Helix-coil-transition in solid polypeptides

Abstract Poly(L-glutamic acid) (PLGA) was synthesized by living anionic ring-opening polymerization of the NCA monomer, which was obtained by reacting diphosgene with an amino acid derivative. The chemical structures and thermal properties were characterized by 1H-NMR, 13C-NMR, TGA and DSC. XRD powder patterns found to be amorphous for all polymers obtained. The molecular weights could be determined under severe limitations due to low solubility and high aggregation tendency. The secondary structure of the PLGA films was analyzed in the solid state by IR spectroscopy; the order was determined mainly by XRD. Uniform bulk films (1-5 µm) were produced by drop-casting of PLGA solutions in TFA on silica. The XRD film analysis indicated the absence of a long range order or an orientation even if a helical microstructure was confirmed by IR spectroscopy. The coil solvent TFA delivered constantly a helical or a β-sheet structure in the solid state depending on the water content of the solvent which was observed for the first time to exhibit a high influence on the crystallization process for PLGA. Temperature dependent in-situ IR measurements were examined to analyze if a helix-coil transition occurs, but there could be no solvent system determined, which resulted in a disordered coil structure in the solid state. General parameters like solvent systems, evaporation conditions, concentration, substrates etc. were analyzed. New crystallizations were obtained on silica prepared by drop-casting of solutions of PLGA in DMF, DMA, TMU, NMP, and pyridine/water mixtures, respectively. PSCBC in DMF, CDCl3/TFA-d, and PSBC in CDCl3/TFA-d exhibited the same crystalline diffraction patterns like PLGA. The long range order in the X-ray diffraction pattern is proven by extremely sharp crystalline signals, which are not changing the shape or the position of the peak by increasing the temperature up to 160°C. The substrate seems to play a decisive role because the crystalline structures were not obtainable on glass. The crystal structure consists probably of two different layered structures based on the intensity ratios of the two series of crystalline signals in the X-ray diffraction patterns. The source of the layered structure remains unclear and needs further studies to investigate the spatial arrangement of the chains in more detail. The secondary structure was still not changing upon heating even if a highly crystalline diffraction pattern occurs. Concluding that even the newly investigated crystallization did not show a helix-coil transition in the solid state by annealing, the phenomenon known in solution has to be claimed as unachievable in the solid state based on the results of this work. A remaining open question represents the observation that the same crystalline pattern can be reproducibly prepared with exhibiting two different ordered secondary structures (helix and β-sheet). After the investigation that the evaporation time cannot be decisive for the crystal growth, the choice of a strong hydrogen bonding interrupting solvent is most probably the key to support and induce the crystallization process.

Development of empirical potentials for amorphous silica

Development of empirical potentials for amorphous silica Amorphous silica (SiO2) is of great importance in geoscience and mineralogy as well as a raw material in glass industry. Its structure is characterized as a disordered continuous network of SiO4 tetrahedra. Many efforts have been undertaken to understand the microscopic properties of silica by classical molecular dynamics (MD) simulations. In this method the interatomic interactions are modeled by an effective potential that does not take explicitely into account the electronic degrees of freedom. In this work, we propose a new methodology to parameterize such a potential for silica using ab initio simulations, namely Car-Parrinello (CP) method [Phys. Rev. Lett. 55, 2471 (1985)]. The new potential proposed is compared to the BKS potential [Phys. Rev. Lett. 64, 1955 (1990)] that is considered as the benchmark potential for silica. First, CP simulations have been performed on a liquid silica sample at 3600 K. The structural features so obtained have been compared to the ones predicted by the classical BKS potential. Regarding the bond lengths the BKS tends to underestimate the Si-O bond whereas the Si-Si bond is overestimated. The inter-tetrahedral angular distribution functions are also not well described by the BKS potential. The corresponding mean value of theSiOSi angle is found to be ≃ 147◦, while the CP yields to aSiOSi angle centered around 135◦. Our aim is to fit a classical Born-Mayer/Coulomb pair potential using ab initio calculations. To this end, we use the force-matching method proposed by Ercolessi and Adams [Europhys. Lett. 26, 583 (1994)]. The CP configurations and their corresponding interatomic forces have been considered for a least square fitting procedure. The classical MD simulations with the resulting potential have lead to a structure that is very different from the CP one. Therefore, a different fitting criterion based on the CP partial pair correlation functions was applied. Using this approach the resulting potential shows a better agreement with the CP data than the BKS ones: pair correlation functions, angular distribution functions, structure factors, density of states and pressure/density were improved. At low temperature, the diffusion coefficients appear to be three times higher than those predicted by the BKS model, however showing a similar temperature dependence. Calculations have also been carried out on crystalline samples in order to check the transferability of the potential. The equilibrium geometry as well as the elastic constants of α-quartz at 0 K are well described by our new potential although the crystalline phases have not been considered for the parameterization. We have developed a new potential for silica which represents an improvement over the pair potentials class proposed so far. Furthermore, the fitting methodology that has been developed in this work can be applied to other network forming systems such as germania as well as mixtures of SiO2 with other oxides (e.g. Al2O3, K2O, Na2O).

