Reduction in total surface area by the develpment of microdroplets during dewetting

To meet the demand of an increasing storage density, the lubricant film for the head disk interface (HDI) needs to be thinner and stronger. In recent years, a new head/disk system, such as the contact type, has been proposed. It is reported that PFPE Zdol coated on a magnetic disk is dewetted and microdroplets are formed due to polar interactions. This makes a flying magnetic head unstable, therefore, the physics and chemistry of the dewetting phenomenon are topics of current interest. We investigated the formation and development of microdroplets using an atomic force microscope (AFM) and an optical microscope. First, we observed the disk surface coated with PFPE Zdol by AFM. From the cross section images of the microdroplets, we found that the microdroplets had a shape similar to a sphere. With this finding, we estimated the contact angle of the microdroplets in each image. The results showed that the contact angle of the microdroplet gradually decreased with time, which indicated the existence of a PFPE thin film in the dewetted area. The thickness of the PFPE film in the dewetted area was then measured using an elliposometer. Next, we investigated the variation in the number and the average diameter of the microdroplets during dewetting using images observed by the optical microscope. The total surface area change was also calculated from the observed results, and it was found that the total surface area, namely the sum of the microdroplet surfaces and dewetted area, was reduced by the development of the microdroplets.     

Ultraviolet bonding of perfluoropolyethers to carbon surfaces investigated using quantum chemical methods

For improving the tribological performance of hard disk drives, nanometer-thick perfluoropolyether (PFPE) lubricant films are generally treated with ultraviolet (UV) irradiation to bond them to the carbon overcoats of the disks. By modeling UV irradiation as an electron emission and attachment process, we investigate the UV bonding of nonfunctional PFPE Z and functional PFPE Zdol to hydrogenated and nitrogenated carbon surfaces with quantum chemical methods. Our calculation results show that, upon electron attachment, Z dissociates at its main chain to two fragments terminated by CF₂CF₂ and CF₂O groups, whereas Zdol dissociates to a hydrogen fluoride and a fragment. The perfluoromethoxy oxygen in one of the Z fragments and the carbon radical and the hydrogen-truncated end group in the Zdol fragment interact strongly with sp² and oxidized sites on carbon surfaces. Imine moieties on the CNx surface also contribute considerably to the UV bonding of Zdol.     

The dynamic behavior of ultrathin lubricant films

Molecular dynamics simulations with the Langevin equation using a coarse-grained, bead-spring model were performed to investigate the dynamic properties of nanoscale lubricant films. The simulated spreading profiles of lubricant nanofilms are in qualitative agreement with previous experimental results. The Einstein’s relationship and Green–Kubo formula provide alternative perspectives for describing the diffusive phenomena of lubricant nanofilms. The effects of molecular weights and their distribution, temperature, and film thickness were examined.     

Adsorption and diffusion of benzene in the nanoporous catalysts FAU, ZSM-5 and MCM-22: a molecular dynamics study

Molecular dynamics (MD) simulations of benzene in siliceous zeolites (FAU, ZSM-5, and MCM-22) were performed at loadings of 1, 2, 4, 8, and 16 molecules per supercell. The potential energy functions for these simulations were constructed in a semi-empirical way from existing potentials and experimental energetic data. The MD simulations were employed to analyze the dynamic properties of the benzene-zeolite systems. The adsorption energies of benzene/siliceous zeolite complexes increase with increasing loading number, due to the intermolecular attraction between benzene molecules. The self-diffusion coefficient of benzene in siliceous zeolites decreases with increasing loading due to the steric hindrance between the sorbates passing each other. From the zeolite-benzene radial distribution functions it was found that the benzene molecules are relatively far from each other, about 5.2A for siliceous FAU, 5.2A for siliceous ZSM-5, and 4.8A for siliceous MCM-22. In the case of FAU, the benzene molecules prefer to be adsorbed parallel to the surface of the sodalite cage above the six-membered-ring. In ZSM-5, we found a T-structure of the benzene molecules at loadings 2, 4, and 8 molecules per supercell. At loadings of 16 molecules per supercell, the molecules are lined up along the straight channel and their movement is highly correlated. For MCM-22 we found adjacent benzene molecules at a loading of 4 molecules with an orientation similar to the stacked conformation of benzene dimer in the gas phase.     

