Identifying the mechanisms of polymer friction through molecular dynamics simulation.

Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused.

Molecular simulation of the frictional behavior of polymer-on-polymer sliding.

Molecular simulations of the sliding processes of polymer-on-polymer systems were performed to investigate the surface and subsurface deformations and how these affect tribological characteristics of nanometer-scale polymer films. It is shown that a very severe deformation is localized to a band of material about 2.5 nm thick at the interface of the polymer surfaces. Outside of this band, the polymer films experience a uniform shear strain that reaches a finite steady-state value of close to 100%. Only after the polymer films have achieved this steady-state shear strain do the contacting surfaces of the films show significant relative slippage over each other. Because severe deformation is limited to a localized band much thinner than the polymeric films, the thickness of the deformation band is envisaged to be independent of the film thickness and hence frictional forces are expected to be independent of the thickness of the polymer films. A strong dependency of friction on interfacial adhesion, surface roughness, and the shear modulus of the sliding system was observed. Although the simulations showed that frictional forces increase linearly with contact pressure, adhesive forces contribute significantly to the overall friction and must therefore be accounted for in nanometer-scale friction. It is also shown that the coefficient of friction is lower for lower-density polymers as well as for polymers with higher molecular weights.

Investigation of the binding preference of reovirus sigma1 for junctional adhesion molecule A by classical and steered molecular dynamics.

Biochemical studies have determined that reoviruses attach to cells by combining attachment protein sigma1 to the binding interface of its receptor protein junctional adhesion molecule A (JAM-A), and the interface normally takes care of the homodimerization of JAM-A. Tighter binding and slower dissociation of for the sigma1-JAM complex than for the JAM-JAM complex have been probed by both biological and atomic force microscopy experiments; however, the mechanism of the binding preference of the attachment protein for JAM-A still remains unclear. With the help of classical and steered molecular dynamics and energy calculations, the unbinding forces and kinetic properties of the complexes are investigated, together with detailed structural information analyses. A multireceptor mechanism is proposed for the binding preference, which can be helpful for future viral infection and vector targeting studies.

Molecular dynamics simulation of ZnO nanowires: size effects, defects, and super ductility.

Molecular dynamics simulations of ZnO nanowires under tensile loading were performed and compared with simulations of TiO(2) wires to present size-dependent mechanical properties and super ductility of metal oxide wires. It is shown that while large surface-to-volume ratio is responsible for their size effects, ZnO and TiO(2) wires displayed opposite trends. Although the stiffness of both wires converged monotonically to their bulk stiffness values as diameter increases, bulk stiffness represented the upper bound for ZnO nanowires as opposed to the lower bound for TiO(2) wires. ZnO nanowires relaxed to either completely amorphous or completely crystalline states depending on wire thickness, whereas a thin amorphous shell is always present in TiO(2) nanowires. It was also found that when crystalline ZnO nanowires are stretched, necking initiated at localized amorphous regions to eventually form single-atom chains which can sustain strains above 100%. Such large elongations are not observed in TiO(2) nanowires. Using the analogy of a clothesline, an explanation is offered for the necessary conditions leading to super ductility.

Buckling of carbon nanotubes at high temperatures.

Presented herein is an investigation into the buckling behavior of single-walled carbon nanotubes (SWCNT) subjected to axial compression and torsion at high temperatures. This study is carried out by performing molecular dynamics (MD) simulations at both room temperature and extremely high temperatures. It is observed that the SWCNT becomes more susceptible to buckling in a higher temperature environment, especially when the SWCNT is subject to axial compression. The high thermal energy enhances the vibration of carbon atoms in the SWCNT significantly, which leads to bond breaking and the formation of sp(3) bonds as well as Stone-Wales (SW) defects in the postbuckling stage.

Atomistic simulations of inorganic nanowires.

Inorganic nanowires, such as those of metals, semiconductors and oxides, have attracted much research interest due to their unique material properties and present many possibilities for the development of revolutionary applications in materials science and technology. There are abundant reports on experimental works covering various aspects of nanowires including fabrication, structural analysis and property characterization. Theoretical studies have also been carried out to provide researchers with a better understanding of nanowire structural characteristics and the mechanisms that affect their properties. This report gives a brief introduction to the numerical methodologies commonly used for the analysis of nanowires followed by a review of theoretical works focusing on the unique structures of nanowires, their stability and related mechanical properties. The current state of research and development of nanowires is presented together with some comments on the future direction of theoretical studies on inorganic nanowires.

Glass transition temperature influence on crosslinked and entangled polymer interfaces.

