Papers by Maria Francesca Zini
Polymer International, 2000
Films of blends of Paraloid 1 B72 (copolymer of ethyl methacrylate and methyl acrylate) and Tecno... more Films of blends of Paraloid 1 B72 (copolymer of ethyl methacrylate and methyl acrylate) and Tecno¯on NM 1 (copolymer of vinylidene¯uoride and hexa¯uoropropene) with different compositions were investigated by means of FT-IR spectroscopy and FT-IR microspectroscopy before and after UV and thermal treatments. Preliminary results of DSC measurements are also reported.
Reactivity of nucleic acids with ozone: An FT-IR microspectroscopy study
Applied Spectroscopy, 1997
ABSTRACT
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surfac... more In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the visualization (Andrei et al) of proteins and other macromolecules, using instruments of computer graphics. A vast number of protein (if not most) exert their function through some extent of motion. Despite recent advances in higly performant methods, it is very difficult to obtain direct information on conformational changes of molecules. However, several systems exist that can shed some light on the variability of conformations of a single peptide chain; among them, NMR methods provide collections of a number of static 'shots' of a moving protein. Starting from this data, and assuming that if a protein exists in more than 1 conformation it must be able to transit between the different states, we have elaborated a system that makes ample use of the computational power of 3D computer graphics technology. Considering information of all (heavy) atoms, we use animation and game engine of Blender to obtain transition states. The model we chose to elaborate our system is Calmodulin, a protein favorite among structural and dynamic studies due to its (relative) simplicity of structure and small dimension. Using Calmodulin we show a procedure that enables the building of a 'navigation map' of NMR models, that can help in the identification of movements. In the process, a number of intermediate conformations is generated, all of which respond to strict bio-physical and bio-chemical criteria. The BioBlender system is available for download from the website www.bioblender.net, together with examples, tutorial and other useful material.
Computing Research Repository, 2010
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins ... more In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the visualization (here) of proteins and other macromolecules, using instruments of computer graphics. The availability of protein structures enables the study of their surfaces and surface properties such as electrostatic potential (EP) and hydropathy (MLP), based on atomic contribution. Recent advances in 3D animation and rendering software have not yet been exploited for the representation of proteins and other biological molecules in an intuitive, animated form. Taking advantage of an open-source, 3D animation and rendering software, Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins' motions with the simultaneous visualization of chemical and physical features. EP and MLP are calculated using physico-chemical programs and custom programs and scripts, organized and accessed within BioBlender interface. A new visual code is introduced for MLP visualization: a range of optical features that permits a photorealistic rendering of its spatial distribution on the surface of the protein. EP is represented as animated line particles that flow along field lines proportional to the total charge of the protein. Our system permits EP and MLP visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges.
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Papers by Maria Francesca Zini