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By employing first-principles calculations that integrate self-consistent phonon theory and the Boltzmann transport equation, we have delved into the thermal transport characteristics of hexagonal anisotropic materials A2B (A = Cs, Rb and B = Se, Te).

The dynamic covalent properties of graphene oxide (GO) are of fundamental interest to a broad range of scientific areas and technological applications. It remains a challenge to access the feasible dynamic reactions for reversibly breaking/reforming covalent bonds of oxygen functional groups on GO, although these reactions can be induced by photonic or mechanical routes, or mediated by adsorbed water. Here, using the density functional theory calculations, we demonstrate the remarkably enhanced dynamic oxygen migration along the basal plane of GO supported by copper substrate (GO@copper), with the C-O bond breaking reaction and proton transfer between the neighboring epoxy and hydroxyl groups. Compared to that on GO, the energy barrier of oxygen migration on GO@copper is sharply reduced to be less than or comparable to thermal fluctuations, and meanwhile the crystallographic match between GO and copper substrate induces new oxygen migration paths on GO@copper. This work sheds light on the understanding of metal substrate-enhanced dynamic properties of GO, and evidences the strategy to tune the activity of two-dimension-interfacial oxygen groups for various potential applications., 5 pages, 4 figures

The oxygen dissociation and the oxidized structure on the pristine C3N monolayer in exposure to air are the inevitably critical issues for the C3N engineering and surface functionalization yet have not been revealed in detail. Using the first-principles calculations, we have systematically investigated the possible O2 adsorption sites, various O2 dissociation pathways and the oxidized structures. It is demonstrated that the pristine C3N monolayer shows more O2 physisorption sites and exhibits stronger O2 adsorption than the pristine graphene. Among various dissociation pathways, the most preferable one is a two-step process involving an intermediate state with the chemisorbed O2 and the barrier is lower than that on the pristine graphene, indicating that the pristine C3N monolayer is more susceptible to oxidation than the pristine graphene. Furthermore, we found that the most stable oxidized structure is not produced by the most preferable dissociation pathway but generated from a direct dissociation process. These results can be generalized into a wide range of temperatures and pressures using ab initio atomistic thermodynamics. Our findings deepen the understanding of the chemical stability of 2D crystalline carbon nitrides under ambient conditions, and could provide insights into the tailoring of the surface chemical structures via doping and oxidation., Comment: 23 pages,8 figures

Combining density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations, we show that oxygen functional groups exhibit unexpected spontaneous dynamic behaviors on the interior surface of single-walled carbon nanotubes (SWCNTs). The hydroxyl and epoxy migrations are achieved by the C–O bond breaking/reforming reactions or the proton transfer reaction between the neighboring epoxy and hydroxyl groups. It is demonstrated that the spontaneous dynamic characteristic is attributed to the sharply reduced energy barrier less than or comparable to thermal fluctuations. We also observe a stable intermediate state with a dangling C–O bond, which permits the successive migration of the oxygen functional groups. However, on the exterior surface of SWCNTs, it is difficult for the oxygen groups to migrate spontaneously because there are relatively high energy barriers, and the dangling C–O bond prefers to transform into the more stable epoxy configuration. The spontaneous oxygen migration is further confirmed by the oxygen migration process using DFT calculations and AIMD simulations at room temperature. Our work provides a new understanding of the behavior of oxygen functional groups at interfaces and gives a potential route to design new carbon-based dynamic materials.

Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)2-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)2-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)2-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.

The dynamic oxygen migration at the interface of carbon allotropes dominated by the periodic hexagonal rings, including graphene and carbon nanotube, has opened up a new avenue to realize dynamic covalent materials. However, for the carbon materials with hybrid carbon rings, such as biphenylene, whether the dynamic oxygen migration at its interface can still be found remains unknown. Using both density functional theory calculations and machine-learning-based molecular dynamics (MLMD) simulations, we found that the oxygen migration departing away from the four-membered carbon (C4) ring is hindered, and the oxygen atom prefers to spontaneously migrate toward/around the C4 ring. This locally spontaneous dynamic oxygen migration on the biphenylene is attributed to the high barrier of about 1.5 eV for the former process and relatively low barrier of about 0.3 eV for the latter one, originating from the enhanced activity of C-O bond near/around the C4 ring due to the hybrid carbon rings structure. Moreover, the locally spontaneous dynamic oxygen migration is further confirmed by MLMD simulations. This work sheds light on the potential of biphenylene as a catalyst for spatial-controlled energy conversion and provides the guidance for realizing the dynamic covalent interface at other carbon-based or two-dimensional materials., 7 pages, 5 figures

