Dynamic transitions in molecularly thin liquid films under frictional sliding

The friction properties of the molecularly thin films of an asymmetric ether, 1,3-dimethylbutyl hexadecyl ether (DBHE), confined between mica surfaces were investigated using the surface forces apparatus. Kinetic friction was measured as a function of normal load and sliding velocity, and the static friction (stiction) was measured as a function of normal load and surface stopping time. Kinetic friction measurements exhibited unstable sliding dynamics: the friction force exhibited cyclic bumps and valleys in the sliding velocity range from about 10(-2) to 1 microm/s, but above and below the velocity range, smooth sliding was observed. Stop-start experiments showed a stiction spike when surface stopping time exceeded a characteristic nucleation time, indicative of the static friction state at very low sliding velocity. These results imply that the friction of the confined DBHE film has at least three responsible friction states--static friction and two different kinetic friction states--depending on the sliding velocity. The unstable sliding (bumps and valleys of the friction force) reflects the dynamic transition between two different kinetic states. The different friction states and their transitions are discussed on the basis of the recent experiments and theories of "inverted" stick-slip friction.     

Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment

Implants invoke inflammatory responses from the body even if they are chemically inert and nontoxic. It has been shown that a crucial precedent event in the inflammatory process is the spontaneous adsorption of fibrinogen (Fg) on implant surfaces, which is typically followed by the presence of phagocytic cells. Interactions between the phagocyte integrin Mac-1 and two short sequences within the fibrinogen gamma chain, gamma190-202 and gamma377-395, may partially explain phagocyte accumulation at implant surfaces. These two sequences are believed to form an integrin binding site that is inaccessible when Fg is in its soluble-state structure but then becomes available for Mac-1 binding following adsorption, presumably due to adsorption-induced conformational changes. The objective of this research was to theoretically investigate this possibility by using molecular dynamics simulations of the gamma-chain fragment of Fg over self-assembled monolayer (SAM) surfaces presenting different types of surface chemistry. The GROMACS software package was used to carry out the molecular simulations in an explicit solvation environment over a 5 ns period of time. The adsorption of the gamma-chain of fibrinogen was simulated on five types of SAM surfaces. The simulations showed that this protein fragment exhibits distinctly different adsorption behavior on the different surface chemistries. Although the trajectory files showed that significant conformational changes did not occur in this protein fragment over the time frame of the simulations, it was predicted that the protein does undergo substantial rotational and translational motions over the surface prior to stabilizing in various preferred orientations. This suggests that the kinetics of surface-induced conformational changes in a protein's structure might be much slower than the kinetics of orientational changes, thus enabling the principles of adsorption thermodynamics to be used to guide adsorbing proteins into defined orientations on surfaces before large conformational changes can occur. This finding may be very important for biomaterial surface design as it suggests that surface chemistry can potentially be used to directly control the orientation of adsorbing proteins in a manner that either presents or hides specific bioactive sites contained within a protein's structure, thereby providing a mechanism to control cellular responses to the adsorbed protein layer.     

Molecular dynamics simulation of the sliding of distamycin anticancer drug along DNA: interactions and sequence selectivity

Molecular dynamics simulations and umbrella sampling have been used to investigate the sliding of distamycin anticancer drug along the DNA minor groove. The potential energy surface calculated for the sliding of drug shows three minima. The global minimum corresponds to the binding of drug to the AT-rich region, which is the origin of sequence selectivity of distamycin. This selectivity originates from both structural factors and energy contributions. The analysis of energy contributions of binding was performed by the MM–PBSA method. The analysis of hydrogen bonds and van der Waals, electrostatic, and solvation interactions show that structural or steric factors are more important in the selectivity of distamycin than energetic factors. The results of this study can be applied in the design of new derivatives of distamycin anticancer drug with improved properties.     

Molecular simulation of the phase behavior of fluids and fluid mixtures using the synthetic method

A new molecular simulation procedure is reported for determining the phase behavior of fluids and fluid mixtures, which closely follows the experimental synthetic method. The simulation procedure can be implemented using Monte Calro or molecular dynamics in either the microcanonical or canonical statistical ensembles. Microcanonical molecular dynamics simulations are reported for the phase behavior of both the pure Lennard-Jones fluid and a Lennard-Jones mixture. The vapor pressures for the pure fluid are in good agreement with Monte Carlo Gibbs ensemble and Gibbs-Duhem calculations. The Lennard-Jones mixture is composed of equal size particles, with dissimilar energy parameters (?(2)∕?(1) = 1∕2, ?(12)∕?(1) = 1∕2). The binary Lennard-Jones mixture exhibits liquid-liquid equilibria at high pressures and the simulation procedure allows us to estimate the coordinates of the high-pressure branch of the critical curve.     

