The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

The refinement and validation of the critical decision making and problem solving scale moral dilema (CDP-MD)

This thesis extended previous research on critical decision making and problem solving by refining and validating a measure designed to assess the use of critical thinking and critical discussion in sociomoral dilemmas. The purpose of this thesis was twofold: 1) to refine the administration of the Critical Thinking Subscale of the CDP to elicit more adequate responses and for purposes of refining the coding and scoring procedures for the total measure, and 2) to collect preliminary data on the initial reliabilities of the measure. Subjects consisted of 40 undergraduate students at Florida International University. Results indicate that the use of longer probes on the Critical Thinking Subscale was more effective in eliciting adequate responses necessary for coding and evaluating the subjects performance. Analyses on the psychometric properties of the measure consisted of test-retest reliability and inter-rater reliability.

Fleshing Out and Losing Flesh: The Decomposing Corpse as Narrative Object in American Hardboiled Detective Fiction

This dissertation examines the corpse as an object in and of American hardboiled detective fiction written between 1920 and 1950. I deploy several theoretical frames, including narratology, body-as-text theory, object relations theory, and genre theory, in order to demonstrate the significance of objects, symbols, and things primarily in the clever and crafty work of Dashiell Hammett (1894-1961) and Raymond Chandler (1888-1959), but also touching on the writings of their lesser known accomplices. I construct a literary genealogy of American hardboiled detective fiction originating in the writings of Edgar Allan Poe, compare the contributions of classic or Golden Age detective fiction in England, and describe the socio-economic contexts, particularly the predominance of the “pulps,” that gave birth to the realism of the Hardboiled School. Taking seriously Chandler’s obsession with the art of murder, I engage with how authors pre-empt their readers’ knowledge of the tricks of the trade and manipulate their expectations, as well as discuss the characteristics and effect of the inimitable hardboiled style, its sharpshooting language and deadpan humour. Critical scholarship has rarely addressed the body and figure of the corpse, preferring to focus instead on the machinations of the femme fatale, the performance of masculinity, or the prevalence of violence. I cast new light on the world of hardboiled detective fiction by dissecting the corpse as the object that both motivates and de-composes (or rots away from) the narrative that makes it signify. I treat the corpse as an inanimate object, indifferent to representation, that destabilizes the integrity and self-possession, as well as the ratiocination, of the detective who authors the narrative of how the corpse came to be. The corpse is all deceptive and dangerous surface rather than the container of hidden depths of life and meaning that the detective hopes to uncover and reconstruct. I conclude with a chapter that is both critical denouement and creative writing experiment to reveal the self-reflexive (and at times metafictional) dimensions of hardboiled fiction. My dissertation, too, in the manner of hardboiled fiction, hopes to incriminate my readers as much as enlighten them.

Empowering development: capabilities and Latin American critical traditions

This thesis theoretically and critically examines the move towards people-centred approaches to development. It offers a critical examination of the work of Amartya Sen using theoretical resources emerging from Latin American traditions. Amartya Sen’s calls to understand Development as Freedom (1999) have significantly influenced mainstream development thinking and practice, constituting the clearest example of people-centred approaches to development today. Overcoming the limitations of previous state-centred notions of development articulated around ideas of economic growth, in Sen’s Capability Approach (CA) development is seen as a process of expanding the real freedoms that people enjoy. In this understanding, the agency of development shifts from the state to individuals and the analytic focus moves from economic growth to individual capabilities. In this manner, this framework is structured towards the central goal of empowerment, wherein the expansion of capabilities is seen both as the means and end of development. Since its inception, the widespread support for the CA has allowed for the expansion of ethical considerations within mainstream development thinking. Even while the remarkable advances offered by Sen’s work should be praised, this thesis argues that these have come with new limitations. These limitations stem from, what is termed here, a “Paradox of Empowerment” that effectively encloses Sen’s approach within Western notions of development. While Sen’s approach is poised to provide a theoretical framework that is built on the expansion of freedom and individual agency, there is little agency here to move beyond the ideas of development fundamentally linked to liberal democracies and market economies. This thesis engages with several critical traditions from Latin America, recovering their often undervalued insights for development thinking. Crucially, this engagement provides the critical framework to illustrate the aforementioned paradox and explore multiple dimensions of empowerment central for contemporary development thinking and practice. In this, the thesis engages Sen’s work with the Liberation Theology of Gustavo Gutierrez, with Paulo Freire’s Critical Pedagogy and with the contemporary discussions of ‘Buen Vivir’ associated with Indigenous philosophies of the Andean region. Throughout its chapters,it uncovers the conceptual baggage within the Paradox of Empowerment in Sen’s work and examines the ethical challenges and boundaries of this approach in relation to the collective dimension of development processes, the possibilities for structural transformation and concerns for sustainability. Progressively engaging the different dimensions of this paradox, this thesis advances the recovery of the transformative potential of the ideas of empowerment for development.