The friction at the liquid-solid interfaces is widely involved in various phenomena ranging from nanometer to micrometer scales. By the molecular dynamic (MD) simulation, the friction properties of liquid-solid interfaces at the molecular level are calculated via the Green-Kubo relation. It is found that the system size will influence the value of the friction coefficient, especially for the solid surfaces with the larger polar charge. The value of the friction coefficient decreases with the increase in the system size and converges at large system sizes. The large polar charge will lead to a significant friction coefficient. However, the diffusion of water molecules on this surface is almost a constant, indicating that the diffusion coefficient seems to be independent of the system size and polar charge. This work provides insights for the selection of the system size in modeling the frictional properties of hydrophobic/hydrophilic surfaces.

Water dissociation is of fundamental importance in scientific fields and has drawn considerable interest in diverse technological applications. However, the high activation barrier of breaking the O-H bond within the water molecule has been identified as the bottleneck, even for the water adsorbed on the graphene oxide (GO). Herein, using the density functional theory calculations, we demonstrate that the water molecule can be spontaneously dissociated on GO supported by the (111) surface of the copper substrate (Copper-GO). This process involves a proton transferring from water to the interfacial oxygen group, and a hydroxide covalently bonding to GO. Compared to that on GO, the water dissociation barrier on Copper-GO is significantly decreased to be less than or comparable to thermal fluctuations. This is ascribed to the orbital-hybridizing interaction between copper substrate and GO, which enhances the reaction activity of interfacial oxygen groups along the basal plane of GO for water dissociation. Our work provides a novel strategy to access water dissociation via the substrate-enhanced reaction activity of interfacial oxygen groups on GO and indicates that the substrate can serve as an essential key to tuning the catalytic performance of various two-dimensional material devices., 13 pages, 5 figures

As with all stylish 2D functional materials, tellurene and tellurides possessing excellent physical and chemical properties such as high environmental stability, tunable narrow bandgap, and lower thermal conductivity, have aroused the great interest of the researchers. These properties of such materials also form the basis for relatively newfangled scholarly fields involving advanced topics, especially for broadband photodetectors. Integrating the excellent properties of many 2D materials, tellurene/telluride-based photodetectors show great flexibility, higher frequency response or faster time response, high signal-to-noise ratio, and so on, which make them leading the frontier of photodetector research. To fully understand the excellent properties of tellurene/tellurides and their optoelectronic applications, the recent advances in tellurene/telluride-based photodetectors are maximally summarized. Benefiting from the solid research in this field, the challenges and opportunities of tellurene/tellurides for future optoelectronic applications are also discussed in this review, which might provide possibilities for the realization of state-of-the-art high-performance tellurene/telluride-based devices.

G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics (MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA. The results show highly heterogeneous hydration patterns in both structure and dynamics; for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ∼ 30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.

Molecular dynamics (MD) simulations were employed to investigate water-ethanol separation through monolayer graphene oxide (GO) membranes with different pore sizes and O/C ratios. The ultrahigh water flux and infinite water separation factors were achieved. The separation properties under 50/50 w/w water-ethanol mixtures reveal that higher O/C ratios favor water selectivity, and water flux is enhanced with O/C ratio and pore size. With the help of highest oxidization, water largely sorption amount governs permeation process. On the contrary, with low oxidization degree of GO membrane, water diffusion effect becomes dominant factor of permeation. We screen an optimal microstructure of GO membrane which equipped with an adequately sized pore (D = 2.4 A) and a highest O/C ratio (R = 0.49). This optimal one D2.4A_R0.49 achieves the highest water flux and fully ethanol rejection in the mimicked experimental system. This simulation study elucidates the role of O/C ratio and pore diameter in water-ethanol separation through porous GO membranes on the microscopic level and uncovers the governing effects for water permeation and also suggests a potential candidate as a water-ethanol separation membrane.

