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Recently, the novel hole-containing carbon nitride C3N3 nanomaterial was successfully synthesized, featuring outstanding and unique mechanical and electrical properties. However, to fully exploit this nanomaterial in biomedical applications, information regarding its biocompatibility is necessary. Herein, by using all-atom molecular dynamics simulations, we evaluate the interactions between a C3N3 nanosheet and a critical cellular component, that is, a lipid membrane bilayer. Our results indicate that the C3N3 nanosheet is able to interact with the lipid bilayer surface without affecting the membrane’s structural integrity. Moreover, our results showed that the C3N3 nanosheet is adsorbed on the surface of the lipid bilayer without inflicting any structural damage to the membrane, regardless of the conditions of the system (that is, with and without restrains in the C3N3 nanosheet). Also, we found that both energy contributions, namely vdW and Coulomb energies, conjointly mediated the C3N3 adsorption process. In comparison and as expected, pristine graphene significantly disturbed the membrane structure. Perpendicularly-oriented-sheet simulations described the significance of the surface charges of the C3N3 nanosheet in prohibiting its insertion into the membrane. Detailed analysis indicated that the electrostatic attraction between the pores in the C3N3 structure and the lipid head amino groups stabilized the interaction restricting the insertion of the C3N3 structure deeper into the membrane. Our results suggested the importance of the negatively charged C3N3 pores when interacting with lipid membranes. Our findings shed light on the potential compatibility of C3N3 with biomembranes and its underlying molecular mechanism, which might provide a useful foundation for the future exploration of this 2D nanomaterial in biomedical applications.

Low-friction but superhydrophilic materials are urgently needed in biomedical and engineering fields because of their nonfouling property and biocompatibility, particularly when the surfaces are definitely superhydrophilic, such as metal or TiO2 as the surface coatings of the intravascular stents. However, generally, there is a higher friction coefficient on the superhydrophilic surfaces than on the hydrophobic surfaces. On the basis of molecular dynamics simulations, we show that the friction on the superhydrophilic surface with appropriate charge patterns is evidently reduced, where the lower friction is similar to that of a rather hydrophobic surface with a contact angle of water droplet of ∼44°. This reduction is attributed to the existence of an ordered water monolayer on the superhydrophilic surface with appropriate charge patterns, and the friction between this ordered water monolayer and the water molecules above is small.

Specific targeting of tumor tissues is essential for tumor imaging and therapeutics but remains challenging. Here, we report an unprecedented method using synthetic sulfonic-graphene quantum dots (sulfonic-GQDs) to exactly target the cancer cell nuclei in vivo without any bio- ligand modification, with no intervention in cells of normal tissues. The key factor for such selectivity is the high interstitial fluid pressure (IFP) in tumor tissues, which allows the penetration of sulfonic-GQDs into the plasma membrane of tumor cells. In vitro, the sulfonic-GQDs are repelled out of the cell membrane because of the repulsive force between negatively charged sulfonic-GQDs and the cell membranes which contributes to the low distribution in normal tissues in vivo. However, the plasma membrane-crossing process can be activated by incubating cells in ultrathin film culture medium because of the attachment of sulfonic-GQDs on cell memebranes. Molecular dynamics simulations demonstrated that, once transported across the plasma membrane, the negatively charged functional groups of these GQDs will leave the membrane with a self-cleaning function retaining a small enough size to achieve penetration through the nuclear membrane into the nucleus. Our study showed that IFP is a previously unrecognized mechanism for specific targeting of tumor cell nuclei and suggested that sulfonic-GQDs may be developed into novel tools for tumor-specific imaging and therapeutics.

Using all-atom molecular dynamics (MD) simulation, we have investigated the adsorption of protein GA module (GA53) onto graphene oxide (GO), compared with similar adsorption onto pristine graphene (PG). We find that: (1) the protein GA53 can be easily and firmly adsorbed onto the surface of GO and PG, but the binding sites are not specific; the main difference is that the secondary structure of GA53 can be well preserved in protein–GO system, while GA53 will partially lose its secondary structure after adsorbed on PG. (2) in protein–GO system, hydroxyl and epoxy groups increase the distance between protein and GO, which weaken their vdW interactions, meanwhile, hydrogen bonds and electrostatic interactions enhance their binding affinity. In protein–PG system, strong vdW interactions between residues of GA53 and PG have destroyed its secondary structure. (3) π–π stacking interactions still exist between aromatic residues and both the basal plane of GO and PG. In comparison with PG, our results suggest that GO presents better biocompatibility to preserve protein secondary structure when simultaneously absorbing protein.