Manufacturing and characterization of amorphous silicon alloys passivation layers for silicon hetero-junction solar cells

Nel presente lavoro di tesi magistrale sono stati depositati e caratterizzati film sottili (circa 10 nm) di silicio amorfo idrogenato (a-Si:H), studiando in particolare leghe a basso contenuto di ossigeno e carbonio. Tali layer andranno ad essere implementati come strati di passivazione per wafer di Si monocristallino in celle solari ad eterogiunzione HIT (heterojunctions with intrinsic thin layer), con le quali recentemente è stato raggiunto il record di efficienza pari a 24.7% . La deposizione è avvenuta mediante PECVD (plasma enhanced chemical vapour deposition). Tecniche di spettroscopia ottica, come FT-IR (Fourier transform infrared spectroscopy) e SE (spettroscopic ellipsometry) sono state utilizzate per analizzare le configurazioni di legami eteronucleari (Si-H, Si-O, Si-C) e le proprietà strutturali dei film sottili: un nuovo metodo è stato implementato per calcolare i contenuti atomici di H, O e C da misure ottiche. In tal modo è stato possibile osservare come una bassa incorporazione (< 10%) di ossigeno e carbonio sia sufficiente ad aumentare la porosità ed il grado di disordine a lungo raggio del materiale: relativamente a quest’ultimo aspetto, è stata sviluppata una nuova tecnica per determinare dagli spettri ellisometrici l’energia di Urbach, che esprime la coda esponenziale interna al gap in semiconduttori amorfi e fornisce una stima degli stati elettronici in presenza di disordine reticolare. Nella seconda parte della tesi sono stati sviluppati esperimenti di annealing isocrono, in modo da studiare i processi di cristallizzazione e di effusione dell’idrogeno, correlandoli con la degradazione delle proprietà optoelettroniche. L’analisi dei differenti risultati ottenuti studiando queste particolari leghe (a-SiOx e a-SiCy) ha permesso di concludere che solo con una bassa percentuale di ossigeno o carbonio, i.e. < 3.5 %, è possibile migliorare la risposta termica dello specifico layer, ritardando i fenomeni di degradazione di circa 50°C.

Charge transport in amorphous organic semiconductors

Organic semiconductors with the unique combination of electronic and mechanical properties may offer cost-effective ways of realizing many electronic applications, e.g. large-area flexible displays, printed integrated circuits and plastic solar cells. In order to facilitate the rational compound design of organic semiconductors, it is essential to understand relevant physical properties e.g. charge transport. This, however, is not straightforward, since physical models operating on different time and length scales need to be combined. First, the material morphology has to be known at an atomistic scale. For this atomistic molecular dynamics simulations can be employed, provided that an atomistic force field is available. Otherwise it has to be developed based on the existing force fields and first principle calculations. However, atomistic simulations are typically limited to the nanometer length- and nanosecond time-scales. To overcome these limitations, systematic coarse-graining techniques can be used. In the first part of this thesis, it is demonstrated how a force field can be parameterized for a typical organic molecule. Then different coarse-graining approaches are introduced together with the analysis of their advantages and problems. When atomistic morphology is available, charge transport can be studied by combining the high-temperature Marcus theory with kinetic Monte Carlo simulations. The approach is applied to the hole transport in amorphous films of tris(8-hydroxyquinoline)aluminium (Alq3). First the influence of the force field parameters and the corresponding morphological changes on charge transport is studied. It is shown that the energetic disorder plays an important role for amorphous Alq3, defining charge carrier dynamics. Its spatial correlations govern the Poole-Frenkel behavior of the charge carrier mobility. It is found that hole transport is dispersive for system sizes accessible to simulations, meaning that calculated mobilities depend strongly on the system size. A method for extrapolating calculated mobilities to the infinite system size is proposed, allowing direct comparison of simulation results and time-of-flight experiments. The extracted value of the nondispersive hole mobility and its electric field dependence for amorphous Alq3 agree well with the experimental results.