Using molecular dynamics simulations, we have studied the effects of salt on the association behavior of solute molecules in nanoconfined aqueous solutions. Three types of solute association states – dispersion, reversible and aggregation states – are still observed in nanoconfined aqueous solutions in the presence of salt. With the increase of ion concentration, the tendency toward the formation of larger clusters is enhanced and the solute critical aggregation number decreases. We even found the transformation of solute association state from the dispersion to the reversible state or from the reversible to the aggregation state within an intermediate range of solute number. This phenomenon is similar to the salting out process and is attributed to the decrease of free water molecules induced by the ion polarization.

Recently, the novel hole-containing carbon nitride C

Generally, the interface friction on solid surfaces is regarded as consistent with wetting behaviors, characterized by the contact angles. Here using molecular dynamics simulations, we find that even a small charge difference (≤0.36 e) causes a change in the friction coefficient of over an order of magnitude on two-dimensional material and lipid surfaces, despite similar contact angles. This large difference is confirmed by experimentally measuring interfacial friction of graphite and MoS2 contacting on water, using atomic force microscopy. The large variation in the friction coefficient is attributed to the different fluctuations of localized potential energy under inhomogeneous charge distribution. Our results help to understand the dynamics of two-dimensional materials and biomolecules, generally formed by atoms with small charge, including nanomaterials, such as nitrogen-doped graphene, hydrogen-terminated graphene, or MoS2, and molecular transport through cell membranes. The interface friction on solid surfaces is generally regarded as consistent with the wetting behaviour. Here the authors use molecular dynamics simulations and experiments to show that a small surface charge difference causes a change in the solid/water friction coefficient of over an order of magnitude, while the contact angles stay similar.

Magnesium (Mg^{2+}) and calcium (Ca^{2+}) are of essential importance in biological activity, but the molecular understanding of their selectivity is still lacking. Here, based on density functional theory calculations and ab initio molecular dynamics simulations, we show that Mg^{2+} binds more tightly to phosphotyrosine (pTyr) and stabilizes the conformation of pTyr, while Ca^{2+} binds more flexibly to pTyr with less structural stability. The key for the selectivity is attributed to the cation-π interactions between the hydrated cations and the aromatic ring together with the synergic interaction between the cations and the side groups in pTyr to form a cation-binding pocket structure, which we refer as side-group-synergetic hydrated cation-π interaction. The existence and relative strength of the cation-π interactions in the pocket structures as well as their structural stability have been demonstrated experimentally with ultraviolet (UV) absorption spectra and ^{1}H NMR spectra. The findings offer insight into understanding the selectivity of Mg^{2+} and Ca^{2+} in a variety of biochemical and physiological essential processes.

The scarcity of freshwater is of great challenge that the world is facing nowadays. The advances of nanomaterial based on the reverse osmosis (RO) technology provide new possibilities for desalination. In this study, using molecular dynamics simulation, we propose and design an excellent RO membrane composed of fluorinated graphene (F-GRA) nanochannels, by which the exceptionally high water permeation (reaching up to 61.1 L/cm2/day/MPa) and the almost complete ion rejection are achieved. Notably, F-GRA nanochannel membranes exhibit a desalination performance much more promising than many other nanomaterials in previously theoretical studies. This superior desalination performance of F-GRA channels is attributed to the negatively charged surface and hydrophobicity of F-GRA, where the electrostatic interactions (attraction or repulsion) between ions and F-GRA surface cause the ideal ion rejection and the ultralow water friction on F-GRA mediated by its hydrophobicity results in the excellent water penetration. Moreover, potential of mean force calculations further reveal that the water molecule reflects the lowest free energy barrier relative to ions when traversing through the F-GRA channel, indicating the energetical favorability of the successful water transport instead of ions. Our theoretical study offers a fascinating approach of molecular sieving design usable for future desalination.