Understanding how nanomaterials interact with cell membranes is related to how they cause cytotoxicity and is therefore critical for designing safer biomedical applications. Recently, graphene (a two-dimensional nanomaterial) was shown to have antibacterial activity on Escherichia coli, but its underlying molecular mechanisms remain unknown. Here we show experimentally and theoretically that pristine graphene and graphene oxide nanosheets can induce the degradation of the inner and outer cell membranes of Escherichia coli, and reduce their viability. Transmission electron microscopy shows three rough stages, and molecular dynamics simulations reveal the atomic details of the process. Graphene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes because of the strong dispersion interactions between graphene and lipid molecules. This destructive extraction offers a novel mechanism for the molecular basis of graphene's cytotoxicity and antibacterial activity.

The evaporation of a tiny amount of water on the solid surface with different wettabilities has been studied by molecular dynamics simulations. From nonequilibrium MD simulations, we found that, as the surface changed from hydrophobic to hydrophilic, the evaporation speed did not show a monotonic decrease as intuitively expected, but increased first, and then decreased after it reached a maximum value. The analysis of the simulation trajectory and calculation of the surface water interaction illustrate that the competition between the number of water molecules on the water-gas surface from where the water molecules can evaporate and the potential barrier to prevent those water molecules from evaporating results in the unexpected behavior of the evaporation. This finding is helpful in understanding the evaporation on biological surfaces, designing artificial surfaces of ultrafast water evaporating, or preserving water in soil.

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.

Molecular dynamic simulations of the chiral transition of a difluorobenzo[c]phenanthrene molecule (C(18)H(12)F(2), D molecule) in single-walled boron-nitride nanotubes (SWBNNTs) revealed remarkable effects of the nanoscale confinement. The critical temperature, above which the chiral transition occurs, increases considerably with the nanotube diameter, and the chiral transition frequency decreases almost exponentially with respect to the reciprocal of temperature. The chiral transitions correlate closely with the orientational transformations of the D molecule. Furthermore, the interaction energy barriers between the D molecule and the nanotube for different orientational states can characterize the chiral transition. This implies that the temperature threshold of a chiral transition can be controlled by a suitable nanotube. These findings provide new insights to the effect of nanoscale confinement on molecular chirality.

Confinement of molecules inside nanoscale pores has become an important method for exploiting new dynamics not happening in bulk systems and for fabricating novel structures. Molecules that are encapsulated in nanopores are difficult to control with respect to their position and activity. On the basis of molecular dynamics simulations, we have achieved controllable manipulation, both in space and time, of biomolecules with aqueous liquids inside a single-walled nanotube by using an external charge or a group of external charges. The remarkable manipulation abilities are attributed to the single-walled structure of the nanotube that the electrostatic interactions of charges inside and outside the single-walled nanotube are strong enough, and the charge-induced dipole-orientation ordering of water confined in the nanochannel so that water has a strong interaction with the external charge. These designs are expected to serve as lab-in-nanotube for the interactions and chemical reactions of molecules especially biomolecules, and have wide applications in nanotechnology and biotechnology.