不同链长烷烃在碳纳米管表面行为的分子动力学模拟

采用分子动力学方法模拟了不同长度的烷烃在单壁碳纳米管表面的吸附和取向过程,直观地给出了过程中很多微观信息,如链与纳米管管轴的夹角,链的弯曲程度等.结果表明短链烷烃能够被吸附在纳米管表面并沿着特定的方向取向;碳纳米管表面起到诱导取向的作用,并且该诱导作用对离表面最近的吸附层作用最明显;在吸附过程中,烷烃链发生弯曲,而吸附以后,取向的烷烃链倾向于采取伸直的状态。     

Molecular order and disorder in the frictional response of alkanethiol self-assembled monolayers

Molecular processes in the frictional response of an alkanethiol monolayer, self-assembled on a Au(111) surface, are studied by means of high-resolution friction force microscopy in ultrahigh vacuum. With increasing load, three regimes are observed on defect-free domains of the monolayer: smooth sliding with negligible friction, regular molecular stick-slip motion with increasing friction, and the onset of wear in the monolayer. Molecular contrast in the lateral force is found for inequivalent molecules within the unit cell of the c(4 × 2) superstructure. Significant differences in the frictional response are found between defect-free domains and areas including a domain boundary. Friction increases by an order of magnitude on domain boundaries in connection with irregular stick-slip motion. This increased friction at domain boundaries is observed at loads below the onset of wear.     

Molecular dynamics simulation on influence of temperature effect on electro-coalescence behavior of nano-droplets

In electric dehydration of crude oil, the dewatering efficiency can be improved by raising emulsion temperature properly which reduces the viscosity of crude oil. However, it should be noticed that the emulsion temperature does not only affect the emulsion viscosity but also nano-droplets dynamics behavior which impacts the coalescence efficiency either. Therefore the influence of temperature effect on the electro-coalescence of nano-droplets is studied by a molecular dynamics method. The results show that the temperature presents an active or negative effect, depending on the competitive relation between electrostatic interaction and thermal motion. Two stages are distinguished according to the dominant mechanism. During stage I, governed by the electrostatic interaction, lower temperature promotes the polarization and leads to an acceleration of the droplets coalescence, but higher temperature restrains the coalescence process due to molecules thermal motion breaking the polarization process. During stage II, governed by the thermal motion, lower temperature improves the coalescence because of a diffusion effect, but higher temperature deteriorates electro-coalescence because of a violent molecular thermal motion. Additionally, hydrogen bond and radial distribution functions are obtained by statistics to describe droplets micromorphology, which explains the reason why the droplet forms longer chain structure at the critical electric field.     

Molecular dynamics simulation of the crystal nucleation behavior of a single chain touching a substrate surface

Molecular dynamics simulation has been used in exploring the crystal nucleation behaviour of a single chain touching a substrate surface. It shows that a polyethylene chain (980 CH₂) changed its overall shape from an isotropic coil to an oriented one in the case of touching a substrate surface of amorphous carbons at 300 K. Most repeats of the chain were aligned and ordered in a zigzag package. Surprisingly, the direction of the package is not parallel to the plane of the substrate, but almost perpendicular to it. This is in accordance with experimental observations.     

Molecular dynamics simulation of dissociation behavior of various crystalline celluloses treated with hot-compressed water

The dissociation behavior of the crystalline cellulose polymorphs I_β, II, III_I, and IV_I (Cell I_β, etc.) at 503 K and 100 bar was studied by molecular dynamics simulation, and the mechanism of the experimental liquefaction during treatment with hot-compressed water was elucidated. The results showed that the mini-crystals of Cell I_β and Cell IV_I exhibited similar resistance to dissociation, which implies the occurrence of crystal transformation from Cell IV_I to Cell I. On the other hand, the mini-crystal of Cell II gradually dissociated into the water environment with the progress of time in the simulation. The water molecules gradually penetrated the Cell II crystal, especially along the (1 \(\overline{1}\) 0) crystal plane. In contrast, the dissolution behavior differed for the surface and the core areas of the mini-crystal of Cell III_I. The cellulose chains on the surface were dissociated into the water environment, whereas the ordered structure of the chains in the core region was maintained for the entire simulation period. The detailed investigation showed that the core part of Cell III_I was transformed into Cell I at an early stage of the simulation: Cell I is resistant to dissociation of the structure even in the hot-compressed water environment. It can be confirmed that the stability of these four crystals under high temperature and pressure conditions follows the order: Cell II < III_I < IV_I ≈ I_β.     