Nonequilibrium critical scaling from quantum thermodynamics

The emerging field of quantum thermodynamics is contributing important results and insights into archetypal many-body problems, including quantum phase transitions. Still, the question whether out-of-equilibrium quantities, such as fluctuations of work, exhibit critical scaling after a sudden quench in a closed system has remained elusive. Here, we take a novel approach to the problem by studying a quench across an impurity quantum critical point. By performing density matrix renormalization group computations on the two-impurity Kondo model, we are able to establish that the irreversible work produced in a quench exhibits finite-size scaling at quantum criticality. This scaling faithfully predicts the equilibrium critical exponents for the crossover length and the order parameter of the model, and, moreover, implies a new exponent for the rescaled irreversible work. By connecting the irreversible work to the two-impurity spin correlation function, our findings can be tested experimentally.

(Quantum-) critical dynamics of magnetoelectric materials

In this thesis the critical dynamics of several magnetoelectric compounds at their phase transition were examined. Mostly measurements of the dielectric properties in the frequency range of below 1 Hz up to 5 GHz were employed to evaluate the critical exponents for both magnetic field and temperature-dependent measurements. Most of the materials that are part of this work show anomalous behavior, especially at very low temperatures where quantum fluctuations are of the order of or even dominate those induced thermally. This anomalous behavior manifests in different forms. In Dy2Ti2O7 we demonstrate the existence of electric dipoles on magnetic monopoles. Here the dynamics at the critical endpoint located at 0.36K and in a magnetic field of 1T parallel to the [111] direction are of special interest. At this critical endpoint the expected critical slowing down of the dynamics could not only not be observed but instead the opposite, critical speeding-up by several orders of magnitude, could be demonstrated. Furthermore, we show that the phase diagram of Dy2Ti2O7 in this field direction can be reproduced solely from the dynamical properties, for example the resonance frequency of the observed relaxation that is connected to the monopole movement. Away from this point of the phase diagram the dynamics are slowing-down with reduction of temperature as one would expect. Additional measurements on Y2Ti2O7, a structurally identical but non-magnetic material, show only slowing down with reduction of temperature and no additional features. A possible explanation for the observed critical speeding-up is a coherent movement of magnetic monopoles close to the critical field that increases the resonance frequency by reducing the damping of the process. LiCuVO4 on the other hand behaves normally at its phase transition as long as the temperature is higher than 0.4 K. In this temperature regime the dynamics show critical slowing-down analogous to classical ferroelectric materials. This analogy extends also towards higher frequencies where the permittivity displays a ‘dispersion’ minimum that is temperature-dependent but of the order of 2 GHz. Below 0.4K the observed behavior changes drastically. Here we found no longer relaxational behavior but instead an excitation with very low energy. This low energy excitation was predicted by theory and is caused by nearly gapless soliton excitations within the 1D Cu2+ chains of LiCuVO4. Finally, in TbMnO3 the dynamics of the phase transition into the multiferroic phase was observed at roughly 27 K, a much higher temperature compared to the other materials. Here the expected critical slowing-down was observed, even though in low-frequency measurements this transition into the ferroelectric phase is overshadowed by the so-called c-axis relaxation. Therefore, only frequencies above 1MHz could be used to determine the critical exponents for both temperatureand magnetic-field-dependent measurements. This was done for both the peak frequency as well as the relaxation strength. In TbMnO3 an electromagnetic soft-mode with small optical weight causes the observed fluctuations, similar to the case of multiferroic MnWO4.

The D(D-3)-anyon chain: integrable boundary conditions and excitation spectra

Chains of interacting non-Abelian anyons with local interactions invariant under the action of the Drinfeld double of the dihedral group D-3 are constructed. Formulated as a spin chain the Hamiltonians are generated from commuting transfer matrices of an integrable vertex model for periodic and braided as well as open boundaries. A different anyonic model with the same local Hamiltonian is obtained within the fusion path formulation. This model is shown to be related to an integrable fusion interaction round the face model. Bulk and surface properties of the anyon chain are computed from the Bethe equations for the spin chain. The low-energy effective theories and operator content of the models (in both the spin chain and fusion path formulation) are identified from analytical and numerical studies of the finite-size spectra. For all boundary conditions considered the continuum theory is found to be a product of two conformal field theories. Depending on the coupling constants the factors can be a Z(4) parafermion or a M-(5,M-6) minimal model.

