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Modelling of chirality propagation in self-assembling systems
Full text linkHierarchical self-assembly is a process in which molecular building blocks form intermediate structures that self organise at macroscopic level. Remarkable examples can be found in nature, like, for instance, DNAs or viruses. Self-assembly offers interesting strategies to build new complex materials: Therefore, it is very important to understand its mechanism to design and control molecular architectures and to build structures with desired properties and morphologies. A major question is how the shape of the building blocks influences self- assembly. In this context, chirality plays a crucial role: It is extremely sensitive to subtleties on the molecular scale and can guide self-assembly; furthermore, chirality can act as an amplifier of changes that occur at the molecular level.
From the theoretical point of view, the difficulty derives from the need of multiscale methods and models, able to connect the different length scales. To take into account the relationship among the building blocks, their supramolecular organization, and the properties of the aggregates, a detailed representation of intermolecular interactions is needed: This description has to be integrated into a suitable modeling of the system behaviour on a much longer length scale.
This thesis deals with the development and implementation of models for chirality propagation from the molecular to the meso- and macroscopic levels in self-assembling systems. In particular, the research has been carried out along three lines. The first deals with self-assembly of hard helices, leading to the formation of anisotropic phases of vari- ous symmetry. The second topic is the linear aggregation and formation of liquid crystal phases by double-stranded nucleic acid oligomers (dsNA): The relationship between the sequence of oligonucleotides, their self-assembly and the properties of their cholesteric phase is investigated. The last topic is the aggregation of porphyrin-polypeptide conjugates in water.
Depending on the problem and the length scale, we used different theoretical and com- putational methods, in particular: Statistical theories of liquids and molecular dynamics simulations (both atomistic and coarse-grained). The first and third topics have been carried out in collaboration with experimentalists, while for the second other groups of theoreticians have been involved.
This thesis is organized in three parts. In Chapter 1, the concepts of self-assembling, chi- rality propagation and multiscale modeling are introduced. Moreover this Chapter presents an outline of the main properties of liquid crystals.
The first Part, from Chapter 2 to Chapter 4, presents the study on the anisotropic phases formed by hard helices. Chapter 2 presents a study of the nematic phase, using an Onsager- like theory. The theoretical results are compared with Monte Carlo simulations. In Chapter 3, a theoretical model for the cholesteric phase is presented and used to investigate the relationship between the helical shape and the properties of the cholesteric phase. In Chapter 4, the complete phase diagram of hard helices is presented, together with the characterization of a novel chiral nematic phase.
The second Part deals with liquid crystal phases formed by dsNA. Chapter 5 focuses on the relation between the sequence of oligonucleotides and their organization in the cholesteric phase, using a molecular theory and coarse-grained modelling based on sequence dependent structural data. Chapter 6 describes the theoretical model for the cholesteric phase formed by self-assembling oligomers, which integrates the theory for cholesteric order presented in Chapter 3 with that for linear aggregation in the nematic phase.
The last Part, from Chapter 7 to Chapter 9, deals with the aggregation of porphyrin- peptide conjugates in water. In Chapter 7 the main concepts of circular dichroism are introduced and the state-of-the-art of self-assembly of porphyrins is reviewed. Chapter 8 describes atomistic molecular dynamics simulation of aggregates of porphyrin-peptide conjugates. Chapter 9 presents a study of the same systems by coarse-grained molecular dynamics simulations, using the MARTINI model. Finally, Chapter 10 presents a summary, which highlights the relevant results obtained in this Thesis, and three Appendices follow
Linker dependent chirality of solvent induced self-assembled structures of porphyrin–α-helical peptide conjugates
No full textThe solvent-promoted aggregation of porphyrins covalently linked to medium length peptides occurs
with the formation of chiral supramolecular structures if the peptide chain can adopt an α-helical secondary
structure. The circular dichroism spectra of different porphyrin–peptide conjugates show that the
chiral arrangement of the porphyrins in the aggregates does not depend on the screw-sense of the
peptide helix. Experimental evidence and molecular dynamic simulations suggest that the linker between
the porphyrin and the peptide helix is responsible for the overall chirality of supramolecular structures. In
particular when the linker is a chiral α-amino acid it is possible to tune the morphology of the chiral
aggregates by inverting the configuration of the chiral center
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Right- and left-handed liquid crystal assemblies of oligonucleotides: phase chirality as a reporter of a change in non-chiral interactions?
No full textUsing molecular theory and coarse grained modelling, based on sequence dependent structural data, we have investigated the relationship between the sequence of oligonucleotides and their organization in the cholesteric phase. Despite the significantly different structure of the double helix, the same result has been found for all the investigated sequences: hard-core interactions would promote a right-handed cholesteric twist, whereas a change to a left-handed twist would be produced by electrostatic interactions. On the other hand, the structural differences between oligomers have been found to strongly influence the concentration at which the cholesteric phase appears. We propose that the sequence dependence of the cholesteric handedness, revealed by recent experiments (G. Zanchetta et al., Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 17497), reflects a change in non-chiral interactions in DNA and RNA solutions under conditions of molecular crowding
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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