Gas adsorption and accumulation on hydrophobic surfaces:Molecular dynamics simulations

Molecular dynamics simulations show that the gas dissolved in water can be adsorbed at a hydrophobic interface and accumulates thereon. Initially, a water depletion layer appears on the hydrophobic interface. Gas molecules then enter the depletion layer and form a high-density gas-enriched layer. Finally, the gas-enriched layer accumulates to form a nanobubble. The radian of the nanobubble increases with time until equilibrium is reached. The equilibrium state arises through a Brenner–Lohse dynamic equilibrium mechanism, whereby the diffusive outflux is compensated by an influx near the contact line. Additionally, supersaturated gas also accumulates unsteadily in bulk water, since it can diffuse back into the water and is gradually adsorbed by a solid substrate.

Molecular Dynamics Simulation of Behaviours of Non-Polar Droplets Merging and Interactions with Hydrophobic Surfaces

This paper presents a molecular dynamics simulation of the behaviours of non-polar droplets merging and also the fluid molecules interacting with a hydrophobic surface. Such behaviours and transport phenomena are popular in general microchannel flow boiling and two-phase flow. The droplets are assumed to be composed of Lennards-Jones type molecules. Periodic boundary conditions are applied in three coordinate directions of a 3-D system, where there exist two liquid droplets and their vapour. The two droplets merge when they come within the prescribed small distance. The merging of two droplets apart from each other at different initial distances is tested and the possible larger （or critical） non-dimensional distance, in which droplets merging can occur, is discussed. The evolution of the merging process is simulated numerically by employing the Molecular Dynamics （MD） method. For interactions with hydrophobic solid wall, a system with fluid confined between two walls is used to study the wetting phenomena of fluid and solid wall. The results are compared with those of hydrophilic wall to show the unique characteristics of hydrophobic interactions by microscopic methods.

Molecular dynamics simulations of the nano-droplet impact process on hydrophobic surfaces

Large-scale molecular dynamics simulations are used to study the dynamic processes of a nano-droplet impacting on hydrophobic surfaces at a microscopic level. Both the impact phenomena and the velocity distributions are recorded and analyzed. According to the simulation results, similar phenomena are obtained to those in macro-experiments. Impact velocity affects the spread process to a greater degree than at a level of contact angle when the velocity is relatively high. The velocity distribution along the X axis during spread is wave-like, either W- or M-shaped, and the velocity at each point is oscillatory; while the edges have the highest spread velocity and there are crests in the distribution curve which shift toward the edges over time. The distribution along the Y axis is 〈- or 〉-shaped, and the segments above the middle have the lowest decrease rate in the spreading process and the highest increase rate in the retraction process.

Formation of nanobubbles generated by hydrate decomposition:A molecular dynamics study

Natural gas hydrate is estimated to have huge reserves. Its exploitation can solve the global oil and gas shortage problem. Hydrates decompose into water and methane, and methane molecules are supersaturated to form nanobubbles.Methane nanobubbles can affect the decomposition efficiency of hydrates. They can provide abundant methane sources for the re-nucleation of hydrates. Molecular dynamics is employed in this study to investigate the decomposition process of type I methane hydrate and the formation of methane nanobubbles generated during decomposition under different methane mole fraction, pressures, and temperatures. The results indicate that external pressure inhibits the diffusion of methane molecules, thereby preventing the formation of nanobubbles. A higher mole fraction of methane molecules in the system requires a higher external pressure to generate stable nanobubbles after the decomposition of the hydrate structure.At 330 K, it is easy to form a nanobubble structure. Results of this study can help provide ideas for the study of efficient extraction and secondary nucleation of hydrates.

Molecular dynamics simulation studies on some topics of water molecules on hydrophobic surfaces

Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in sin- gle-walled carbon nanochannels are exploited. Molecular simulations show that the density of the N2 and H2 are quite high, which is critical for the stability of the nanobubbles and may have potential applications, such as hydrogen storage, incorporated with recent experimental method to controllably produce hydrogen nanobubbles. The water molecules inside the nanochannel show an unexpected directed motion with long time period, which is indispensable in the future study of the dynamics of biological channels.