Kinetics of tidal resuspension of microbiota: Testing the effects of sediment cohesiveness and bioturbation using flume experiments

Resuspension of the top few sediment layers of tidal mud flats is known to enhance planktonic biomass of microbiota (benthic diatoms and bacteria). This process is mainly controlled by tidal shear stress and cohesiveness of mud, and is also influenced by bioturbation activities. Laboratory experiments in a race track flume were performed to test the interactive effects of these factors on both the critical entrainment and resuspension kinetics of microbiota from silt-clay sediments from the Marennes-Oleron Bay, France. The marine snail Hydrobia ulvae was used to mimic surface bioturbation activities. As expected, the kinetics of microbial resuspension versus shear stress were largely controlled by the cohesiveness of silt-clay sediments. However, our results indicate that the effect of surface tracking by H. ulvae on microbial resuspension was clearly dependent on the interaction between sediment cohesiveness and shear velocity. Evidence was also found that microphytobenthos and bacteria are not simultaneously resuspended from silt-clay bioturbated sediments. This supports the theory that diatoms within the easily eroded mucus matrix behave actively and bacteria adhering to fine silt particles eroded at higher critical shear velocities behave passively.

Critical behavior of the three-dimensional Ising spin glass

We have simulated, using parallel tempering, the three-dimensional Ising spin glass model with binary couplings in a helicoidal geometry. The largest lattice (L520) has been studied using a dedicated computer (the SUE machine). We have obtained, measuring the correlation length in the critical region, strong evidence for a second-order finite-temperature phase transition, ruling out other possible scenarios like a KosterlitzThouless phase transition. Precise values for the ν and ƞ critical exponents are also presented.

Multi-scalar critical theories: first steps for a non perturbative functional renormalization group analysis

In this work the fundamental ideas to study properties of QFTs with the functional Renormalization Group are presented and some examples illustrated. First the Wetterich equation for the effective average action and its flow in the local potential approximation (LPA) for a single scalar field is derived. This case is considered to illustrate some techniques used to solve the RG fixed point equation and study the properties of the critical theories in D dimensions. In particular the shooting methods for the ODE equation for the fixed point potential as well as the approach which studies a polynomial truncation with a finite number of couplings, which is convenient to study the critical exponents. We then study novel cases related to multi field scalar theories, deriving the flow equations for the LPA truncation, both without assuming any global symmetry and also specialising to cases with a given symmetry, using truncations based on polynomials of the symmetry invariants. This is used to study possible non perturbative solutions of critical theories which are extensions of known perturbative results, obtained in the epsilon expansion below the upper critical dimension.

Inhibitory Effects Of A Cured Antibacterial Bonding System On Viability And Metabolic Activity Of Oral Bacteria.

To evaluate the antimicrobial efficacy of Clearfil SE Protect (CP) and Clearfil SE Bond (CB) after curing and rinsed against five individual oral microorganisms as well as a mixture of bacterial culture prepared from the selected test organisms. Bacterial suspensions were prepared from single species of Streptococcus mutans, Streptococcus sobrinus, Streptococcus gordonii, Actinomyces viscosus and Lactobacillus lactis, as well as mixed bacterial suspensions from these organisms. Dentin bonding system discs (6 mm×2 mm) were prepared, cured, washed and placed on the bacterial suspension of single species or multispecies bacteria for 15, 30 and 60 min. MTT, Live/Dead bacterial viability (antibacterial effect), and XTT (metabolic activity) assays were used to test the two dentin system's antibacterial effect. All assays were done in triplicates and each experiment repeated at least three times. Data were submitted to ANOVA and Scheffe's f-test (5%). Greater than 40% bacteria killing was seen within 15 min, and the killing progressed with increasing time of incubation with CP discs. However, a longer (60 min) period of incubation was required by CP to achieve similar antimicrobial effect against mixed bacterial suspension. CB had no significant effect on the viability or metabolic activity of the test microorganisms when compared to the control bacterial culture. CP was significantly effective in reducing the viability and metabolic activity of the test organisms. The results demonstrated the antimicrobial efficacy of CP both on single and multispecies bacterial culture. CP may be beneficial in reducing bacterial infections in cavity preparations in clinical dentistry.

