Surface-charge-governed electrolyte transport in carbon nanotubes

The transport behavior of pressure-driven aqueous electrolyte solution through charged carbon nanotubes(CNTs) is studied by using molecular dynamics simulations. The results reveal that the presence of charges around the nanotube can remarkably reduce the flow velocity as well as the slip length of the aqueous solution, and the decreasing of magnitude depends on the number of surface charges and distribution. With 1-M KCl solution inside the carbon nanotube, the slip length decreases from 110 nm to only 14 nm when the number of surface charges increases from 0 to 12 e. This phenomenon is attributed to the increase of the solid–liquid friction force due to the electrostatic interaction between the charges and the electrolyte particles, which can impede the transports of water molecules and electrolyte ions. With the simulation results,we estimate the energy conversion efficiency of nanofluidic battery based on CNTs, and find that the highest efficiency is only around 30% but not 60% as expected in previous work.     

Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins

Molecular dynamics simulation(MDS)is a powerful technology for investigating evolution dynamics of target proteins,and it is used widely in various fields from materials to biology.This mini-review introduced the principles,main preforming procedures,and advances of MDS,as well as its applications on the studies of conformational and allosteric dynamics of proteins especially on that of the mechanosensitive integrins.Future perspectives were also proposed.This review could provide clues in understanding the potentiality of MD simulations in structure–function relationship investigation of biological proteins.     

Ethylene glycol solution-induced DNA conformational transitions

We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.     

How to identify dislocations in molecular dynamics simulations?

Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals.With the development of computational facilities and technologies,the observations of dislocations at atomic level through numerical simulations are permitted.Molecular dynamics(MD)simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects.However,the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures.Thus,it is a big challenge for the beginners in this community to choose a proper method to start their investigations.In this review,we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids.A comprehensive comparison was made between the advantages and disadvantages of these typical techniques.We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing.It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.     

Atomistic simulations on adhesive contact of single crystal Cu and wear behavior of Cu-Zn alloy

Atomistic simulations are carried out to investigate the nano-indentation of single crystal Cu and the sliding of the Cu-Zn alloy.As the contact zone is extended due to adhesive interaction between the contact atoms,the contact area on a nanoscale is redefined.A comparison of contact area and contact force between molecular dynamics(MD)and contact theory based on Greenwood-Williamson(GW)model is made.Lower roughness causes the adhesive interaction to weaken,showing the better consistency between the calculated results by MD and those from the theoretical model.The simulations of the sliding show that the substrate wear decreases with the mol%of Zn increasing,due to the fact that the diffusion movements of Zn atoms in substrate are blocked during the sliding because of the hexagonal close packed(hcp)structure of Zn.     

Liquid to glass transition of tetrahydrofuran and 2-methyltetrahydrofuran

Both tetrahydrofuran(THF) and 2-methyltetrahydrofuran(MTHF) are studied systematically at desired temperatures using molecular dynamics simulations.The results show that the calculated densities are well consistent with experiment.Their glass transition temperatures are obtained:115K ～ 130K for THF and 131K ～ 142K for MTHF.The calculated results from the dipolar orientational time correlation functions indicate that the "long time" behavior is often associated with a glass transition.From the radial and spatial distributions,we also find that the methyl has a direct impact on the structural symmetry of molecules,which leads to the differences of physical properties between THF and MTHF.     

Abnormal breakdown of Stokes–Einstein relation in liquid aluminium

We present the results of systematic molecular dynamics simulations of pure aluminium melt with a well-accepted embedded atom potential. The structure and dynamics were calculated over a wide temperature range, and the calculated results(including the pair correlation function, self-diffusion coefficient, and viscosity) agree well with the available experimental observations. The calculated data were used to examine the Stokes–Einstein relation(SER). The results indicate that the SER begins to break down at a temperature T_x(~1090 K) which is well above the equilibrium melting point(912.5 K).This high-temperature breakdown is confirmed by the evolution of dynamics heterogeneity, which is characterised by the non-Gaussian parameter α_2(t). The maximum value of α 2(t), α_(2,max), increases at an accelerating rate as the temperature falls below Tx. The development of α_(2,max) was found to be related to the liquid structure change evidenced by local fivefold symmetry. Accordingly, we suggest that this high-temperature breakdown of SER has a structural origin. The results of this study are expected to make researchers reconsider the applicability of SER and promote greater understanding of the relationship between dynamics and structure.     

Processes of DNA condensation induced by multivalent cations： Approximate annealing experiments and molecular dynamics simulations

The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.     

Strain Rate Sensitivities of Face-Centred-Cubic Metals Using Molecular Dynamics Simulation

We use dislocation theory and molecular dynamics （MD） simulations to investigate the effect of atom properties on the macroscopic strain rate sensitivity of f cc metals. A method to analyse such effect is proposed. The stress dependence of dislocation velocity is identified as the key of such study and is obtained via 2-D MD simulations on the motion of an individual dislocation in an fcc metal. Combining the simulation results with Orowan＇s relationship, it is concluded that strain rate sensitivities of fcc metals are mainly dependent on their atomic mass rather than the interatomic potential. The order of strain rate sensitivities of five fcc metals obtained by analysing is consistent with the experimental results available.     

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

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.     