Dynamic conformations of fluorocarbon molecules on magnetic hard disk surfaces with charged sites

To meet the demand of extremely high recording density of magnetic storage device, magnetic head is expected to reduce its flying height to sub 5 nm. Lubricant films in such system become more important and the conformation characteristics of lubricant molecules, which receive attractive forces both from the disk and the head, must be clarified for the stable flying of the head. In this report molecular dynamics simulations are carried out to investigate the conformation of lubricant molecules. The model is composed of solid surface and polar-ended fluorocarbon molecules. The surface has several reactive sites, which interact with polar end groups of fluorocarbon molecules. Varying the number of reactive sites, the processes that the reactive sites attract molecules are simulated. Results from the present simulations indicate that lubricant molecules tend to gathered and piled up. It is difficult to achieve 100% coverage.     

Flap opening mechanism of HIV-1 protease

The active site of aspartic proteases, such as HIV-1 protease (PR), is covered by one or more flaps, which restrict access to the active site. For HIV-1 PR, X-ray diffraction studies suggested that in the free enzyme the two flaps are packed onto each other loosely in a semi-open conformation, while molecular dynamics (MD) studies observed that the flaps can also separate into open conformations. In this study, the mechanism of flap opening and the structure and dynamics of HIV-1 PR with semi-open and open flap conformations were investigated using molecular dynamics simulations. The flaps showed complex dynamic behavior as two distinct mechanisms of flap opening and various stable flap conformations (semi-open, open and curled) were observed during the simulations. A network of weakly polar interactions between the flaps were proposed to be responsible for stabilizing the semi-open flap conformation. It is hypothesized that such interactions could be responsible for making flap opening a highly sensitive gating mechanism which control access to the active site.     

Micro-rheometry of pressurized lubricants and micro-nanorheology

In the present study, micro-rheometry of pressurized lubricants employing a diamond-anvil pressure cell and a laser confocal displacement sensor of 0.4 μm resolution was shown. High pressure viscosity was obtained up to 2 GPa at 200°C for traction oils and PFPE oils. The linearity between logarithmic viscosity and pressure is confirmed. Viscosity-pressure coefficient α at room temperature was almost twice larger than that at 100°C. α for hard disk oil, Zdol2000, was 13/GPa at 24°C ~ 5/GPa at 150°C and was similar to that of paraffinic mineral oil. The feature of the obtained high pressure volume was different for each oil up to 6 GPa. Zdol2000 was the most compressible of all the sample lubricants and its high pressure refractive index increased about 10% at 4.8 GPa. Zdol2000 remained transparent up to 4.8 GPa under isothermal loading. Some considerations for lubricant’s micro-nanorheology were also mentioned with high pressure lubricant’s rheology.     

Structural and water diffusion of poly(acryl amide)/poly(vinyl alcohol) blend films: Experiment and molecular dynamics simulations

To study the effects of composition ratios and temperature on the diffusion of water molecules in PVA/PAM blend films, five simulation models of PVA/PAM with ten water molecules at different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using a molecular dynamics (MD) simulation. The diffusion behavior of water molecules in blends were investigated from the aspects of the diffusion coefficient, free volume, pair correlation function (PCF) and trajectories of water molecules, respectively. And the hydrophilicity of blend composite was studied based on the contact angle and equilibrium water content (EWC) of the blend films. The simulation results show that the diffusion coefficient of water molecules and fractional free volume (FFV) of blend membranes increase with the addition of PAM, and a higher temperature can also improve the diffusion of water molecules. Additionally, the analysis of PCFs reveals the main reason why the diffusion coefficient of water in blend system increases with the addition of PAM. The measurement results of contact angle and EWC of blend films indicate that the hydrophilicity of blend films decreases with the addition of PAM, but the EWC of blends increases with the addition of PAM.     