We perform a comparative theoretical study of benzene and its homologues (toluene, para-xylene, and mesitylene) adsorbed on Cu/Al/Pd(111)-supported graphene using density functional theory (DFT). The long-range attraction is handled by semiempirical dispersion correction method (PBE-D3) and ab initio van der Waals density functionals (vdW-DF2, optB86b-vdW, optB88-vdW, and SCAN-rVV10). Our results show a systematic increase in the adsorption energy of organic molecules on graphene in the presence of underlaying metal substrates. In the case of strong metal-graphene contact, such as Pd(111)-graphene, the adsorption energy of benzene even increases 0.44 eV, which presents suitable platform for filtering harmful molecules such as benzene. Besides, we find out that the dispersion-corrected functionals play a fundamental role in the structure and adsorption energy. Furthermore, the adsorption energy increases linearly with the number of methyl groups on the benzene ring.

Previous work showed that solid polar surfaces with a very small dipole length still might be quite hydrophobic even with large values of charge. Using molecular dynamics simulations, we have found that the presence of the point defects on a solid polar surface greatly influences the wetting behavior of water, even at a very low defect ratio of 1%. As the defect ratio increases, the coverage of the water layer over the solid surface also increases. Because of the breakdown of steric exclusion, the water molecules strongly bind to the solid surface mainly through electrostatic interactions between their hydrogen atoms and the negative charges near the positive-vacancy defects on the surface, or between their oxygen atoms and the positive charges near the negative-vacancy defects.

Phase transitions of water molecules are commonly expected to occur only under extreme conditions, such as nanoconfinement, high pressure, or low temperature. We herein report the disordered-ordered phase transition of two-dimensional interfacial water molecules under ambient conditions using molecular-dynamics simulations. This phase transition is greatly dependent on the charge dipole moment, production of both charge values, and the dipole length of the solid surface. The phase transition can be identified by a sharp change in water-water interaction energies and the order parameters of the two-dimensional interfacial water monolayer, under a tiny dipole moment change near the critical dipole moment. The critical dipole moment of the solid material surface can classify a series of materials that can induce distinct ordered phases of surface water, which may also result in surface wetting, friction, and other properties.

G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics (MD), and steered MD (SMD) simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions (K+/Na+) is about the base stacking free energies indicates that there will be a competition among the binding of M+-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+ was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.

We develop a new Gibbs free energy-based association model and perform series of molecular dynamics (MD) simulations to study the association behavior of Lennard-Jones (LJ) particles in nanoconfined aqueous solution. In the association model, the total Gibbs free energy is the sum of free energy cost in the nucleation of a densely packed cluster with an isotropic shape and a radius dependent interfacial tension coefficient, and the translation entropy of dispersed particles outside the cluster. Two key theoretical expressions – total Gibbs free energy formula and the thermodynamic equilibrium equation – are obtained to estimate the cluster aggregation number for a given LJ particle number and the corresponding total Gibbs free energy. Using MD simulations, we observe that the association state transforms from the stable dispersion state, through the reversible state, finally to the stable aggregation state as the LJ particle number increases. In the reversible state, the system reversibly switch in between the dispersion and aggregation states. The existence of three types of association states is also found for LJ particles with the varied well depth. According to our model, the Gibbs free energy curve shows from a single minimum, through two minima, finally to a single minimum, leading to the transformation of association states. The occurrence of reversible state transition is attributed to the free energy barrier of the order of thermal fluctuation in water between the dispersion and aggregation states. These findings deepen the understanding of nucleation/aggregation of hydrophobic gas molecules or particles in solution under nanoconfinement.

We theoretically and experimentally show that, with water being adsorbed, the graphene oxide (GO) is converted to a spontaneously dynamic covalent material under ambient conditions, where the dominated epoxy and hydroxyl groups are mediated by water molecules to spontaneously break/reform their C–O bonds to achieve dynamic oxygen migration. This dynamic material presents structural adaptivity for response to biomolecule adsorption. Both density functional theory calculations and ab initio molecular dynamics simulations demonstrate that this spontaneously dynamic characteristics is attributed to the adsorption of water molecules, which sharply reduces the barriers of these oxygen migration reactions on GO to the level less than or comparable to the hydrogen bonding energy in liquid water.