The influence of glass transition temperature (Tg) on crosslinked and entangled polymer interfaces was investigated using coarse grained molecular dynamics (MD). A crosslinked polymer interface and an entangled polymer interface were built and the Tg for each system were obtained by confining a thin film between two rigid walls. The physical properties of each system above and under Tg were compared. The mechanical properties were also explored by pulling the interfaces apart at different temperature. The results are qualitatively agreed with experimental observations. Furthermore, the present results show that, when under tensile loading at temperature higher than Tg, the entangled interface exhibits strain softening while the crosslinked thin film is still able to show strain hardening. The different performances may due to that, at high temperature, the high mobility of monomers tend to unravel the entangled chain in linear polymer system while in crosslinked system, monomers with high mobility tend to arrest the void and decrease the void propagation.

Multiscale modeling of polymers-bridging the molecular continuum divide.

A method to reduce the degrees freedom in molecular mechanics simulation is presented. Although the approach is formulated for amorphous materials, it is equally applicable to crystalline materials. The method is selectively applied to regions where molecular displacements are expected to be small while simultaneously using classical molecular mechanics for regions undergoing large deformation. Its accuracy and computational efficiency are demonstrated through the simulation of a polymer-like substrate indented by a rigid indentor. The region directly below the indentor is modelled by classical molecular mechanics while the region further away has the degrees of freedom reduced by about 50 times.

Buckling of carbon nanotubes: a literature survey.

This survey paper comprises 5 sections. In Section 1, the reader is introduced to the world of carbon nanotubes where their structural form and properties are highlighted. Section 2 presents the various buckling behaviors exhibited by carbon nanotubes that are discovered by carbon nanotube researchers. The main factors, such as dimensions, boundary conditions, temperature, strain rate and chirality, influencing the buckling behaviors are discussed in Section 3. Section 4 presents the continuum models, atomistic simulations and experimental techniques in studying the buckling phenomena of carbon nanotubes. A summary as well as recommendations for future research are given in Section 5. Finally a large body of papers, over 200, is given in the reference section. It is hoped that this survey paper will provide the foundation knowledge on carbon nanotube buckling and inspire researchers to advance the modeling, simulation and design of carbon nanotubes for practical applications.

Numerical investigations into the tensile behavior of TiO(2) nanowires: structural deformation, mechanical properties, and size effects.

The mechanisms governing the tensile behavior of TiO(2) nanowires were studied by molecular dynamics simulations. Nanowires below a threshold diameter of about 10 A transformed into a completely disordered structure after thermodynamic equilibration, whereas thicker nanowires retained their crystalline core. Initial elastic tensile deformation was effected by the reconfiguration of surface atoms while larger elongations resulted in continuous cycles of Ti-O bond straightening, bond breakage, inner atomic distortion, and necking until rupture. Nanowires have much better mechanical properties than bulk TiO(2). Nanowires below the threshold diameter exhibit extraordinarily high stiffness and toughness and are more sensitive to strain rate.

Significance of water molecules in the inhibition of cylin-dependent kinase 2 and 5 complexes.

Interest in CDK2 and CDK5 has stemmed mainly from their association with cancer and neuronal migration or differentiation related diseases and the need to design selective inhibitors for these kinases. In the present paper, eight Molecular Dynamics (MD) simulations are carried out to examine the importance of structure and dynamics of water in the active site of both CDK2 and CDK5 complexes with roscovitine and indirubin analogues. Together with previous results, the current work shows a highly conserved water-involved hydrogen bonding (HB) network in both CDK2- and CDK5-indirubin combinations to complete information from the X-ray crystallography. The simulations suggest the importance of such a network for combining the inhibitor to the host protein as well as the significance of using an activated CDK as a template when designing new inhibitors. Different binding patterns of roscovitine in CDK2 and CDK5 are detected during the simulations because of the different binding conformations of the group on the C2 side chain, which might offer a clue toward finding highly selective inhibitors with regards to CDK2 and CDK5.

The activation and inhibition of cyclin-dependent kinase-5 by phosphorylation.

Despite the very similar 3-dimensional structures as reflected by the more than 60% identity in amino acid sequences, CDK2 and CDK5 have very different functions and characteristics. Phosphorylation on a conserved Thr14 can inhibit activities of both the kinases, but phosphorylating another conserved Tyr15, however, can lead to totally opposite inhibition and stimulation consequences in CDK2 and CDK5. Our molecular dynamics (MD) simulations suggest a similar inhibition mechanism of phosphorylation on the Thr14 as in the CDK2 system. In both the systems, the kinase activities are inhibited by the phosphorylation because it causes ATP phosphate moiety misalignment and changes in the Mg2+ ion coordination sphere, which have been proven to be critical for the phosphate group of the ATP transferring to the hydroxyl group on the serine in the substrate peptide. The calculations indicate that ATP adopts a more favorable conformation and location in the phosphorylated Tyr15 complex to facilitate the interactions with the substrate and the Mg2+ is wrapped more strongly by the phosphate group than in the unphosphorylated system, which might be favored by the transfer reaction.