Single-file transportation of water across narrow nanochannels such as carbon nanotubes has attracted much attention in recent years. Such permeation can be greatly affected by the water-channel interactions; despite some progress, this issue has not been fully explored. Herein we use molecular dynamics simulations to investigate the effects of water-channel attractions on occupancy, translational (transportation) and orientational dynamics of water inside narrow single-walled carbon nanotubes (SWNTs). We use SWNTs as the model nanochannels and change the strength of water-nanotube attractions to mimic the changes in the hydrophobicity/polarity of the nanochannel. We investigate the dependence of water occupancy inside SWNTs on the water-channel attraction and identify the corresponding threshold values for drying states, wetting-drying transition states, and stably wetting states. As the strength of water-channel attractions increases, water flow increases rapidly first, and then decreases gradually; the maximal flow occurs in the case where the nanochannel is predominately filled with the 1D water wire but with a small fraction of 'empty states', indicating that appropriate empty-filling (drying-wetting) switching can promote water permeation. This maximal flow is unexpected, since in traditional view, the stable and tight hydrogen-bonding network of the water wire is the prerequisite for high permeability of water. The underlying mechanism is discussed from an energetic perspective. In addition, the effect of water-channel attractions on reorientational dynamics of the water wire is studied, and a negative correlation between the flipping frequency of water wire and the water-channel attraction is observed. The underlying mechanism is interpreted in term of the axial total dipole moment of inner water molecules. This work would help to better understand the effects of water-channel attractions on wetting properties of narrow nanochannels, and on single-file water permeation through nanochannels, which might be helpful in designs of high-flux nanochannels.

The dynamics of water molecules confined in nanochannels is of great importance for designing novel molecular devices/machines/sensors, which have wide applications in nanotechnology, such as water desalination, chemical separation, sensing. In this chapter, inspired by the aquaporins, which are proteins embedded in the cell membrane that regulate the flow of water but stop the protons, we will discuss the mechanism of water channel gating and water channel pumping, where water molecules form single-filed structure. The single-filed water molecules can also serve as molecular devices for signal transmission, conversion, and multiplication. Moreover, the water in the channel may have great potential applications in designing the lab-in-tube to controllable manipulation of biomolecules.

The mechanism of signal transmission, conversion and multiplication at molecular level has been of great interest lately, due to its wide applications in nanoscience and nanotechnology. The interferences between authentic signals and thermal noises at the nanoscale make it difficult for molecular signal transduction. Here we review some of our recent progress on the signal transduction mediated by water and other polar molecules confined in nanochannels, such as Y-shaped carbon nanotubes. We also explore possible future directions in this emerging field. These studies on molecular signal conduction might have significance in future designs and applications of nanoscale electronic devices, and might also provide useful insights for a better understanding of signal conduction in both physical and biological systems.

Molecular scale signal conversion and multiplication is of particular importance in many physical and biological applications, such as molecular switches, nano-gates, biosensors, and various neural systems. Unfortunately, little is currently known regarding the signal processing at the molecular level, partly due to the significant noises arising from the thermal fluctuations and interferences between branch signals. Here, we use molecular dynamics simulations to show that a signal at the single-electron level can be converted and multiplied into 2 or more signals by water chains confined in a narrow Y-shaped nanochannel. This remarkable transduction capability of molecular signal by Y-shaped nanochannel is found to be attributable to the surprisingly strong dipole-induced ordering of such water chains, such that the concerted water orientations in the 2 branches of the Y-shaped nanotubes can be modulated by the water orientation in the main channel. The response to the switching of the charge signal is very rapid, from a few nanoseconds to a few hundred nanoseconds. Furthermore, simulations with various water models, including TIP3P, TIP4P, and SPC/E, show that the transduction capability of the Y-shaped carbon nanotubes is very robust at room temperature, with the interference between branch signals negligible.

The molecular scale signal conversion, transmission, and amplification by a single external charge through a water-mediated Y-shaped nanotube have been studied using molecular dynamics simulations. Our results show that the signal converting capability is highly sensitive to the magnitude of the charge, while the signal transmitting capability is independent of the charge signal. There is a sharp two-state-like transition in the signal converting capacity for both positive and negative charges. When the charge magnitude is above a threshold (|q| ≥ ~0.7 e), the water dipole orientations in the main tube can be effectively controlled by the signaling charge (i.e., signal conversion), and then be transmitted and amplified through the Y-junction, despite the thermal noises and interferences between branch signals. On the other hand, the signal transmitting capability, characterized by the correlation between the two water dipole orientations in the two branches, is found to be always larger than 0.6, independent of charge signals, indicating that the water-mediated Y-tube is an excellent signal transmitter. These findings may provide useful insights for the future design of molecular scale signal processing devices based on Y-shaped nanotubes.