High density gas state at water/graphite interface studied by molecular dynamics simulation

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different monolayers （SAMs） are studied by molecular dynamics hydrophilic and hydrophobic surfaces of well ordered self-assembled simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon（111） substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups （-CH3, -COOH）. In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results sug- gest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better or- dering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hy- droxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of in- terfacial water.

Fabrication of Super Hydrophobic Surfaces on Copper by Solution-immersion

Super hydrophobic copper wafer was prepared by means of solution immersion and surface self-assembly methods. Different immersion conditions were explored for the best hydrophobic surface. Scanning electron microscopy (SEM), X-ray diffraction (XRD), energy dispersive spectrometer (EDS) and water contact angle measurements were used to investigate the morphologies, microstructures, chemical compositions and hydrophobicity of the produced films on copper substrates, respectively. Results show that the super hydrophobic surface is composed of micro structure of Cu 7 S 4 . The films present a high water contact angle larger than 150°, a low sliding angle less than 3°, good abrasion resistance and storage stability. The molecular dynamics simulation confirms that N-dodecyl mercaptan molecules link up with Cu 7 S 4 admirably, compared with Cu, which contributes to the stable super hydrophobic surface.

Size-dependent surface tension of a cylindrical nanobubble in liquid Ar

In view of the continued disputes on the fundamental question of whether the surface tension of a vapour bubble in liquid argon increases, or decreases, or remains unchanged with the increase of curvature radius, a cylindrical vapour bubble of argon is studied by molecular dynamics simulation in this paper instead of spherical vapour bubble so as to reduce the statistical error. So far, the surface tension of the cylindrical vapour bubble has not been studied by molecular dynamics simulation in the literature. Our results show that the surface tension decreases with radius increasing. By fitting the Tolman equation with our data, the Tolman length σ = -0.6225 sigma is given under cut-off radius 2.5σ, where σ = 0.3405 nm is the diameter of an argon atom. The Tolman length of Ar being negative is affirmed and the Tolman length of Ar being approximately zero given in the literature is negated, and it is pointed out that this error is attributed to the application of the inapplicable empirical equation of state and the neglect of the difference between surface tension and an equimolar surface.

Influence mechanism of Fe^(3+)doping on the hydrophobic regulation of kaolinite/water interface:Experiments and MD simulations

The surface/interfacial reactivity of clay is a critical factor influencing the sedimentation of coal slurry water.To achieve efficient sedimentation of coal slurry water,this paper introduces a novel approach that regulates the hydrophobicity of defective active sites in clay minerals.Fe^(3+)-doped kaolinite(Fe^(3+)-Kao)was synthesized by hydrothermal methods.Subsequently,tests were conducted on the adsorption capacity,surface wettability,and agglomeration sedimentation of alkyl amine/ammonium salts(AAS)on Fe^(3+)-Kao surfaces.Fe^(3+)doping significantly enhances AAS adsorption and alters surface properties from hydrophilic to hydrophobic,promoting kaolinite particle aggregation and sedimentation,thereby improving coal slurry water treatment efficiency.Molecular dynamics(MD)simulations were performed to analyze the statistical adsorption behavior of AAS on Fe^(3+)-Kao surfaces.The simulation results indicate that the mechanism by which Fe^(3+)doping influences the hydrophobic regulation of kaolinite surfaces is due to the enhanced interfacial interactions between the kaolinite surface and AAS,where the interfacial effects are more pronounced on surfaces closer to the dopant sites.The findings of this research offer valuable insights for future studies on other types of lattice defects in clay minerals,as well as for the development of more efficient treatment chemicals for coal slurry water.

INVESTIGATION OF INFLUENCE OF WETTABILITY ON POISEUILLE FLOW VIA MOLECULAR DYNAMICS SIMULATION

In this article,the influence of wettability on a liquid flow between two parallel plane walls were studied by using Non-Equilibrium Molecular Dynamics（NEMD） simulation.The wettability of the solid surfaces can be described as the contact angle.The liquid flow rate,the slip velocity and the slip length which are affected by the contact angle were investigated.The results show that the boundary condition at a microscopic level is different from a ＂no-slip＂ condition at a macroscopic level.There exits a slippage of a liquid flow for the hydrophobic boundary and an external force is needed to overcome threshold pressure for the hydrophilic boundary.And the orderly layered distributions of the liquid particles near the hydrophilic surface vary from a place near the hydrophobic surface.The study indicates that the surface wettability plays a significant role on possibilities of forming a viscous layer and the direct slip at the solid surface.The resistance of liquid flow can be decreased by changing the wettability of boundary surface.