Kinesiographic Study Of Masticatory Movements In Denture Wearers With Normal And Resorbed Denture-bearing Areas.

An unfavorable denture-bearing area could compromise denture retention and stability, limit mastication, and possibly alter masticatory motion. The purpose of this study was to evaluate the masticatory movements of denture wearers with normal and resorbed denture-bearing areas. Completely edentulous participants who received new complete dentures were selected and divided into 2 groups (n=15) according to the condition of their denture-bearing areas as classified by the Kapur method: a normal group (control) (mean age, 65.9 ± 7.8 years) and a resorbed group (mean age, 70.2 ± 7.6 years). Masticatory motion was recorded and analyzed with a kinesiographic device. The patients masticated peanuts and Optocal. The masticatory movements evaluated were the durations of opening, closing, and occlusion; duration of the masticatory cycle; maximum velocities and angles of opening and closing; total masticatory area; and amplitudes of the masticatory cycle. The data were analyzed by 2-way ANOVA and the Tukey honestly significant difference post hoc test (α=.05). The group with a resorbed denture-bearing area had a smaller total masticatory area in the frontal plane and shorter horizontal masticatory amplitude than the group with normal denture-bearing area (P<.05). Denture wearers with resorbed denture-bearing areas showed reduced jaw motion during mastication.

Magnetic resonant x-ray diffraction study of europium telluride

Here we use magnetic resonant x-ray diffraction to study the magnetic order in a 1.5 mu m EuTe film grown on (111) BaF(2) by molecular-beam epitaxy. At Eu L(II) and L(III) absorption edges, a resonant enhancement of more than two orders was observed for the sigma ->pi(') diffracted intensity at half-order reciprocal-lattice points, consistent with the magnetic character of the scattering. We studied the evolution of the (1/21/21/2) magnetic reflection with temperature. When heating toward the Neel temperature (T(N)), the integrated intensity decreased monotonously and showed no hysteresis upon cooling again, indicating a second-order phase transition. A power-law fit to the magnetization versus temperature curve yielded T(N)=9.99(1) K and a critical exponent beta=0.36(1), which agrees with the renormalization theory results for three-dimensional Heisenberg magnets. The fits to the sublattice magnetization dependence with temperature, disregarding and considering fourth-order exchange interactions, evidenced the importance of the latter for a correct description of magnetism in EuTe. A value of 0.009 was found for the (2j(1)+j(2))/J(2) ratio between the Heisenberg J(2) and fourth-order j(1,2) exchange constants. The magnetization curve exhibited a round-shaped region just near T(N) accompanied by an increase in the magnetic peak width, which was attributed to critical scattering above T(N). The comparison of the intensity ratio between the (1/21/21/2) and the (1/21/21/2) magnetic reflections proved that the Eu(2+) spins align within the (111) planes, and the azimuthal dependence of the (1/21/21/2) magnetic peak is consistent with the model of equally populated S domains.

Nonuniversal behavior for aperiodic interactions within a mean-field approximation

We study the spin-1/2 Ising model on a Bethe lattice in the mean-field limit, with the interaction constants following one of two deterministic aperiodic sequences, the Fibonacci or period-doubling one. New algorithms of sequence generation were implemented, which were fundamental in obtaining long sequences and, therefore, precise results. We calculate the exact critical temperature for both sequences, as well as the critical exponents beta, gamma, and delta. For the Fibonacci sequence, the exponents are classical, while for the period-doubling one they depend on the ratio between the two exchange constants. The usual relations between critical exponents are satisfied, within error bars, for the period-doubling sequence. Therefore, we show that mean-field-like procedures may lead to nonclassical critical exponents.

Continuous structural transitions in quasi-one-dimensional classical Wigner crystals

We study the structural phase transitions in confined systems of strongly interacting particles. We consider infinite quasi-one-dimensional systems with different pairwise repulsive interactions in the presence of an external confinement following a power law. Within the framework of Landau's theory, we find the necessary conditions to observe continuous transitions and demonstrate that the only allowed continuous transition is between the single-and the double-chain configurations and that it only takes place when the confinement is parabolic. We determine analytically the behavior of the system at the transition point and calculate the critical exponents. Furthermore, we perform Monte Carlo simulations and find a perfect agreement between theory and numerics.