The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method that allows very fast calculations and can be easily applied to arbitrarily complex knots. As an application, the specific energy and heat capacity of the trefoil, the figure-eight and the 81 knots are calculated at different temperatures and for different lengths. Short-range repulsive interactions between the monomers are assumed. The knots configurations are generated on a three-dimensional cubic lattice and sampled by means of the Wang-Landau algorithm and of the pivot method. The obtained results show that the topological effects play a key role for short-length polymers. Three temperature regimes of the growth rate of the internal energy of the system are distinguished.

Nanometre-size cobalt columns with tilt angle ranging from ∼0º to ∼40º and fixed density on Si(100) were fabricated by combining oblique-angle physical evaporation with controlled substrate motion. The column tilt angle can be controlled by the speed and phase of substrate rotation in addition to the angle of the incident vapour beam. A simple geometrical model is proposed to describe the relationship between the tilt angle of the cobalt columns and the rotational parameters (speed and phase), and is consistent with our experimental results.

As the on-chip interconnect linewidth and film thickness shrink below 0.1 µm, the size effect on Cu resistivity becomes important, and the electrical performance deliverable by such narrow metal lines needs to be assessed critically. From the fabrication viewpoint, it is also crucial to determine how structural parameters affect resistivity in the sub-0.1 µm feature size regime. To evaluate the scaling of resistivity with thickness, we have fabricated a series of Ta/Cu/Ta/SiO2 thin film structures with Cu thickness ranging from 1 µm to 0.02 µm. These test structures revealed a far larger (∼2.3 ×) size effect than that expected from surface scattering. We have also fabricated test structures containing 50-nm-wide Cu lines wrapped in Ta-based liners and embedded in insulating SiO2 using e-beam lithography, high-density plasma etching, ionized PVD Cu deposition, and chemical-mechanical planarization processes. Direct current (16 nA) resistance measurements from these 50-nm-wide Cu lines have also shown a higher- than-expected distribution of resistivity. Cross-sectional TEM and surface AFM observations suggest that the observed extra resistivity increase can be attributed to small grain sizes in ultra- thin Cu films and to Cu/Ta interface roughness. Monte Carlo simulations are used to quantify the extra resistivity resulting from interface roughness.

The folding of proteins with a complex knot is still an unresolved question. Based on representative members of Ubiquitin C-terminal Hydrolases (UCHs) that contain the 52 knot in the native state, we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model. In particular, we identify two, topologically different folding/unfolding pathways and corroborate our results with experiment, recreating the chevron plot. We show that confinement effect of chaperonin or weak crowding greatly facilitates folding, simultaneously slowing down the unfolding process of UCHs, compared with bulk conditions. Finally, we analyze the existence of knots in the denaturated state of UCHs. The results of the work show that the crowded environment of the cell should have a positive effect on the kinetics of complex knotted proteins, especially when proteins with deeper knots are found in this family.