Contact angle and stability of interfacial nanobubble supported by gas monolayer

Since solid-liquid interfacial nanobubbles(INBs)were first imaged,their long-term stability and large contact angle have been perplexing scientists.This study aimed to investigate the influence of internal gas density and external gas monolayers on the contact angle and stability of INB using molecular dynamics simulations.First,the contact angle of a water droplet was simulated at different nitrogen densities.The results showed that the contact angle increased sharply with an increase in nitrogen density,which was mainly caused by the decrease in solid-gas interfacial tension.However,when the nitrogen density reached 2.57 nm^(-3),an intervening gas monolayer(GML)was formed between the solid and water.After the formation of GML,the contact angle slightly increased with increasing gas density.The contact angle increased to 180°when the nitrogen density reached 11.38 nm^(-3),indicating that INBs transformed into a gas layer when they were too small.For substrates with different hydrophobicities,the contact angle after the formation of GML was always larger than 140°and it was weakly correlated with substrate hydrophobicity.The increase in contact angle with gas density represents the evolution of contact angle from macro-to nano-bubble,while the formation of GML may correspond to stable INBs.The potential of mean force curves demonstrated that the substrate with GML could attract gas molecules from a longer distance without the existence of a potential barrier compared with the bare substrate,indicating the potential of GML to act as a gas-collecting panel.Further research indicated that GML can function as a channel to transport gas molecules to INBs,which favors stability of INBs.This research may shed new light on the mechanisms underlying abnormal contact angle and long-term stability of INBs.

Molecular dynamics simulations exploring drug resistance in HIV-1 proteases

Although HIV-1 subtype B still dominates the epidemic AIDS in developed countries,an increasing number of people in developing countries are suffering from an epidemic of non-subtype B viruses.What is worse,the efficacy of the combinational use of antiretroviral drugs is gradually compromised by the rapid development of drug resistance.To gain an insight into drug resistance, 10-ns MD simulations were simultaneously conducted on the complexes of the TL-3 inhibitor with 4 different proteases(Bwt,Bmut, Fwt and Fmut),among which the complex of the Bwt protease with the TL-3 inhibitor was treated as the control group.Detailed analyses of MD data indicated that the drug resistance of Bmut against TL-3 mainly derived from loss of an important hydrogen bond and that of Fwt was caused by the decrease of hydrophobic interactions in S1/S1'pocket,while both of the two reasons mentioned above were the cause of the Fmut protease's resistance.These results are in good agreement with the previous experiments, revealing a possible mechanism of drug resistance for the aforementioned protease subtypes against the TL-3 inhibitor.Additionally,another indication was obtained that the mutations of M36I,V82A and L90M may induce structural transforms so as to alter the inhibitor's binding mode.

Computational study of laser fragmentation in liquid:Phase explosion,inverse Leidenfrost effect at the nanoscale,and evaporation in a nanobubble

Laser fragmentation in liquid is an effective and environment-friendly processing technique capable of yielding colloidal nanoparticles and atomic clusters with a narrow size distribution. The advancement of this technique can be facilitated by an improved understanding of processes that control the sizes, shapes, and structures of the produced nanoparticles. In this work, the dependence of the fragmentation mechanisms on the energy density deposited by the laser pulse is investigated in atomistic simulations performed for 20 nm Au nanoparticles irradiated in water by 10 ps laser pulses. The simulations reveal that the decrease in the absorbed laser energy leads to sequential transitions from the regime of “strong” phase explosion, when all products of an explosive phase decomposition of the irradiated nanoparticle are promptly injected into the water surrounding a nanobubble formed around the nanoparticle, to two distinct regimes of nanoparticle fragmentation leading to the formation of a large central nanoparticle surrounded by smaller satellite fragments. First, in the regime of “mild” phase explosion, the central nanoparticle is produced by the reflection of some of the hot metal droplets generated by the explosive decomposition of the nanoparticle from the boundary of the nanobubble. This reflection is attributed to the inverse Leidenfrost effect acting at the nanoscale. The reflected droplets converge in the center of the nanobubble and coalesce into a single droplet that solidifies shortly after the collapse of the nanobubble. Further decrease in the absorbed laser energy brings the irradiation conditions below the threshold for the phase explosion and results in the formation of a core-satellite structure of the fragmentation products through an interplay of the intense evaporation from the surface of the irradiated nanoparticle, evolution of the nanobubble, and condensation of the metal vapor into clusters and small satellite nanoparticles. The computational predictions are related to the experimental observations, and the connections between the fragmentation mechanisms, the nanoparticle size distribution, and the generation of internal crystal defects are discussed.