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics(MD) simulation in aqueous solution four fragments cut out of a protein G, including oneα-helix(seq B: KVFKQYAN), two β-turns(seq A: LNGKTLKG and seq C: YDDATKTF), and one β-strand(seq D:DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seq A and seq B have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seq D alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seq C is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seq C in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.     

Aggregation of fullerene(C60) nanoparticle:A molecular-dynamic study

We present the results of molecular dynamics simulations of net positively charged fullerene nanoparticles in salt- free and salt-added solution. The aggregation of fullerene （C60）-like nanoparticle and counterion are studied in detail as a function of temperatures and a finite salt concentration. Our simulations show that the strong conformation changes as temperature changes. The net positively-charged nanoparticles do not repel each other but are condensed under proper temperatures. If salts are added, the aggregated nanoparticles will be disaggregated due to the Debye screening effect.     

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA(ss DNA). In this paper, based on the molecular dynamics simulations, we find that ss DNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ss DNA molecule and the graphene-based surface, which is accompanied with the π–π stacking and hydrogen bond formation. The number of π–π stacking between ss DNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ss DNA on the GO surface. Furthermore, it is found that the absorbed ss DNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ss DNA's physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.     

Dynamics of quantum discord in a two-qubit system under classical noise

We study the quantum discord dynamics of two noninteracting qubits that are, respectively, subject to classical noise. The results show that the dynamics of quantum discord are dependent on both the coupling between the qubits and classical noise, and the average switching rate of the classical noise. In the weak-coupling Markovian region, quantum discord exhibits exponent decay without revival, and can be well protected by increasing the average classical noise switching rate. While in the strong-coupling non-Markovian region, quantum discord reveals slowly decayed oscillations with quick revival by decreasing the average switching rate of the classical noise. Thus, our results provide a new method of protecting quantum discord in a two-qubit system by controlling the coupling between the qubits and classical noise, and the average switching rate of the classical noise.     

Molecular-Dynamics Simulations of Droplets on a Solid Surface

By using a semi-empirical Lennard-Jones embedded-atom-method potential, we study the influence of many-body forces and atomic size mismatch on the wetting behavior of nano droplets on a solid surface. With molecular dynamics simulations, we find that the contact angle decreases with increasing many-body forces. The increase of atomic size mismatch between solid and liquid results in the decrease of contact angles. Our calculation also shows that the interface structure is strongly affected by the interaction between liquid and solid as well as the atomic size mismatch. For weak solid-liquid interaction, the interface layer of the droplet nearest to the solid exhibits a typical simple liquid structure regardless of the size mismatch. For strong solid-liquid interaction, evident ordering in the interface layer is observed for well matched cases.     

Influence of external load on friction coefficient of Fe-polytetrafluoroethylene

A coarse-grained molecular dynamics simulation model was developed in this study to investigate the friction process occurring between Fe and polytetrafluoroethylene(PTFE).We investigated the effect of an external load on the friction coefficient of Fe–PTFE using the molecular dynamics simulations and experimental methods.The simulation results show that the friction coefficient decreases with the external load increasing,which is in a good agreement with the experimental results.The high external load could result in a larger contact area between the Fe and PTFE layers,severer springback as a consequence of the deformed PTFE molecules,and faster motion of the PTFE molecules,thereby affecting the friction force and normal force during friction and consequently varying the friction coefficient.     

Spatial heterogeneity in liquid–liquid phase transition

Molecular dynamics simulations are performed to investigate the liquid–liquid phase transition(LLPT) and the spatial heterogeneity in Al–Pb monotectic alloys. The results reveal that homogeneous liquid Al–Pb alloy undergoes an LLPT,separating into Al-rich and Pb-rich domains, which is quite different from the isocompositional liquid water with a transition between low-density liquid(LDL) and high-density liquid(HDL). With spatial heterogeneity becoming large, LLPT takes place correspondingly. The relationship between the cooling rate, relaxation temperature and percentage of Al and the spatial heterogeneity is also reported. This study may throw light on the relationship between the structure heterogeneity and LLPT, which provides novel strategies to control the microstructures in the fabrication of the material with high performance.     

Depinning Dynamics of Two-Dimensional Charged Colloids on a Random Laser-Optical Substrate

Using Langevin simulations, we. investigate the depinning dynamics of two-dimensional charged colloids on a random laser-optical substrate. With an increase in the strength of the substrate, we find a transition from crystal to smectic flows above the depinning. A power-law scaling relationship between average velocity and applied driving force could be obtained for both flows, and we find that the scaling exponents are no bigger than 1 for the crystal and are bigger than 1 for the smectic flows.     

Non-monotonic temperature evolution of nonlocal structure–dynamics correlation in CuZr glass-forming liquids

The structure–dynamics correlations in a nonlocal manner were investigated in CuZr metallic glass-forming liquids via classical molecular dynamics simulations. A spatial coarse-graining approach was employed to incorporate the nonlocal structural information of given structural order parameters in the structure–dynamics relationship. It is found that the correlation between structure order parameters and dynamics increases with increasing coarse-graining length and has a characteristic length scale. Moreover, the characteristic correlation length exhibits a non-monotonic temperature evolution as temperature approaches glass transition temperature, which is not sensitive to the considered structure order parameters.Our results unveil a striking change in the structure–dynamics correlation, which involves no fitting theoretical interpretation. These findings provide new insight into the structure–dynamics correlation in glass transition.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.