Haiping（方海平） Fang

Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets

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 graphenes cytotoxicity and antibacterial activity.

Intercalation and diffusion of lithium ions in a carbon nanotube bundle by ab initio molecular dynamics simulations

The intercalation and diffusion of lithium ions in a bundle of carbon nanotubes (CNTs) are investigated via an ab initio molecular dynamics simulation method based on the density functional theory. We found that lithium ions quickly penetrate into the CNTs and the space between neighboring CNTs. With a low Li ion density, the Li ions tend to stay close to the nanotube ends. Interestingly, Li ions are able to penetrate through the carbon nanotube and move from one end to the other. We also discovered that Li ions may remain between two neighboring CNTs, which presents a new approach for Li ion intercalation and storage. Importantly, Li ions located among three neighboring CNTs have very strong adsorption potentials that are a factor of four larger than those of Li ions located along the central axis of a single-walled nanotube (SWNT). This indicates that Li ions located among three neighboring CNTs would be very difficult to remove from a nanotube bundle, which suggests that Li storage capacity in this case is possibly irreversible, and that keeping the nanotubes apart with an appropriate distance would hinder or promote the formation of irreversible intercalation. Our findings contribute to the understanding of lithium intercalation and diffusion in CNTs, which has implications for the experimental development and application of rechargeable Li ion batteries.

Ion Enrichment on the Hydrophobic Carbon-based Surface in Aqueous Salt Solutions due to Cation-π Interactions

By incorporating cation-π interactions to classic all-atoms force fields, we show that there is a clear enrichment of Na+ on a carbon-based π electron-rich surface in NaCl solutions using molecular dynamics simulations. Interestingly, Cl− is also enriched to some extend on the surface due to the electrostatic interaction between Na+ and Cl−, although the hydrated Cl−-π interaction is weak. The difference of the numbers of Na+ and Cl− accumulated at the interface leads to a significant negatively charged behavior in the solution, especially in nanoscale systems. Moreover, we find that the accumulation of the cations at the interfaces is universal since other cations (Li+, K+, Mg2+, Ca2+, Fe2+, Co2+, Cu2+, Cd2+, Cr2+, and Pb2+) have similar adsorption behaviors. For comparison, as in usual force field without the proper consideration of cation-π interactions, the ions near the surfaces have a similar density of ions in the solution.

Reversible tuning of the hydrophobic–hydrophilic transition of hydrophobic ionic liquids by means of an electric field

In this work, we demonstrate for the first time that hydrophobic ILs can be strikingly tuned to be hydrophilic under a strong external electric field, with the use of nonequilibrium molecular dynamics (MD) simulations and atomic force microscopy (AFM) experiments. With increase of the electric field strength, the cation–anion and water–water interactions are both attenuated. The cations and anions gradually evolve from an IL interface to a water medium, leading to surprisingly hydrophilicity with high intersolvent mixing. This novel hydrophilic mixing process can be reversibly tuned to phase separation by reversing the electric field. These simulations suggest that the driving force of this hydrophobic–hydrophilic transition derived from a different tuning effect for the cations and the anions.

Ice or water: thermal properties of monolayer water adsorbed on a substrate

Adsorbed water molecules on an ionic surface may exhibit an ordered monolayer on the surface. The ordered structure gives it many unique properties that are distinct from either liquid water or ice. We use molecular dynamics simulations to investigate the thermal properties of monolayer water, and find that its thermal conductivity is more similar to ice than to liquid water. The dependence of the thermal conductivity on the charge on the substrate and the temperature are studied. This study explores the density distribution of the water molecules to explain the dependence relations, and examines the effect of bulk water on the structure and thermal properties of monolayer water. Furthermore, kinetic energy transportation in monolayer water is studied.

