Effect of surface functionalization on DNA sequencing using MXene-based nanopores.

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. 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 two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore.

Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.

Controlling ion transport in a C2N-based nanochannel with tunable interlayer spacing.

Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C2N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C2N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C2N-based nanodevices in nanofiltration.

Tailoring the component of protein corona via simple chemistry.

Control over the protein corona of nanomaterials allows them to function better. Here, by taking graphene/gold as examples, we comprehensively assessed the association of surface properties with the protein corona. As revealed by in vitro measurements and computations, the interaction between graphene/gold and HSA/IgE was inversely correlated with the hydroxyl group availability, whereas the interaction between that and ApoE was comparatively less relevant. Molecular simulations revealed that the number and the distribution of surface hydroxyl groups could regulate the manner in which nanomaterials interact with proteins. Moreover, we validated that ApoE pre-adsorption before injection enhances the blood circulation of nanomaterials relative to their pristine and IgE-coated counterparts. This benefit can be attributed to the invulnerability of the complementary system provided by ApoE, whose encasement does not increase cytotoxicity. Overall, this study offers a robust yet simple way to create protein corona enriched in dysopsonins to realize better delivery efficacy.

Designing a nanoparticle-containing polymeric substrate for detecting cancer cells by computer simulations.

Efficient and accurate detection of cancer cells (from normal cells) is of great importance in cancer diagnosis and prognosis. In this work, we design a new type of polymeric substrate containing nanoparticles for detecting cancers by the dissipative particle dynamics (DPD) simulation. It is found that the cancer cells and the normal cells can be indeed distinguished since the uptake number of nanoparticles from the substrate is different. The competition between the nanoparticle-cell specific interaction and nanoparticle-polymer non-specific interaction is the main factor for different uptake behaviors. Moreover, the dynamics of the nanoparticle diffusion in the polymer layer also plays an important role in the detection. To improve the detection accuracy, we further investigate the effect of the polymer type and density as well as the ligand type on the detection, and find that there may exist an optimal parameter to maximize the difference between cancer cells and normal cells. The present study may provide useful insights into the design of functionalized substrate-based nanodevices in biomedicine.

Counteranion Modulated Crystal Growth and Function of One-Dimensional Homochiral Coordination Polymers: Morphology, Structures, and Magnetic Properties.

Four pairs of enantiomeric dysprosium(III) phosphonates, namely, R- or S-[Dy3(pempH2)2(pempH)7]2(NO3)4·12H2O ( R-1 or S-1), R- or S-[Dy3(pempH)7(pempH2)2]Cl2·2H2O ( R-2 or S-2), R- or S-[Dy3(pempH)7(pempH2)2]Br2·2H2O ( R-3 or S-3), and R- or S-[Dy11(pempH2)6(pempH)27](CF3SO3)6·22H2O ( R-4 or S-4) are reported, where R- or S-pempH2 represent R- or S-(1-phenylethyl)amino] methylphosphonic acid. All show homochiral chain structures, charge-balanced by counteranions. A comparison of the crystal morphologies of the R-isomers reveals that the overall shapes are quite similar for the four compounds, but the aspect ratio changes remarkably following the sequence: R-1 < R-2 < R-3 < R-4. The sequence is in agreement with the decreasing interchain interactions related to different counteranions, which is rationalized by molecular simulations. The counteranions also influence the intrachain structures and the local coordination environments of the DyIII ions. As a result, compounds R-2 and R-3 exhibit distinct dual relaxation processes at zero dc field with the effective energy barriers for the slow- and fast-relaxation being 79.1 and 37.6 K for R-2, and 80.0 and 39.1 K for R-3, respectively. For compounds R-1 and R-4, however, slow magnetic relaxation is also observed at zero dc field but without the appearance of maxima down to 1.8 K.

Computational investigation on DNA sequencing using functionalized graphene nanopores.

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.

Ion transport through a nanoporous C2N membrane: the effect of electric field and layer number.

Ion transport through a two-dimensional membrane with nanopores plays an important role in many scientific and technical applications (e.g., water desalination, ion separation and nanofiltration). Although there have been many two-dimensional membranes for these applications, the problem of how to controllably fabricate nanopores with proper shape and size still remains challenging. In the present work, the transport of ions through a C2N membrane with intrinsically regular and uniformly distributed nanopores is investigated using all-atom molecular dynamic simulations. It was found that the monolayer C2N membrane possesses higher ion permeability compared to the graphene membrane because of its higher density of nanopores. In addition, it exhibits excellent ion selectivity under a low electric field due to the distinct dehydration capabilities and interaction behaviors (with the pore edges) of the different ions. Furthermore, we found that multilayer C2N membranes have weak ion selectivity, but show promising potential for desalination. The present study may provide some physical insights into the experimental design of C2N-based nanodevices in nanofluids.