Depletion of monolayer liquid lubricant films induced by high-frequency pulsed-laser heating in thermally assisted magnetic recording

In this study, lubricant depletion due to high-frequency pulsed-laser heating was investigated for lubricant films with thicknesses of both more than and less than one monolayer. A conventional lubricant, Zdol2000, was used. It was found that the critical temperature at which the lubricant begins to deplete owing to laser heating was strongly dependent on the lubricant film thickness. In the case in which the thickness of the lubricant film was less than one monolayer, this temperature was approximately 170?°C higher than it was when the thickness was more than one monolayer. To analyze the lubricant depletion mechanism, we examined the tested lubricant film using temperature programmed desorption (TPD) spectroscopy. It was found that the lubricant depletion characteristics due to laser heating could be explained using the experimental TPD results for the tested lubricant film, and that the depletion mechanism involves the desorption or decomposition of the lubricant molecules, which interact with the diamond-like carbon thin films when the lubricant film thickness is less than one monolayer. Further, the results of TPD and of a thermogravimetric analysis (TGA) of the lubricant were compared. The thermal robustness of the ultra-thin liquid lubricant films was found to be greater than that of the bulk lubricant materials.     

Measurement of spreading characteristics of molecularly thin lubricant films over grooved solid surfaces based on diffraction simulations

Characteristics of molecularly thin lubricant films are basically determined by their interactions with solid surfaces. Since these interactions can be modified by engineered microscopic surface textures, it is expected that rational design of the textures will make it possible to attain desired tribological functions and performance. In this research, with the aim of applying it to head-disk interface of hard disk drives, we propose a method based on diffraction simulations that enables thickness measurement of molecularly thin films coated on grooved solid surfaces. Using this method, we experimentally investigate the spreading characteristics of nanometer-thick polymeric liquid lubricant films on grooved surfaces. The results revealed that the average thicknesses of the films dip-coated on the grooved and smooth surfaces under identical conditions were approximately the same, whereas lubricant spreading on grooved surfaces was significantly faster than that on smooth surfaces.     

Tribological characteristics of novel branched perfluoropolyether lubricant films in hard disk drives

In this study, the basic tribological characteristics of novel branched perfluoropolyether (PFPE) lubricant films such as TA-30 and QA-40 were examined. Their surface free energy characteristics and adhesive and friction forces were investigated using an atomic force microscope. The interactions between the lubricant molecules and the water molecules were also examined by monitoring the changes in the contact angle of distilled water on the test lubricant films. The interactive forces such as the adhesive and friction forces of a film that is approximately one monolayer thick were found to be strongly dependent on the conformation of the lubricant molecules on diamond-like carbon thin films. In addition, the TA-30 and QA-40 lubricant molecules appeared to interact with the water molecules more actively than conventional Ztetraol2000 molecules. These results afforded fundamental insight into the tribological performance of novel branched PFPE lubricants in the head-disk interface.     

Fabrication of layered polydimethylsiloxane/perfluoropolyether microfluidic devices with solvent compatibility and valve functionality

The development of multilayer soft lithography methodology has seen polydimethysiloxane (PDMS) as the preferred material for the fabrication of microfluidic devices. However, the functionality of these PDMS microfluidic chips is often limited by the poor chemical resistance of PDMS to certain solvents. Here, we propose the use of a photocurable perfluoropolyether (PFPE), specifically FOMBLIN^® MD40 PFPE, as a candidate material to provide a solvent-resistant buffer layer to make the device substantially impervious to chemically induced swelling. We first carried out a systematic study of the solvent resistance properties of FOMBLIN^® MD40 PFPE as compared with PDMS. The comparison presented here demonstrates the superiority of FOMBLIN^® MD40 PFPE over PDMS in this regard; moreover, the results permitted to categorize solvents in four different groups depending on their swelling ratio. We then present a step-by-step recipe for a novel fabrication process that uses multilayer lithography to construct a comprehensive solvent-resistant device with fluid and control channels integrated with a valve structure and also permitting easy establishment of outside connections.     

