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Molecular dynamics (MD) simulations were performed to investigate the adsorption behavior and dynamics of Arg-Gly-Asp (RGD) tripeptide onto the rutile TiO(2) (110) perfect and grooved surfaces in aqueous solution. The simulation results suggest that, driven by the electrostatic attractions between charged groups of the tripeptide and opposite-type charges of the surface atoms, RGD substitutes the adsorbed water molecules and binds to TiO(2) surface strongly through direct interactions of carboxyl oxygen (O(coo(-))) atoms with nearby titanium atoms in the interface, in agreement with some experimental observations and theoretical data. Once bonded to both perfect and grooved surfaces, RGD tripeptides show a reasonable propensity to remain there with the carboxyl groups providing anchors to the substrate surface, while the amide groups (NH(3)(+) and NH(2)) with larger separations from the attached portions, undergo relatively remarkable fluctuations during the whole simulation time. The trajectories for atom-surface distances, backbone dihedral angles and root-mean-squared deviations from the initial structure have revealed less mobility and more stable adsorption of RGD onto grooved surface than onto perfect surface, which is confirmed again by greater values of adsorption energy for available grooved surfaces.

Three-dimensional molecular dynamics simulations are conducted to investigate the effect of reciprocating nanomachining process on the subsurface damaged layers, surface integrity, cutting force, stress variation of subsurface, and changes of energy and defects in the workpiece. Results show that there is no obvious shear zone ahead the tool during nanomachining. Dislocation nucleations are near the free surface ahead the tool and the interface of the tool and the workpiece and propagate in the surface and downward in the workpiece. There are the generations of dislocation jog and dislocation loops ahead the tool during the reciprocating cutting. The values of the reciprocating cutting force for the (111) orientation and (100) orientation under offset distance of 0a0 are not zero but 11.756 and 13.0498 nN, respectively. When the offset distance of the tool is up to 10a0, the ratio of primary cutting force to reciprocating force is nearly 90%. The shape of the machined groove in the (111) orientation remains better than that in the (111) orientation in cases of both the primary cutting process and the reciprocating process. Reciprocating cutting with the offset distance of 5a0 of the tool results in the pile-up atoms filling in the primary machined groove and forming the order lattice by surface reconstruction. Primary cutting force decreases with the reduction of workpiece sizes, which shows the size effects. With the increasing cutting depths, average primary cutting force and average reciprocating force increase. It is noted that reciprocating cutting force in the case of the (111) workpiece is larger than that of the (100) orientation except for the offset distance of 0a0. With the increasing offset distance of the tool, the residual shear stress increases in the subsurface of the workpiece, and the order degree of subsurface atoms of the workpiece decreases in the cases of both the (111) orientation and (100) orientation. It is denoted that, with the offset distance at 5a0, the peak of the average shear stress is highest during the reciprocating cutting. Meanwhile, the order degree of subsurface atoms in the case of the (111) orientation is better than that of the (100) orientation.

Molecular dynamics simulations were performed to investigate the relaxed structures and surface energies of perfect and pit anatase TiO2 surfaces. It is shown that the slab containing more than two unit-cell layers away from the fixed layer expresses the surface characteristics of perfect anatase TiO2 (1 0 1) and (1 0 0) surfaces well, while the slab containing more than one unit-cell layer away from the fixed layer expresses the surface characteristics of the (0 0 1) surface well. Their surface energies follow the sequence (0 0 1) < (1 0 1) < (1 0 0). Simulation results also indicate that the pit edges expose many undercoordinated atoms, and the more highly undercoordinated atoms exhibit the larger displacement vectors. Moreover, the surface energy of the pit surface is higher than that of the perfect surface. The surface energies of pit anatase (1 0 1) surfaces are linearly related to the pit sizes along the [ ] and [0 1 0] directions, and the changes in their surface energies are less than 0.05 J m−2, while the surface energies increase sharply with the increase in pit depth within 1 nm. Therefore, for anatase (1 0 1) surface, in order to obtain a higher surface energy, one may increase the pit sizes, particularly along the [1 0 1] direction.