Yusong Tu

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.

Water-mediated signal multiplication with Y-shaped carbon nanotubes

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.

Manipulating biomolecules with aqueous liquids confined within single-walled nanotubes.

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.

Critical Dipole Length for the Wetting Transition Due to Collective Water-dipoles Interactions

The wetting behavior of water on the solid surfaces is fundamental to various physical, chemical and biological processes. Conventionally, the surface with charges or charge dipoles is hydrophilic, whereas the non-polar surface is hydrophobic though some exceptions were recently reported. Using molecular dynamics simulations, we show that there is a critical length of the charge dipoles on the solid surface. The solid surface still exhibited hydrophobic behavior when the dipole length was less than the critical value, indicating that the water molecules on the solid surface seemed not “feel” attractive interactions from the charge dipoles on the solid surface. Those unexpected observations result from the collective interactions between the water molecules and charge dipoles on the solid surface, where the steric exclusion effect between water molecules greatly reduces the water-dipole interactions. Remarkably, the steric exclusion effect is also important for surfaces with charge dipole lengths greater than this critical length.

Galilean invariant fluid-solid interfacial dynamics in lattice Boltzmann simulations

Galilean invariance is a fundamental property; however, although the dynamics of lattice Boltzmann equation in the hydrodynamic limit is Galilean invariant, this property is usually not taken into account in the treatment of the fluid-solid interface. Here, we show that consideration of Galilean invariance in fluid-solid interfacial dynamics can greatly enhance the computational accuracy and robustness in a numerical simulation. Surprisingly, simulations are so vastly improved that the force fluctuation is very small and a time average becomes unnecessary.

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.

Alcohol-induced drying of carbon nanotubes and its implications for alcohol/water separation: A molecular dynamics study

Alcohols are important products in chemical industry, but separating them from their aqueous solutions is very difficult due to the hydrophilic nature of alcohols. Based on molecular dynamics simulations, we observe a striking nanoscale drying phenomenon and suggest an energy-saving and efficient approach toward alcohol∕water separation by using single-walled carbon nanotubes (SWNTs). We use various common linear alcohols including C1-C6 1-alcohols and glycerol for demonstration (the phenol is also used as comparison). Our simulations show that when SWNTs are immersed in aqueous alcohols solutions, although the alcohols concentration is low (1 M), all kinds of alcohols can induce dehydration (drying) of nanotubes and accumulate inside wide [(13, 13)] and narrow [(6, 6) or (7, 7)] SWNTs. In particular, most kinds of alcohols inside the narrow SWNTs form nearly uniform 1D molecular wires. Detailed energetic analyses reveal that the preferential adsorption of alcohols over water inside nanotubes is attributed to the stronger dispersion interactions of alcohols with SWNTs than water. Interestingly, we find that for the wide SWNT, the selectivity for 1-alcohols increases with the number of alcohols carbon atoms (Ncarbon) and exhibits an exponential law with respect to Ncarbon for C1-C5 1-alcohols; for narrow SWNTs, the selectivity for 1-alcohols is very high for methanol, ethanol, and propanol, and reaches a maximum when Ncarbon = 3. The underlying physical mechanisms and the implications of these observations for alcohol∕water separation are discussed. Our findings provide the possibility for efficient dehydration of aqueous alcohols (and other hydrophilic organic molecules) by using SWNT bundles∕membranes.

Different water scenarios for a primitive model with two types of hydrogen bonds

Using a primitive water model, we find that the strength of tetrahedral interactions can change the behavior of liquid water from the liquid-liquid critical point scenario to the singularity-free scenario. Specifically, we find that the strongly tetrahedral model has a liquid-liquid critical point from which the Widom line emanates with a negative slope, but that the weakly tetrahedral model lacks the second critical point and the line of the specific heat maxima analogous to the Widom line has a positive slope. The strongly tetrahedral interaction is characterized by a double-step potential that depends on hydrogen-bond bending, while the weakly tetrahedral interaction has a uniform single-step potential.

Modeling the rupture of a capillary liquid bridge between a sphere and plane

The capillary force due to a liquid bridge, and the breaking of this bridge, are of importance due to the widespread existence of capillary menisci in macro-, micro-, and even nano-scale applications. In this paper, a model was developed to predict the rupture distance between a micro- to nano-sized sphere and a plane. There was good agreement between the theoretical prediction and experimental results for the change in normalized capillary force with separation distance. This partly demonstrates the accuracy and robustness of the model. Based on the model, we found that the rupture distance increased with stronger particle hydrophobicity, increasing particle radius, and increasing environmental humidity. The dependence of the rupture distance on the hydrophobicity of the particle and particle radius was particularly enhanced with nano-sized particles. The model we developed and the observations from this model are helpful in the development of nanotechnology such as the nanoparticle separations, nanoparticle picking up and atomic microscopy manipulations.

Evaporation of Tiny Water Aggregation on Solid Surfaces with Different Wetting Properties

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.