We present atomistic molecular dynamics simulation study of the self-assembly behavior of toll-like agonist lipopeptides (Pam nCSK4) in aqueous solutions. The variable number of hexadecyl lipid chains ( n = 1, 2, 3) per molecule has been experimentally suggested to have remarkable influence on their self-assembled nanostructures. Starting from preassembled spherical or bilayer configurations, the aggregates of lipopeptides, PamCSK4 and Pam2CSK4, which contain peptide sequences CSK4 linked to either mono- or dilipid chains (Pam), evolve into spherical-like micelles within 30 ns, whereas the self-assembled structure of trilipidated lipopeptides, Pam3CSK4, relaxes much slower and reaches an equilibrium state of flattened wormlike micelle with a bilayer packing structure. The geometric shapes and sizes, namely the gyration radii of spherical micelles and thickness of the flattened wormlike micelle, are found to be in good agreement with experimental measurements, which effectively validates the simulation models and employed force fields. Detailed analyses of molecular packing reveal that these self-assembled nanostructures all consist of a hydrophobic core constructed of lipid chains, a transitional layer, and a hydrophilic interfacial layer composed of peptide sequences. The average area per peptide head at the interfaces is found to be nearly constant for all micellar structures studied. The packing parameter of the lipopeptide molecules thus increases with the increase of the number of linked lipid chains, giving rise to the distinct micellar shape transition from spherical-like to flattened wormlike geometry with bilayer stacking, which is qualitatively different from the shape transitions of surfactant micelles induced by variation of concentration or salt type. To facilitate the close-packing of the lipid chains in the hydrophobic core, the lipopeptide molecules typically take the bent conformation with average tilt angles between the peptide sequences and the lipid chains ranging from 110° to 140°. This consequently affects the orientation angles of the lipid chains with respect to the radial or normal direction of the spherical-like or flattened wormlike micelles. In addition, the secondary structures of the peptides may also be altered by the number of lipid chains to which they are linked and the resultant micellar structures. Our simulation results on the microscopic structural features of the lipopeptide nanostructures may provide potential insights into their bioactivities and contribute to the design of bioactive medicines or drug carriers. The force fields built for these lipopeptides and the geometric packing discussions could also be adopted for simulating and understanding the self-assembly behavior of other bioactive amiphiphiles with similar chemical compositions.

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.

Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on GO surfaces. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface. The adsorption process shows a dynamic cooperation adsorption behavior; the ssDNA segment first captures the oxidized groups of the GO surface by hydrogen bonding interaction, and then the configuration relaxes to maximize the π-π stacking interactions between the aromatic rings of the nucleobases and those of the GO surface. We attributed this behavior to the faster forming hydrogen bonding interaction compared to π-π stacking; the π-π stacking interaction needs more relaxation time to regulate the configuration of the ssDNA segment to fit the aromatic rings on the GO surface.

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.

Using molecular dynamics simulations, we show that free diffusion of a nanoscale particle (molecule) with asymmetric structure critically depends on the orientation in a finite timescale of picoseconds to nanoseconds. In a timescale of ~100 ps, there are ~10% more possibilities for the particle moving along the initial orientation than moving opposite to the orientation; and the diffusion distances of the particle reach ~1 nm. We find that the key to this observation is the orientation-dependence of the damping force to the moving of the nanoscale particle and a finite time is required to regulate the particle orientation. This finding extends the work of Einstein to nano-world beyond random Brownian motion, thus will have a critical role in the understanding of the nanoscale world., Comment: 16 pages, 2 figures

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.

Using molecular dynamics simulations, we show that an asymmetrically shaped nanoparticle in dilute solution possesses a spontaneously curved trajectory within finite time interval, instead of the generally expected random walk. This unexpected dynamic behavior has a similarity to that of active matters, such as swimming bacteria, cells or even fishes, but is of a different physical origin. The key to the curved trajectory lies in the non-zero resultant force originated from the imbalance of the collision forces acted by surrounding solvent molecules on the shaped nanoparticle during its orientation regulation. Theoretical formulae based on the microscopic observation have been derived to describe this non-zero force and the resulted motion of the nanoparticle., Comment: 7 pages, 2 figures