physical data in the study area, the reservoirs in Shan-1 member and He-8 member have typical characteristics of low porosity and low permeability. According to that microscopic observation of sandstone thin section and cast thin section combined with the analysis of scan electron microscope, the results show that both Shan-1 member and He-8 member of Sudong area 2 in Sulige gas field are dominated by class I reservoirs and class II reservoirs. Especially, class I reservoirs are widely distributed, with the cumulative area of this type of reservoirs accounting for 70.12% of the total area in Shan section and 64.12% in He-8 section. Class I reservoirs are scattered in the study area, accounting for 0.27% of the total area in the mountain section and 0.36% in the He-8 section. Class IV reservoirs are distributed dispersedly and have a small distribution area. The cumulative area of reservoirs in mountain section accounts for 5.38% of the total area and that in He-8 section accounts for 5.46%. Therefore, Sudong area 2 in Sulige gas field is a typical low porosity and low permeability reservoir. On the basis of geological background, sedimentary microfacies, diagenesis, and pore structure characteristics of the study area, it is considered that the pore structure of sandstone in the study area is mainly controlled by sedimentary characteristics and diagenesis of sandstone.

Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores

Gating in ion transport is at the center of many vital living-substance transmission processes, and understanding how gating works at an atomic level is essential but intricate. However, our understanding and finite experimental findings of subcontinuum ion transport in subnanometer nanopores are still limited, which is out of reach of the classical continuum nanofluidics. Moreover, the influence of ion density on subcontinuum ion transport is poorly understood. Here we report the ion density-dependent dynamic conductance switching process in biomimetic graphene nanopores and explain the phenomenon by a reversible ion absorption mechanism. Our molecular dynamics simulations demonstrate that the cations near the graphene nanopore can interact with the surface charges on the nanopore, thereby realizing the switching of high- and low-conductance states. This work has deepened the understanding of gating in ion transport.

Material Evolution with Nanotechnology, Nanoarchitectonics, and Materials Informatics: What will be the Next Paradigm Shift in Nanoporous Materials?

Materials science and chemistry have played a central and significant role in advancing society. With the shift toward sustainable living, it is anticipated that the development of functional materials will continue to be vital for sustaining life on our planet. In the recent decades, rapid progress has been made in materials science and chemistry owing to the advances in experimental, analytical, and computational methods, thereby producing several novel and useful materials. However, most problems in material development are highly complex. Here, the best strategy for the development of functional materials via the implementation of three key concepts is discussed: nanotechnology as a game changer, nanoarchitectonics as an integrator, and materials informatics as a super-accelerator. Discussions from conceptual viewpoints and example recent developments, chiefly focused on nanoporous materials, are presented. It is anticipated that coupling these three strategies together will open advanced routes for the swift design and exploratory search of functional materials truly useful for solving real-world problems. These novel strategies will result in the evolution of nanoporous functional materials.

Two-dimensional materials as solid-state nanopores for chemical sensing

Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.

Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore

Amplification-free genome analysis can revolutionize biology and medicine by uncovering genetic variations among individuals. Here, the authors report on a 3D-integrated nanopore for electrolysis to in situ detection of single-molecule DNA in a cell by ionic current measurements. It consists of a SiO₂ multipore sheet and a SiN_x nanopore membrane stacked vertically on a Si wafer. Single cell lysis is demonstrated by 10⁶  V m^-1 -level electrostatic field focused at the multinanopore. The intracellular molecules are then directly detected as they move through a sensing zone, wherein the authors find telegraphic current signatures reflecting folding degrees of freedom of the millimeter-long polynucleotides threaded through the SiN_x nanopore. The present device concept may enable on-chip single-molecule sequencing to multi-omics analyses at a single-cell level.

Single-Entity Detection With TEM-Fabricated Nanopores

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.