Prediction of three-dimensional structures and structural flexibilities of wild-type and mutant cytochrome P450 1A2 using molecular dynamics simulations

In this study, we investigated the effect of genetic polymorphism on the three-dimensional (3D) conformation of cytochrome P450 1A2 (CYP1A2) using molecular dynamics (MD) simulations. CYP1A2, a major drug-metabolizing enzyme among cytochrome P450 enzymes (CYPs), is known to have many variant alleles. The genetic polymorphism of CYP1A2 may cause individual differences in the pharmacokinetics of medicines. By performing 100 ns or longer MD simulations, we investigated the influence of amino acid mutation on the 3D structures and the dynamic properties of proteins. The results show that the static structures were changed by the mutations of amino acid residues, not only near the mutated residues but also in distant portions of the proteins. Moreover, the mutation of only one amino acid was shown to change the structural flexibility of proteins, which may influence the substrate recognition and enzymatic activity. Our results clearly suggest that it is necessary to investigate the dynamic property as well as the static 3D structure for understanding the change of the enzymatic activity of mutant CYP1A2.     

Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations

The brevity of molecular dynamics simulations often limits their utility in developing and evaluating structural models of proteins. The duration of simulations can be increased greatly using discrete molecular dynamics (DMD). However, the trade off is that coarse graining, implicit solvent, and other time-saving procedures reduce the accuracy of DMD simulations. Here we address some of these issues by comparing results of DMD and conventional all atom MD simulations on proteins of known structure and misfolded proteins. DMD simulations were performed at a range of temperatures to identify a 'physiological' temperature for DMD that mimicked molecular motions of conventional MD simulations at 310K. We also compared results obtained with a new implicit solvent model developed here based on Miyazawa-Jernigan interaction pair potential to those obtained with a previously used model based on Kyte-Doolittle hydropathy scale. We compared DMD and all atom molecular dynamics with explicit water by simulating both correctly and incorrectly folded structures, and monomeric and dimeric α β-barrel structures to analyze the ability of these procedures to distinguish between good and bad models. Deviations from the correct structures were substantially greater with DMD, as would be expected from coarse-graining and longer simulation time. Deviations were smallest for β-strands and greatest for coiled loops. Structures of the incorrectly folded models were very poorly preserved during the DMD simulations; but both methods were able to distinguish between the correct and the incorrect structures based on differences in the magnitudes of the root mean squared deviation (RMSD) from the starting conformation.     

Exploring the molecular basis of the enantioselective binding of penicillin G acylase towards a series of 2-aryloxyalkanoic acids: a docking and molecular dynamics study

In the present paper, molecular modeling studies were undertaken in order to shed light on the molecular basis of the observed enantioselectivity of penicillin G acylase (PGA), a well known enzyme for its industrial applications, towards 16 racemic 2-aryloxyalkanoic acids, which have been reported to affect several biological systems. With this intention docking calculations and MD simulations were performed. Docking results indicated that the (S)-enantiomers establish several electrostatic interactions with SerB1, SerB386 and ArgB263 of PGA. Conversely, the absence of specific polar interactions between the (R)-enantiomers and ArgB263 seems to be the main reason for the different binding affinities observed between the two enantiomers. Results of molecular dynamics simulations demonstrated that polar interactions are responsible for both the ligand affinity and PGA enantiospecificity. Modeling calculations provided possible explanations for the observed enantioselectivity of the enzyme that rationalize available experimental data and could be the basis for future protein engineering efforts.     

How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?

Aiming at understanding the molecular properties of the encapsulation of the anticancer drug gemcitabine in the single-walled carbon nanotube (SWCNT), molecular dynamics (MD) simulations were applied to the two scenarios; that of gemcitabine filling inside the SWCNT, and that of the drug in the free state. Inside the SWCNT, the cytosine ring of gemcitabine was found to form a π-π stacking conformation with the SWCNT surface, and this movement is not along the centerline of the tube from one end to the other of the tube where the distance from the center of gravity of the molecule to the surface is 4.7 ?. A tilted angle of 19° was detected between the cytosine ring of gemcitabine and the inner surface of SWCNT. In comparison to its conformation in the free form, no significant difference was observed on the torsion angle between the five- (ribose) and the six- (cytosine) membered rings. However, gemcitabine inside the SWCNT was found to have a lower number of solvating water molecules but with a stronger net solvation than the drug in the free state. This is due to the collaborative interactions between gemcitabine and the surface of the SWCNT. In addition, the steered molecular dynamics simulation (SMD) approach was employed to investigate the binding free energy for gemcitabine moving from one end to another end throughout the SWCNT. In excellent agreement with that yielded from the classical MD, the SMD energy profile confirms that the drug molecule prefers to locate inside the SWCNT.     