Alternative derivative expansion in Functional RG and application

We give a brief review of the Functional Renormalization method in quantum field theory, which is intrinsically non perturbative, in terms of both the Polchinski equation for the Wilsonian action and the Wetterich equation for the generator of the proper verteces. For the latter case we show a simple application for a theory with one real scalar field within the LPA and LPA' approximations. For the first case, instead, we give a covariant "Hamiltonian" version of the Polchinski equation which consists in doing a Legendre transform of the flow for the corresponding effective Lagrangian replacing arbitrary high order derivative of fields with momenta fields. This approach is suitable for studying new truncations in the derivative expansion. We apply this formulation for a theory with one real scalar field and, as a novel result, derive the flow equations for a theory with N real scalar fields with the O(N) internal symmetry. Within this new approach we analyze numerically the scaling solutions for N=1 in d=3 (critical Ising model), at the leading order in the derivative expansion with an infinite number of couplings, encoded in two functions V(phi) and Z(phi), obtaining an estimate for the quantum anomalous dimension with a 10% accuracy (confronting with Monte Carlo results).

NCX-1000, a nitric oxide-releasing derivative of UDCA, does not decrease portal pressure in patients with cirrhosis: results of a randomized, double-blind, dose-escalating study

NCX-1000 (2(acetyloxy) benzoic acid-3(nitrooxymethyl)phenyl ester) is an nitric oxide (NO)-releasing derivative of ursodeoxycholic acid (UDCA), which showed selective vasodilatory effect on intrahepatic circulation in animal models of cirrhosis. This study was aimed at testing the efficacy and tolerability of this compound in patients with cirrhosis and portal hypertension.

Clinical Outcomes Following Treatment of Non-contained Intrabony Defects with Enamel Matrix Derivative (EMD) or Guided Tissue Regeneration (GTR). A 12-month Randomized Controlled Clinical trial

The purpose of this study is to compare the healing of deep, non-contained intrabony defects (i.e., with a ?80% 1-wall component and a residual 2- to 3-wall component in the most apical part) treated with either an enamel matrix derivative (EMD) or guided tissue regeneration (GTR) after 12 months.

Healing of two and three wall intrabony periodontal defects following treatment with an enamel matrix derivative combined with autogenous bone

BACKGROUND: There are still limited data on the outcomes of regenerative periodontal surgery using a combination of an enamel matrix protein derivative (EMD) and autogenous bone (AB). AIM: To evaluate the healing of deep intrabony defects treated with either a combination EMD+AB or EMD alone. MATERIALS AND METHODS: Forty patients with advanced chronic periodontitis, with one deep intrabony defect, were randomly treated with either EMD+AB (test) or EMD (control). Clinical assessments were performed at baseline and at 1 year after treatment. The primary outcome variable was relative attachment level (RAL). RESULTS: Healing was uneventful in all patients. The test sites showed a reduction in the mean probing pocket depth (PPD) of 5.6 +/- 0.9 mm (p<0.001), a gain in the mean RAL of 4.2 +/- 1.1 mm (p<0.001) and a gain in the mean probing bone level (PBL) of 3.9 +/- 1.0 mm (p<0.001). The control group displayed a mean PPD reduction of 4.6 +/- 0.4 mm (p<0.001), a mean RAL gain of 3.4 +/- 0.8 mm (p<0.001) and a mean PBL gain of 2.8 +/- 0.8 mm (p<0.001). RAL gains of > or =4 mm were measured in 90% of the test defects and in 55% of the controls. PBL gains of > or =4 mm were obtained in 85% of the test defects and in 25% of the control ones. The test treatment resulted in statistically higher PPD reductions, RAL gains and PBL gains compared with the control (p<0.01). CONCLUSIONS: Within their limits, the present results indicate that: (i) at 1 year after surgery, both therapies resulted in statistically significant clinical improvements compared with baseline and (ii) although the combination of EMD+AB resulted in statistically significant higher soft and hard tissue improvements compared with treatment with EMD, the clinical relevance of this finding is unclear.

