Classification of Epigenetic Biomarkers with Atomically Thin Nanopores

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.

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.

Nanoconfined Fluids: What Can We Expect from Them?

Nanoconfined fluids (NCFs), which are confined in nanospaces, exhibit distinctive nanoscale effects, including surface effects, small-size effects, quantum effects, and others. The continuous medium hypothesis in fluid mechanics is not valid in this context because of the comparable characteristic length of spaces and molecular mean free path, and accordingly, the classical continuum theories developed for the bulk fluids usually cannot describe the mass and energy transport of NCFs. In this Perspective, we summarize the nanoscale effects on the thermodynamics, mass transport, flow dynamics, heat transfer, phase change, and energy transport of NCFs and highlight the related representative works. The applications of NCFs in the fields of membrane separation, oil and gas production, energy harvesting and storage, and biological engineering are especially indicated. Currently, the theoretical description framework of NCFs is still missing, and it is expected that this framework can be established by adopting the classical continuum theories with the consideration of nanoscale effects.

Recent Progress of Biomarker Detection Sensors

Early cancer diagnosis and treatment are crucial research fields of human health. One method that has proven efficient is biomarker detection which can provide real-time and accurate biological information for early diagnosis. This review presents several biomarker sensors based on electrochemistry, surface plasmon resonance (SPR), nanowires, other nanostructures, and, most recently, metamaterials which have also shown their mechanisms and prospects in application in recent years. Compared with previous reviews, electrochemistry-based biomarker sensors have been classified into three strategies according to their optimizing methods in this review. This makes it more convenient for researchers to find a specific fabrication method to improve the performance of their sensors. Besides that, as microfabrication technologies have improved and novel materials are explored, some novel biomarker sensors-such as nanowire-based and metamaterial-based biomarker sensors-have also been investigated and summarized in this review, which can exhibit ultrahigh resolution, sensitivity, and limit of detection (LoD) in a more complex detection environment. The purpose of this review is to understand the present by reviewing the past. Researchers can break through bottlenecks of existing biomarker sensors by reviewing previous works and finally meet the various complex detection needs for the early diagnosis of human cancer.

Selective Molecular Sieving through a Large Graphene Nanopore with Surface Charges

The precise control of the pore sizes at an atomic level has proved to be the biggest challenge of all for nanoporous graphene membranes for gas separation. Here, we propose a simple method to realize the selective molecular sieving through originally nonselective graphene nanopores by adding charges on the graphene surfaces. Molecular dynamic simulations show that the CO₂/N₂ selectivity of the graphene nanopore with a diameter of 0.52 nm increases up to 22.78 for a surface charge density of only -5.934 e/nm². The selectivity improvement is related to the distinctive adsorption intensities of CO₂ and N₂ molecules on the charge-loaded graphene surfaces. This work points toward a promising road to tune the selectivity of graphene nanopores and therefore promotes the realization of porous graphene membranes and other two-dimensional porous membranes by accepting the pores with a wide size distribution and reducing the requirements in the control of pore sizes.

Microfluidic epigenomic mapping technologies for precision medicine

Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.

Perforating Freestanding Molybdenum Disulfide Monolayers with Highly Charged Ions

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.