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1.
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Ario de Marco, Miguel Soler, Sara Fortuna, 2016, izvirni znanstveni članek

Opis: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Najdeno v: ključnih besedah
Ključne besede: nanobodies, molecular dynamics, modeling, antibody solubility
Objavljeno: 11.10.2016; Ogledov: 1076; Prenosov: 100
.pdf Polno besedilo (1,95 MB)

2.
Efficient de-agglomeration of polysilane macromolecules in solution and their molecular size
Matjaž Valant, Mattia Fanetti, Artem V. Badasyan, Andraž Mavrič, 2017, objavljeni povzetek znanstvenega prispevka na konferenci

Najdeno v: ključnih besedah
Povzetek najdenega: ...polysilane, solubility, de-agglomeration, dynamic light scattering...
Ključne besede: polysilane, solubility, de-agglomeration, dynamic light scattering
Objavljeno: 03.07.2017; Ogledov: 958; Prenosov: 0
.pdf Polno besedilo (1,81 MB)

3.
FROM SPINODAL DECOMPOSITION AND MOLECULAR DISPERSION OF POLYSILANES TO SUPER-HARD NANOCOATING
Artem V. Badasyan, Boštjan Mavrič, Matjaž Valant, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: Conformations of polymer molecules in solution crucially depend on the sign of the effective potential energy of interaction between the monomers, also known as the quality of solvent. Therefore in “poor” solvent regime, when effective attraction overwhelms, the experimental measurements of polymer sizes are complicated by the agglomeration of macromolecules, followed by precipitation. This phenomenon, also known as spinodal decomposition, causes serious problems when the goal is to determine properties of individual macromolecules. Interestingly, while in the case of carbon-based polymers the precipitation-related problems can be easily avoided with dilution, this is not the case for polysilanes, i.e. polymeric chains on basis of silicon. Although the linear polysilanes were first synthesized in early 1920’s, the aggregationrelated problems have hampered their studies and applicability until recently. In the Materials Research Laboratory of University of Nova Gorica we have developed a technology to strengthen the scratch-resistance nanocoating for glass on the basis of polysilane dendritic polymers we synthesized. Through the prism of the Flory-Huggins theory, that provides a miscibility phase diagram in temperature-volume fraction variables, the quality of polymer solution can be manipulated by changing the temperature. Using Dynamic Light Scattering (DLS) and Differential Scanning Calorimetry (DSC) we have managed to show, that at temperatures in the range of 40- 50 C the deagglomeration of the dendritic polysilane takes place in tetrahydrofuran (THF) [1], and the system becomes a true molecular dispersion with particles 20 nm in size [2]. Introducing such molecular dispersion into the alumina precursor solution yields an amorphous nanocomposite stabilized by a high level of strain. This resulted in an extraordinary increase of hardness and scratch resistance of the alumina – polymer nanocomposite coating that can be used for glass protection [3].
Najdeno v: ključnih besedah
Ključne besede: Polysilane, dendrimer, solubility
Objavljeno: 12.09.2017; Ogledov: 740; Prenosov: 0
.pdf Polno besedilo (53,55 KB)

4.
Amorphous nanocomposite of polycarbosilanes and aluminum oxide
Andraž Mavrič, 2018, doktorska disertacija

Opis: This work presents a paradigm for high temperature stabilization of bulk amorphous aluminium oxide. The thermodynamic stabilization is achieved by preparing a nanocomposite, where polymethylsilane dendritic molecules are dispersed in an aluminium hydroxide gel. Upon heat-treatment the gel transforms to the amorphous aluminium oxide that is stable up to 900°C. The dispersion of the macromolecules and their covalent bonding to the alumina matrix induce homogeneously distributed strain fields that keep the alumina amorphous. The first part of the thesis focuses on the synthesis, characterization and solubility properties of the dendritic polymethylsilane. The polymethylsilane is synthetized by electrochemical polymerization from trichloromethylsilane monomer. The polymerization mechanism, involving a single polymerization pathway, is identified. The polymer growth proceeds through reduction of the monomers to the silyl anions and their addition to the growing polymer. The solubility of three chemically related but topologically different polysilanes (linear, dendritic and network) were studied by dynamic light scattering. At room temperature the agglomerates in a range from 500 to 1300 nm are present. They undergo de-agglomeration at slightly elevated temperatures of around 40°C. The de-agglomeration results in formation of stable solutions, where a hydrodynamic diameter of the individual polymer molecules was measured to be in a range from 20 to 40 nm. The obtained diameters of two dendritic polymethylsilane macromolecules, synthesized under different electrolysis conditions, are much larger than the theoretical size estimated for an ideal dendrimer. We determined by 29Si NMR that the reason for this is in a large number of branching irregularities (defects) contained in the molecular structure. Combining the experimental values obtained by DLS and density measurements with a structural model that considers the branching irregularities, it is shown that the inclusion of the defects allows the dendritic polymer to exceed the sterical limitations and form the hyperbranched dendritic structure. The final size depends on a relative amount of the branching defects. In the second part, the synthetized polymethylsilane molecules were successfully used for the nanocomposite formation. The aluminium hydroxide gel with the dispersed polymethylsilane molecules was prepared as a precursor. Upon heat-treatment it gives the amorphous aluminium oxide stable up to 900°C. The dispersed macromolecules induce homogeneously distributed strain fields that keep the aluminium oxide amorphous during the thermal treatment the dispersed macromolecules covalently bind to the matrix, inducing the interface strain. The amorphous state was confirmed by the presence of penta-coordinated aluminium detected by 27Al NMR and a low bandgap measured by UV-vis absorption spectroscopy.
Najdeno v: ključnih besedah
Povzetek najdenega: ...thesis focuses on the synthesis, characterization and solubility properties of the dendritic polymethylsilane. The polymethylsilane...
Ključne besede: amorphous aluminium oxide, polymethylsilane, nanocomposite, electropolymerization, solubility, agglomeration, de-agglomeration, dendrimer, hyperbranched dendritic structure, dynamic light scattering, thermal analysis, transmission electron microscopy, scanning electron microscopy, X-ray diffraction, infrared spectroscopy, UV-Vis spectroscopy
Objavljeno: 19.07.2018; Ogledov: 810; Prenosov: 43
.pdf Polno besedilo (5,07 MB)

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