Investigating Interaction Between Biochanin A and Human Serum Albumin by Multi-spectroscopic and Molecular Simulation Methods

Biochanin A (BCA), the most abundant isoflavone in chickpeas, presents a wide range of biological activities, such as hypolipidaemic, anti-oxidative, anti-proliferative, and estrogen-like effects. We investigated the interaction between BCA and human serum albumin (HSA) via several techniques. UV–Vis absorption spectroscopy verified the conformational variation of HSA after BCA addition, and fluorescence spectroscopy revealed the relevant binding parameters. Circular dichroism spectroscopy was used to estimate the secondary structural changes of HSA with and without BCA. Molecular docking and dynamics simulations were then applied to study the characteristics of HSA with BCA. Energy decomposition analysis was used to prove that Trp214 in subdomain IIA of HSA is the most likely binding site of BCA. Van der Waals forces and hydrophobic interactions may play important roles during the binding process. All of our results showed that BCA presents significant binding affinity to HSA, thus confirming that the role of HSA has as an efficient transporter of biomolecules. © 2017, Tianjin University and Springer-Verlag Berlin Heidelberg.

纳米气泡浮选过程强化研究进展

浮选是低品质矿及煤分选提质的有效手段,其中微细粒浮选难题突出,而纳米气泡则是解决该难题的重要途径,但关于纳米气泡浮选过程强化的诸多基础科学问题仍未解决。为促进微细粒纳米气泡浮选过程强化技术的开发,重点围绕浮选过程中纳米气泡的界面选择性成核动力学、界面纳米气泡超常稳定性机理及纳米气泡强化颗粒-气泡捕获效率微观作用机制等三个关键科学问题,介绍了笔者团队在纳米气泡浮选过程强化方向的最新研究进展。研究结果表明:纳米气泡的选择性成核是纳米气泡浮选过程强化的关键,而纳米气泡的稳定性则是纳米气泡浮选过程强化的前提;纳米气泡浮选过程强化的机制主要包括促进颗粒絮团与缩短诱导时间,其内在作用机制来自纳米气泡长程疏水引力与边界滑移的协同作用。笔者团队的研究阐明了纳米气泡固-液界面选择性成核的能量作用机制,提出了基于界面高密度气层自动补偿的界面纳米气泡稳定性机理,建立了微纳力学-边界滑移协同驱动的纳米气泡强化浮选界面作用机制,进一步丰富发展了现代浮选基础理论,为开发微细粒纳米气泡浮选过程强化技术提供了一定的指导。

基于亚稳态液膜空化的长程疏水力作用机制

疏水力作为胶体物理化学及生物大分子体系中重要作用力,具有典型的多尺度作用程特征,其中亚稳态液膜空化气泡桥接诱发长程疏水力和固液界面水分子重排熵效应诱导短程疏水力假说占据着当前学术主流,但仍缺少系统理论研究.为进一步阐明基于亚稳态液膜空化的长程疏水力作用机制,借助原子力显微镜(AFM)及分子动力学模拟对全氟辛基三氯硅烷疏水化颗粒与表面间长程疏水力进行了系统研究.AFM力测试结果表明:长程疏水力作用程随接近次数增加而逐渐增大并逐渐趋于稳定,第十次接触时进针曲线跳入黏附距离达到502.01 nm,退针曲线中观察到了预示空化气泡毛细桥断裂的台阶.此外,发现经典毛细力数学模型可以较好地拟合进针曲线,通过计算得到毛细桥体积约为0.30μm^(3),从理论角度直接验证了亚稳态液膜空化气泡毛细桥的存在.进一步借助GROM ACS(GROningen M A chine for Chemical Simulations)大尺度牵引分子动力学模拟从分子尺度探索疏水颗粒分离过程中空化气泡毛细桥产生、演化过程与力学行为的内在关联机制,结果表明:疏水颗粒从基板表面跳出分离瞬间,产生的局部压降吸引氮气分子向液膜内部扩散从而形成空化气泡毛细桥,同时,在毛细桥断裂时刻在计算弹簧势力曲线中观察到了力跳跃行为.最后研究了溶液气体含量对长程疏水力的影响规律,发现气体分子含量和空化气泡毛细桥体积增长速率与毛细桥拉伸断裂长度呈现正相关关系,进一步表明了长程疏水力的气体浓度依赖效应.基于亚稳态液膜空化的长程疏水力作用机制的揭示有助于进一步完善胶体物理化学及生物大分子间相互作用理论体系,同时对调控实际矿物浮选过程具有重要指导意义.

