Tailoring the properties of PECVD deposited terpinen-4ol thin films

Polymer thin films have been of significant research interest in the field of, mechanics, optics, electronics and medicine. Bioactive coatings are extensively used in marine and medical field for the prevention of biofouling which is colonization of any wetted surface by flora and fauna. Fouling of the surfaces has severe implications for the performance of the material and biocide based coating have been used in the prevention of marine fouling. However, these coatings have adverse environmental effects. Natural antifouling products derived from organisms have been found to be an excellent alternative to biocide based strategies. Terpinen-4-ol derived from Australian Tea tree oil has antimicrobial properties. The Plasma enhanced chemical vapor deposition (PECVD) method has been used to develop environmentally friendly antifouling coating from Terpinen-4-ol. The effect of Process variables such as substrate temperature have been investigated on the PECVD of terpinen-4-ol. The influence of surface functionalization and the deposition mode of terpinen-4-ol plasma polymer on its antibacterial property has been studied. Coating created in the form of bilayer are tested for their marine antifouling behavior. The substrate temperature was found to influence the deposition mechanism of Terpinen-4-ol plasma polymers. Hydro Stable terpinen-4-ol plasma polymers were found to be formed at higher substrate temperature. Pulse plasma deposited films exhibited enhanced antibacterial performance. Grafting of ZnO nanoparticles onto the surface of the terpinen-4-ol polymer boosted the antibacterial and UV absorbing properties. The deposited bilayer coatings were effective in preventing the primary stage of marine biofouling. The bilayer acted as biocidal self-polishing coating

Modeling vitreous silica bilayers

We computer model a free-standing vitreous silica bilayer which has recently been synthesized and characterized experimentally in landmark work. Here we model the bilayer using a computer assembly procedure that starts from a single layer of amorphous graphene, generated using a bond switching algorithm from an initially crystalline graphene structure. Next each bond is decorated with an oxygen atom and the carbon atoms are relabeled as silicon. This monolayer can be now thought of as a two dimensional network of corner sharing triangles. Next each triangle is made into a tetrahedron, by raising the silicon atom above each triangle and adding an additional singly coordinated oxygen atom at the apex. The final step is to mirror reflect this layer to form a second layer and then attach the two layers together to form the bilayer. We show that this vitreous silica bilayer has the additional macroscopic degrees of freedom to easily form a network of identical corner sharing tetrahedra if there is a symmetry plane through the center of the bilayer going through the layer of oxygen ions that join the upper and lower layers. This has the consequence that the upper rings lie exactly above the lower rings, which are tilted in general. The assumption of a network of perfect corner sharing tetrahedra leads to a range of possible densities that we have previously characterized in three dimensional zeolites as a flexibility window. Finally, using a realistic potential, we have relaxed the bilayer to determine the density, and other structural characteristics such as the Si-Si pair distribution functions and the Si-O-Si bond angle distribution, which are compared to the experimental results obtained by direct imaging

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

Surface patterning for enhanced protein stability

by Avishek KumarM.Tech

Fabrication and characterisation of solid-phase crystallised plasma-deposited silicon thin films on glass for photovoltaic application

Ph.DDOCTOR OF PHILOSOPH