催化裂解过程分子尺度的反应动力学模拟： 原料油分子尺度的模拟

以工业实测数据为基础,运用结构导向集总方法构造分子,对催化裂解原料油进行了分子尺度上的蒙特卡罗模拟.结果表明,Monte Carlo方法可以在分子尺度上实现对催化裂解原料很好的模拟.两种工况下原料的平均分子量、饱和烃、芳烃、胶质沥青、碳、氢、硫、氮含量等性质的计算值与实际值吻合,且由此产生的分子矩阵将为后续反应网络的建立打下基础.     

碳纳米管内N2吸附行为及等量吸附热的GCMC分子模拟研究

碳纳米管及石墨烯具有高比表面积、高化学稳定性以及高耐蚀性等优点,被认为是一种理想的吸附材料。分子模拟技术的发展和应用丰富了人们对吸附机理研究的方式,而简单气体吸附体系的吸附机理研究对吸附理论的发展有着重要的推动作用。本文以单壁碳纳米管（SWCNT）-N₂吸附体系为研究对象,首先通过透射扫描电镜和氮气吸/脱附测试对所选用碳纳米管的微观孔形貌及吸/脱附等温线进行了表征,然后根据对应孔径参数采用巨正则蒙特卡罗方法对该体系的吸附过程进行了分子模拟,并详细研究了碳纳米管孔径和温度对该体系吸附行为的影响。结果显示,SWCNT孔径越小,吸附能力则越强;孔半径为0.746nm的SWCNT的吸附体系发生凝聚相变的临界温度为66K。通过对等量吸附热进行计算发现,孔半径0.746、1.15、1.56和1.83 nm的SWCNT-N₂吸附体系对应的初始固-液等量吸附热分别为10.9、9.2、8.6和8.4 kJ/mol。67.5K时,孔半径1.56和1.83 nm的吸附体系的等量吸附热有热峰出现。     

Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite

Molecular dynamics simulations are applied to study the adsorption of polyethylene with different chain lengths on patterned graphite surfaces that contain nanoscale protrusions. The influence of the nanostructure on the strong attractive interaction inherently in the hydrophobic polyethylene and hydrophobic graphite system is investigated by modifying the top surface area and the height and the shape of the protrusions. The results are analyzed in terms of the chain configuration, the adsorption energy, the global orientational order parameter, and the normalized surface-chain contacting pair number in the first adsorption layer. When the size of the protrusion increases, the adsorption energy, the order parameter, and the normalized surface-chain contacting pair number decrease at a fixed chain length. When the size of the protrusion is fixed, the average adsorption energy per monomer and the order parameter decrease with increasing chain length because of the stronger intramolecular interactions between the monomers. Changing the protrusion shape in a suitable way will effectively reduce the strong surface-chain interaction.     

Molecular dynamics simulation of ferronanofluid behavior in a nanochannel in the presence of constant and time-dependent magnetic fields

Journal of Thermal Analysis and Calorimetry - For the first time, double phosphates(V) Zn3Cr4(PO4)6 and Mg3Cr4(PO4)6 were synthesized by non-waste solid-state reaction, performed in the temperature...     

Molecular tilting and its impact on frictional properties of n-alkane self-assembled monolayers

Hydrophobic, methyl-terminated self-assembled monolayer (SAM) surfaces can be used to reduce friction. Among methyl-terminated SAMs, the frictional properties of alkanethiol SAMs and silane SAMs have been well-studied. In this research, we investigated friction of methyl-terminated n-hexatriacontane (C36) SAM and compared its friction properties with the alkanethiol and silane SAMs. Alkane SAM does not have an anchoring group. The alkane molecules stand on the surface by physical adsorption, which leads to a higher surface mobility of alkane molecules. We found that C36 SAM has a higher coefficient of friction than that of octadecyltrichlorosilane (OTS) silane. When an atomic force microscope (AFM) tip was swiped across the alkane SAM with a loading force, we found that the alkane SAM can withstand the tip loading pressure up to 0.48 GPa. Between 0.48 and 0.49Ga, the AFM tip partially penetrated the SAM. When the tip moved away, the deformed SAM healed and maintained the structural integrity. When the loading pressure was higher than 0.49 GPa, the alkane SAM was shaved into small pieces by the tip. In addition, we found that the molecular tilting of C36 molecules interacted with the tribological properties of the alkane SAM surface. On one hand, a higher loading force can push the rod-like alkane molecules to a higher tilting angle; on the other hand, a higher molecular tilting leads to a lower friction surface.     