基于分子模拟方法的纳米气泡溃灭过程分析

采用分子动力学模拟方法研究纳米气泡逐渐凹陷并发展至溃灭的过程,本文主要研究冲击速度和气泡尺寸对纳米气泡溃灭的动力学特性影响机制.结果表明:纳米气泡溃灭大体上经历三个阶段.首先是气泡外侧水分子压缩阶段,然后是冲击波导致液膜稳定结构被破坏阶段,最终发展至气泡完全溃灭阶段;在冲击速度较大时,较小尺寸气泡在更强的冲击效果作用下,气泡溃灭时间更短;纳米气泡溃灭后高速射流后在速度等高线右端形成凸起,随着气泡尺寸和冲击速度增大,凸起程度就越大,水分子向气泡中心汇集,在气泡上方和下方形成涡旋结构,有效的增强了流体内部传质作用;随着气泡尺寸和冲击速度的增大,气泡周围密度也逐渐增大,气泡完全时溃灭时局部密度可达1.5 g/cm^(3)附近;当气泡体系衰减至一半时,出现水锤冲击效应,随着气泡尺寸和冲击速度的增大,水锤冲击作用愈发明显,对于u_(p)=3.0 km/s,D=10 nm的纳米气泡结构塌陷后射流水锤冲击所形成的局部压强可达30 GPa.

分子动力学模拟研究氨基酸亲疏水性质对蛋白质结构的影响

目的:从氨基酸的侧链大小、带电性、二硫键的形成等方面研究氨基酸的亲疏水性质对蛋白质结构的影响。方法:利用VMD软件构建由不同亲疏水性氨基酸组成的蛋白质模型,并采用分子动力学方法对体系进行模拟。结果:体系键伸缩能与键弯曲能的大小仅与氨基酸的侧链原子数目有关,与氨基酸的亲疏水性质无明显相关性,但疏水型氨基酸构建的蛋白质链其范德华能低于亲水型氨基酸构建的蛋白质链。同时,氨基酸的亲疏水性质会直接影响蛋白质链的二级结构,通过对蛋白质链的均方根涨落和均方根偏差分析得到,疏水型氨基酸构建的蛋白质链能够维持稳定的α螺旋结构。结论:对氨基酸的亲疏水性质与蛋白质链能量及结构参数的关系的研究结果,可为后续进一步理解蛋白质的三级结构特征和动力学行为提供理论支持。

Residual occurrence and energy property of proteins in HNP model

Four categories of globular proteins, including all-a, all-β, α＋β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of three types of residues, i.e., H, N, and P to form a secondary structure is investigated based on 146 protein samples. We find that P residues are easy to form a-helices, whereas H residues have a higher tendency to construct β-sheets. The statistical analysis also indicates that the occurrence of P residues is invariably higher than that of H residues, which is independent of protein category. Changes in bond- and non-bonded potential energies of all protein samples under a wide temperature range are presented by coarse-grained molecular dynamics （MD） simulation. The simulation results clearly show a linear relationship between the bond-stretching/bending potential energy and the reduced temperature. The bond-torsional and non-bonded potential energies show distinct transitions with temperature. The bond-torsional energy increases to the maximum and then decreases with the increase of temperature, which is opposite to the change in non-bonded potential energy. The transition temperature of non-bonded potential energy is independent of the protein category, while that of bond-torsional energy is closely related to the protein secondary structure, i.e., α-helix or E-sheet. The quantitatively bonded- and semi- quantitatively non-bonded potential energy of 24 α＋β and 23 α/β protein samples are successfully predicted according to the statistical results obtained from MD simulations.