Diffusion of water molecules in crystalline beta-cyclodextrin hydrates

To understand the rapid diffusion mechanism of water molecules in the crystal lattice of hydrated beta-cyclodextrin (beta-CD), molecular dynamics (MD) simulations of crystalline beta-CD were performed at five different relative humidities corresponding to hydration states ranging from beta-CD-9.4H2O to beta-CD-12.3H2O, and in aqueous solution. The trajectories for the crystalline beta-CD hydrates had lengths of 4 ns each, whereas the simulation in aqueous solution extended to 2 ns. Transport of water molecules in the crystal was characterized in terms of a spatially varying diffusion constant and the main direction of diffusion, which were evaluated using newly developed algorithms. The main diffusion pathway winds through the cavities of adjacent doughnut shaped beta-CD molecules and is slightly slanted with respect to the crystallographic b-axis. Water molecules outside the beta-CD cavities have access to the main diffusion pathway. The diffusion constant for transport of water molecules along the main pathway calculated from the MD simulation data adopts 1/30 of the value in bulk water at room temperature. This is in agreement with estimates that can be made from experimental data on the adjustment of a beta-CD crystal to changes in relative humidity.     

Exploring the molecular basis of the enantioselective binding of penicillin G acylase towards a series of 2-aryloxyalkanoic acids: A docking and molecular dynamics study

In the present paper, molecular modeling studies were undertaken in order to shed light on the molecular basis of the observed enantioselectivity of penicillin G acylase (PGA), a well known enzyme for its industrial applications, towards 16 racemic 2-aryloxyalkanoic acids, which have been reported to affect several biological systems. With this intention docking calculations and MD simulations were performed. Docking results indicated that the (S)-enantiomers establish several electrostatic interactions with SerB1, SerB386 and ArgB263 of PGA. Conversely, the absence of specific polar interactions between the (R)-enantiomers and ArgB263 seems to be the main reason for the different binding affinities observed between the two enantiomers. Results of molecular dynamics simulations demonstrated that polar interactions are responsible for both the ligand affinity and PGA enantiospecificity. Modeling calculations provided possible explanations for the observed enantioselectivity of the enzyme that rationalize available experimental data and could be the basis for future protein engineering efforts.     

Separation based adsorption of ethanol–water mixture in azeotropic solution by single–walled carbon,boron-nitride and silicon-carbide nanotubes

The separation of the azeotropic ethanol-water mixture (95.57 wt% ethanol) over a wide range of pressures (100–100000 kPa) was studied on armchair SWCNTs, SWSiCNTs and SWBNNTs with different diameters at 351.30 K using GCMC simulations. The GCMC results demonstrated that ethanol and water molecules form a monolayer single-file, chain together in the center of (6,6) SWCNT, while a spiral ring of ethanol and water is formed in the center of (8,8), (10,10) and (12,12) SWCNTs. It was found that in SWCNTs, the adsorption of ethanol reduces the function of pressure, while water adsorption increases its function. Water selectivity rises as a function of pressure. Also, in SWBNNTs, the adsorption of water increases as a function of pressure, while ethanol adsorption is almost constant. However, in the case of SWSiCNTs, ethanol and water adsorptions are very similar to those of SWBNNTs, whereas the adsorptivities of SWSiCNTs are more than those of SWBNNTs. Our findings regarding adsorption and slope of adsorption indicate that higher pressures are favorable for separating water and ethanol by SWCNTs, while SWBNNTs and SWSiCNTs are demonstrate higher ethanol adsorptivities in lower pressures. Also, MD simulations have been performed to study the microscopic structure and diffusion of binary mixtures of water and ethanol within SWCNTs, SWSiCNTs and SWBNNTs. The MD simulations imply that the oxygen atoms are highly well-organized around themselves. Also, the MD results illustrate a similar tendency for oxygen of water (OW) and oxygen of ethanol (OE) to the wall of the nanotubes in all the pressures. In addition, from the MD results, self-diffusion of water and ethanol in all nanotubes were calculated and discussed.