The quassinoid derivative NBT-272 targets both the AKT and ERK signaling pathways in embryonal tumors

The quassinoid analogue NBT-272 has been reported to inhibit MYC, thus warranting a further effort 7to better understand its preclinical properties in models of embryonal tumors (ET), a family of childhood malignancies sharing relevant biological and genetic features such as deregulated expression of MYC oncogenes. In our study, NBT-272 displayed a strong antiproliferative activity in vitro that resulted from the combination of diverse biological effects, ranging from G(1)/S arrest of the cell cycle to apoptosis and autophagy. The compound prevented the full activation of both eukaryotic translation initiation factor 4E (eIF4E) and its binding protein 4EBP-1, regulating cap-dependent protein translation. Interestingly, all responses induced by NBT-272 in ET could be attributed to interference with 2 main proproliferative signaling pathways, that is, the AKT and the MEK/extracellular signal-regulated kinase pathways. These findings also suggested that the depleting effect of NBT-272 on MYC protein expression occurred via indirect mechanisms, rather than selective inhibition. Finally, the ability of NBT-272 to arrest tumor growth in a xenograft model of neuroblastoma plays a role in the strong antitumor activity of this compound, both in vitro and in vivo, with its potential to target cell-survival pathways that are relevant for the development and progression of ET.

Effect of enamel matrix derivative and parathyroid hormone on bone formation in standardized osseous defects: an experimental study in minipigs

Previous experimental studies have indicated that locally administered enamel matrix derivative (EMD) and parathyroid hormone (PTH) may have a stimulatory effect on bone formation. However, it is not clear if the positive effect of EMD is related to its effect on the periodontium as a whole or directly on the bone-forming cells. In addition, it is not known if the presentation of PTH by adding the amino acid sequence Arg-Gly-Asp (RGD) is essential for its osteopromotive effect. Local delivery of a bioactive substance at the right time and in the right concentration often constitutes a major challenge. Polyethylene glycol-based hydrogel (PEG) is a degradable vehicle developed for delivery of bioactive proteins. To enhance the mechanical stability of the PEG-bioactive substance complex, an osteoconductive bone substitute material is often needed.

Four-year results following treatment of intrabony periodontal defects with an enamel matrix derivative alone or combined with a biphasic calcium phosphate

The aim of this study was to evaluate the 4-year clinical outcomes following regenerative surgery in intrabony defects with either EMD + BCP or EMD. Twenty-four patients with advanced chronic periodontitis, displaying one-, two-, or three-walled intrabony defect with a probing depth of at least 6 mm, were randomly treated with either EMD + BCP (test) or EMD alone (control). The following clinical parameters were evaluated at baseline, at 1 year and at 4 years after regenerative surgery: plaque index, gingival index, bleeding on probing, probing depth, gingival recession, and clinical attachment level (CAL). The primary outcome variable was CAL. No differences in any of the investigated parameters were observed at baseline between the two groups. The test group demonstrated a mean CAL change from from 10.8 ± 1.6 mm to 7.4 ± 1.6 mm (p < 0.001) and to 7.6 ± 1.7 mm (p < 0.001) at 1 and 4 years, respectively. In the control group, mean CAL changed from 10.4 ± 1.3 at baseline to 6.9 ± 1.0 mm (p < 0.001) at 1 year and 7.2 ± 1.2 mm (p < 0.001) at 4 years. At 4 years, two defects in the test group and three defects in the control group have lost 1 mm of the CAL gained at 1 year. Compared to baseline, at 4 years, a CAL gain of ≥3 mm was measured in 67% of the defects (i.e., in 8 out of 12) in the test group and in 75% of the defects (i.e., in 9 out of 12) in the control group. There were no statistically significant differences in any of the investigated parameters at 1 and at 4 years between the two groups. Within their limits, the present results indicate that: (a) the clinical improvements obtained with both treatments can be maintained over a period of 4 years, and (b) in two- and three-walled intrabony defects, the addition of BCP did not additionally improve the outcomes obtained with EMD alone. In two- and three-walled intrabony defects, the combination of EMD + BCP did not show any advantage over the use of EMD alone.

Pharmacokinetics and pharmacodynamic effects of meloxicam in piglets subjected to a kaolin inflammation model

The pharmacokinetics and the analgesic, anti-inflammatory and antipyretic effects of meloxicam were investigated in a placebo controlled study in 2-week-old piglets. Inflammation was induced by a subcutaneous injection of kaolin in the left metacarpus, and 16 h later, meloxicam (0.6 mg/kg) or saline was administered intramuscularly. The absorption half-life was relatively short (0.19 h) and the elimination half-life was 2.6 h. Mechanical nociceptive threshold testing was used to evaluate the analgesic effect, but no significant effect of the meloxicam treatment was found. The skin temperature of the inflamed area increased after the kaolin injection, but no significant decrease in temperature was found after administration of meloxicam. Only limited pyresis was observed after the kaolin injection, and no significant antipyretic effect of meloxicam was found. The results indicated that this dose of meloxicam had very limited anti-inflammatory and analgesic effects in piglets.