Anisotropic Dielectric Relaxation of the Water Confined in Nanotubes for Terahertz Spectroscopy Studied by Molecular Dynamics Simulations

The dynamics and structure of the hydrogen-bond network in confined water are of importance in understanding biological and chemical processes. Recently, terahertz (THz) time domain spectroscopy was widely applied for studying the kinetics of molecules and the hydrogen-bond network in water. However, the characteristics of the THz spectroscopy varying with respect to the confinement and the mechanism underlying the variation are still unclear. Here, on the basis of molecular dynamics simulations, the relationship between the anisotropic dielectric relaxation and the structure of the water confined in a carbon nanotube (CNT) was investigated. The results show that there are two preferred hydrogen-bond orientations of the confined water in the nanotube: (1) parallel to the CNT axis and (2) perpendicular to the CNT axis, which are clearly different. Moreover, the response of the orientations to the increment of the CNT diameters is opposite, leading to the opposite variations of the dielectric relaxation times along the two directions. The anisotropy in the relaxation time can be presented by the anisotropic dielectric permittivity which is able to be observed through THz spectroscopy. The anormal behaviors above are attributed to the special structure of the water close to the nanotube wall due to the confinement and hydrophobicity of CNT. These studies contribute an important step in understanding the THz experiments of water in nanoscales, and designing a chamber for specific chemical and biological reactions by controlling the diameters and materials of the nanotube.

Aggregated Gas Molecules: Toxic to Protein?

The biological toxicity of high levels of breathing gases has been known for centuries, but the mechanism remains elusive. Earlier work mainly focused on the influences of dispersed gas molecules dissolved in water on biomolecules. However, recent studies confirmed the existence of aggregated gas molecules at the water-solid interface. In this paper, we have investigated the binding preference of aggregated gas molecules on proteins with molecular dynamics simulations, using nitrogen (N2) gas and the Src-homology 3 (SH3) domain as the model system. Aggregated N2 molecules were strongly bound by the active sites of the SH3 domain, which could impair the activity of the protein. In contrast, dispersed N2 molecules did not specifically interact with the SH3 domain. These observations extend our understanding of the possible toxicity of aggregates of gas molecules in the function of proteins.

Ethanol promotes dewetting transition at low concentrations

Recent studies have suggested important roles for nanoscale dewetting in the stability and self-assembly dynamics of both physical and biological systems. Less known is the cosolvent (such as ethanol) effect on nanoscale dewetting. Here, we use molecular dynamics simulations to investigate the dewetting behavior in-between two hydrophobic plates immersed in ethanol aqueous solutions, particularly at low concentrations. Unexpectedly, the existence of a small amount of ethanol molecules promotes the dewetting transition in the inter-plate region at a greater separation that is otherwise non-existent in pure water or pure ethanol. We find that a competition for ethanol molecules at equilibrium among the inter-plate region, the outer-surfaces of the plates and the bulk solution results in a depletion of ethanol molecules in the inter-plate region. Meanwhile, the preferred inward orientations of the ethanol ethyl groups at the liquid–vapor interface located at the edge of the plates make the inter-plate core more hydrophobic so that water molecules are more favored to be expelled, thus resulting in an enhancement of the dewetting. These findings provide a deeper understanding of the effects of cosolvents on the hydrophobic interaction.

DNA base pair hybridization and water-mediated metastable structures studied by molecular dynamics simulations.

The base pair hybridization of a DNA segment was studied using molecular dynamics simulation. The results show the obvious correlation between the probability of successful hybridization and the accessible surface area to water of two successive base pairs, including the unpaired base pair adjacent to paired base pair and this adjacent paired base pair. Importantly, two metastable structures in an A-T base pair were discovered by the analysis of the free energy landscape. Both structures involved addition of a water molecule to the linkage between the two nucleobases in one base pair. The existence of the metastable structures provide potential barriers to the Watson-Crick base pair, and numerical simulations show that those potential barriers can be surmounted by thermal fluctuations at higher temperatures. These studies contribute an important step toward the understanding of the mechanism in DNA hybridization, particularly the effect of temperature on DNA hybridization and polymerase chain reaction. These observations are expected to be helpful for facilitating experimental bio/nanotechnology designs involving fast hybridization.