1,721,186 research outputs found
Spin-selective chemical reactions in radical pair magnetoreception
Full text linkMany animals on earth need to navigate in their own environments for breeding and foraging. The ability to determine a correct heading and the current location for a migratory bird is critical for its survival. Animals that are sensitive to the Earth’s magnetic field can use it to obtain their direction of travel. In 2000, a paper suggested that radical pair reaction could form the basis for magnetoreception in migratory birds and a flavoprotein, cryptochrome, was proposed as the candidate for the radical pair precursor. Recent in vivo experimental results strongly support the hypothesis that radical pairs formed in the eyes of migratory birds are responsible for their magnetic compass sense. Cryptochrome has also been located in the UV-cones in the retinas of two different species of bird. Radical pairs in living cells are influenced mainly by Zeeman interaction, hyperfine interaction, rotational modulation, etc., and together they influence the recombination reactions of the radical pairs. This thesis considers the possible role of radical pairs in avian magnetoreception, using computer simulations of the quantum mechanical evolution of a radical pair under a variety of conditions. Chapter 1 contains the introductions to spin chemistry, avian magnetoreception, and the mathematical description of the quantum evolution of a radical pair. Chapter 2 describes the four different theoretical models for a general non-diffusion-controlled radical pair reaction and the product yields of a radical pair reaction predicted by these four models are analysed and compared. Chapter 3 introduces a model for avian magnetoreception that integrates photoselection with the radical pair reaction and the model is used to predict the retinal patterns that a bird may be able to use for magnetoreception. The anisotropic singlet product yields of a radical pair comprises the flavin chromophore and the tryptophan of a cryptochrome are also presented in this chapter. A paper based on some parts of this chapter is published [1] in the Journal of The Royal Society Interface. Chapter 4 describes a modified version of an algorithm that is used to calculate the product yields detected in a reaction yield detected magnetic resonance (RYDMR) experiment. The new algorithm is used to analyse the results of two sets of RYDMR experiments in which two radical pair systems, pyrene/1,3-dicyanobenzene and chrysene/1,4-dicyanobenzene, were used. The modulated detection technique used in the RYDMR experiments is also discussed in this chapter. A section of this chapter is published [2] in a paper in the journal Physical Chemistry Chemical Physics
Nuclear magnetic resonance data processing methods
Full text linkThis thesis describes the application of a wide variety of data processing methods, in particular the Maximum Entropy Method (MEM), to data from Nuclear Magnetic Resonance (NMR) experiments. Chapter 1 provides a brief introduction to NMR and to data processing, which is developed in chapter 2. NMR is described in terms of the classical model due to Bloch, and the principles of conventional (Fourier transform) data processing developed. This is followed by a description of less conventional techniques. The MEM is derived on several grounds, and related to both Bayesian reasoning and Shannon information theory. Chapter 3 describes several methods of evaluating the quality of NMR spectra obtained by a variety of data processing techniques; the simple criterion of spectral appearance is shown to be completely unsatisfactory. A Monte Carlo method is described which allows several different techniques to be compared, and the relative advantages of Fourier transformation and the MEM are assessed. Chapter 4 describes in vivo NMR, particularly the application of the MEM to data from Phase Modulated Rotating Frame Imaging (PMRFI) experiments. In this case the conventional data processing is highly unsatisfactory, and MEM processing results in much clearer spectra. Chapter 5 describes the application of a range of techniques to the estimation and removal of splittings from NMR spectra. The various techniques are discussed using simple examples, and then applied to data from the amino acid iso-leucine. The thesis ends with five appendices which contain historical and philosophical notes, detailed calculations pertaining to PMRFI spectra, and a listing of the MEM computer program
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
Spin dynamics calculations applied to systems of potential biological significance
Full text linkMagnetic fields interact with biological systems, often in unexplored and surprising ways. In this thesis I develop and employ a range of quantum mechanical spin dynamics tools for simulating these magnetic spin interactions, modelling a diverse set of systems of potential biological relevance.
Nuclear spins in calcium phosphates known as Posner molecules form the basis of a proposed mechanism for human neural processing. This theory requires that phosphorus nuclei in different Posner molecules become entangled and remain so for periods far longer than typical nuclear spin relaxation times. In Chapter 3 I model the coherent and relaxation spin dynamics of this molecule, deriving a strict upper bound on the entanglement lifetime and arguing that other relaxation effects will further limit this lifetime.
Spin relaxation is also relevant to studies into the chemical compass sense possessed by migratory birds. Certain evidence indicates that a flavin-superoxide radical pair may be better suited for detecting the Earth’s magnetic field than the flavin-tryptophan system more commonly assumed. Studies into this alternative radical pair often ignore the particularly rapid electron spin relaxation expected for superoxide. In Chapter 4 I simulate the sensitivity of this superoxide radical pair to an Earth-strength magnetic field, deriving a set of strict conditions on the local environment and molecular dynamics of the radicals that will need to be satisfied if it does play a role in geomagnetic sensing.
In Chapter 5 I simulate the effect of a magnetic field on the electrocatalytic reduction of carbon dioxide, demonstrating that an experimentally observed field effect cannot be accounted for by the mechanism originally proposed. By including spin relaxation, I am able to fit the experimental results and derive a set of physically reasonable parameters that quantitatively account for the observed field effect.
In many systems these observed magnetic effects are of a relatively small magnitude. In Chapter 6 I examine autocatalysis in oscillating chemical reactions as a means of amplifying weak field effects. A minute change in one of the rate constants for the initiation step in a model oscillating system that involves a radical pair is found to produce a dramatically large change in the amplitude of reaction intermediate oscillations
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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