Molecular dynamics simulation study on zwitterionic structure to maintain the natural behavior of polyalanine13 in aqueous environment

Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."     

Molecular simulation of the glass transition of polyphosphazenes

Molecular dynamics simulation (NPT ensemble) has been used to obtain specific volume as a function of temperature for four polyphosphazenes. From these results, the volumetric glass transition temperature has been determined as the temperature marking the discontinuity in slope of the V–T simulation data. The molecular mechanics force field used in this study was COMPASS (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies) which has been extensively parameterized and validated for phosphazenes in a previous communication. The polyphosphazenes include poly[bis(2,2,2-trifluoroethoxy)phosphazene] (PTFEP) and three isomers of poly(dibutoxyphosphazene)—poly[bis(n-butoxy)phosphazene] (PnBuP), poly[bis(iso-butoxy)phosphazene)] (PiBuP), and poly[bis(sec-butoxy)phosphazene] (PsBuP). In all cases, there was reasonable agreement between experimental results and values of density and T_g obtained from the simulations. In the case of PnBuP, two different methods for amorphous cell building are compared to explore the relationship between the state of equilibration and the T_g obtained from simulation.     

Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail

To study the effect of the alkyl tail and the terminal dipole on the stability of the liquid crystalline phase of mesogens, we have carried out molecular dynamics simulations for 1CB(4-methyl-4'-cyanobiphenyl) and 5CB(4-n-pentyl-4'-cyanobiphenyl) by using a coarse-grained model. In the coarse-grained model, a 5CB molecule is divided into the rigid part of 1CB moiety, which is represented by an ellipsoid, and the remaining flexible part which is represented by a chain of united atoms. The nonbonded potential between coarse-grained segments is represented by the generalized Gay-Berne (GB) potential and the potential parameters are determined by directly comparing the GB potential with the atomistic potentials averaged over the rotation of the mesogen around its axis. In addition, a dipole moment is placed at one end of the ellipsoid opposite to the flexible tail. The ordered state obtained in the polar 5CB model was assigned as the nematic phase, and the experimental static and dynamical properties were reproduced well by using this coarse-grained model. Both the dipole-dipole interactions and the thermal fluctuation of the flexible tail increase the positional disorder in the director direction, and stabilize the nematic phase. Thus, the nematic phase in the polar 5CB is induced by a cooperative effect of the flexible tail and the terminal dipole. It is noted that a local bilayer structure with head-to-head association is formed in the nematic phase, as experimentally observed by x-ray diffraction measurements.     

Structural-phenomenological simulation of the mechanical behavior of rubbers

It is hypothesized that, during deformation of rubbers, polymer chains slip off the layers at filler particles into voids between inclusions and high-strength polymer fibers in the uniaxially oriented state are formed in the voids. As a result, the macroscopic strength of elastomers increases by an order of magnitude and the elongation at break simultaneously increases relative to the unfilled elastomer. Aggregates of carbon black particles that occur close to one another in the initial sample depart to very large distances upon stretching the material. The fibers that tie the aggregates must extend their length by a factor of a few tens in this case. A mathematical model that takes into account these processes is proposed. It was shown that the set of constitutive equations makes it possible to simulate with good accuracy both the viscoelastic behavior of rubbers and the Mullins softening effect under finite strain conditions.     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

Molecular simulation of cross-nucleation between polymorphs

Recent experiments report that an early nucleating crystalline structure (or polymorph) may nucleate another polymorph. We use molecular dynamics simulations to model this phenomenon known as cross-nucleation. We study the onset of crystallization in a liquid of Lennard-Jones particles cooled at a temperature 22% below the melting temperature. We show that growth proceeds through the successive cross-nucleation of the metastable hexagonal close-packed (hcp) polymorph on the stable face-centered cubic (fcc) polymorph and of the stable fcc polymorph on the metastable hcp polymorph. This finding is in agreement with the experimental results which demonstrated that the cross-nucleation of a stable polymorph on a metastable polymorph is just as likely as the cross-nucleation of a metastable polymorph on a stable polymorph. We then extend our findings established in the case of the homogeneous crystal nucleation to a situation of practical interest, i.e., when a seed of the stable polymorph is used. By studying the crystal growth from the (111) plane of a perfect fcc crystal, we show that, again, growth proceeds through the cross-nucleation of the hcp and fcc structures.