No description available.

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Here, we present the program QContacts, which implements Voronoi polyhedra to determine atomic and residue contacts across the interface of a protein-protein interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge interactions, we focus on QContacts’ identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible Surface Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface. The results were assessed based on a set of 71 double cycle mutants. QContacts excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and the delta-SASA methods performed well at picking out direct contacts; however, QContacts was the most accurate in excluding false positives. The significance of the differences identified between QContacts and previous methods was assessed using pair-wise contact frequencies in a broader set of 592 protein interfaces. The inaccuracies introduced by commonly used radial cutoff methods were found to produce misleading bias in the residue frequencies. This bias could compromise pair-wise potentials that are based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons (Fischer et al., 2006).

No description available.

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 7 uppsatser.

Isotherms of one atom thick film of adsorption for propane on purified Hipco single-walled carbon nanotube were experimentally studied at 6 different temperatures ranging from 190K up to 280K. In these isotherm measurements, two substeps were clearly present at temperatures between 190K and 220K. For propane adsorption, two different groups of binding energy sites on the nanotubes were determined by the outcome. Also, we found that those substeps were gradually smearing as the temperature increases. These features of propane adsorption were compared to the same features that were present for the case of ethane and butane adsorption on the same sample. In comparison, high binding energy sites revealed by low pressure substeps were clearly visible in all the cases. However, the high pressure substep that represents a low binding energy site, external surface site, was smearing as carbon chain length of adsorbed alkanes increase. For the case of butane adsorption, the substep was not pronounced in the alkanes' isotherms at the relative temperatures. We also determined a decrease in the values of specific surface area of the nanotubes and an increase in the values of binding energies of alkanes on the substrate were increased as the sizes and lengths of linear carbon alkanes were increased.

Nanoporous polymer fibres are currently attracting increasing interest due to their unique characteristics. Increased specific surface area, improved mechanical properties and improved cellular growth are amongst the advantages that set porous fibres as ideal candidates in applications like catalysis, separation and tissue engineering. This work explores the single step production of porous poly(ε-caprolactone) (PCL) fibres through combinative electrospinning and Non-solvent Induced Phase Separation (NIPS) technique. Theoretical models, based on three different contact models (Hertzian, DMT, JKR), correlating the fibrous network specific surface area to material properties (density, surface tension, Young s modulus, Poisson s ratio) and network physical properties (density) and geometrical characteristics (fibre radius, fibre aspect ratio, network thickness) were developed in order to calculate the surface area increase caused by pore induction. Experimental results proved that a specific surface area increase of up to 56% could be achieved, compared to networks composed of smooth surfaced fibres. The good solvent effect on electrospun fibre surface morphology and size was examined through experimental investigation of four different good solvent (chloroform, dichloromethane, tetrahydrofuran and formic acid) based solutions at various good/poor solvent ratios. Chloroform was proven to be the most suitable solvent for good /poor solvent ratios varying from 75-90% v/v, whereas alternative mechanisms leading to different fibre morphologies were identified, interpreted and discussed. Evaporation rate of the good solvent was identified as the key parameter of the process. Second order polynomial equations, derived from the experimental data, correlating the feed solution physical parameters (viscosity, conductivity, surface tension) to the fibre average diameter produced were developed and validated. Response surface methodology was implemented for the design and conduction of electrospinning experiments on a 12.5 % w/v Chloroform/DMSO solution 90/10 % v/v in order to determine the individual process parameters (spinning distance, applied voltage, solution flow rate) effect in fibre surface morphology and size. The increase in any of these parameters results in increase of both the fibre size and the tendency for pore generation, whereas applied voltage was the parameter with the strongest effect. Findings from this thesis expand the knowledge about both phenomena occurring during the production process and end product properties, and can be used for the production of controlled morphology and size porous poly(ε-caprolactone) (PCL) fibres.

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