25 research outputs found

    Theoretical Investigation of Interactions and Relaxation in Biological Macromolecules

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    One of the major challenges posed to our quantitative understanding of structure, dynamics, and function of biological macromolecules has been the high level of complexity of biological structures. In the present work, we studied interactions between G protein-coupled receptors (GPCRs), and also introduced a theoretical model of relaxation in complex systems, in order to help understand interactions and relaxation in biological macromolecules. GPCRs are the largest and most diverse family of membrane receptors that play key roles in mediating signal transduction between outside and inside of a cell. Oligomerization of GPCRs and its possible role in function and signaling currently constitute an exciting area of research, with implications on development of therapeutic regimens. We performed molecular dynamics (MD) simulations of fluorescent proteins attached through short linkers to GPCRs, in order to obtain distances between them and orientation factors of their transition dipole moments. Used in conjunction with Förster resonance energy transfer (FRET) experiments, this information is used for determination of binding interfaces between GPCR protomers (i.e., single molecules) within an oligomer. We simulated, with coarse-grained resolution, several configurations of dimers and tetramers of the M2 muscarinic acetylcholine receptor fused to the green fluorescent protein (GFP, a donor of energy in FRET) and yellow fluorescent protein (YFP, an acceptor of energy). From simulated distances and orientation factors for oligomers with different relative orientations of the protomers, we computed apparent FRET efficiencies for mixtures of monomers, dimers and tetramers based on the simulated data, and then compared them to experimental FRET data. Comparing the fitting residuals obtained for all tested oligomer configurations, we were able to determine, for the first time, the most probable quaternary structure of the M2 muscarinic receptor in living cells. The study of relaxation processes is still insufficiently developed for the case of complex systems. Although it is currently firmly established that the dielectric behavior of systems of coupled dipoles or systems with complex biological structures deviates markedly from classical Debye (in the frequency domain) or pure exponential decay (in the time domain), the exact ways in which these deviations occur and their significance are still debated issues. In the second part of my thesis, we use a new approach to this problem for systems that present hierarchical relationships between their parts, also known as fractals. We formulated a set of differential equations of physical quantities in the hierarchical structure and developed a method of solving it. As a test case, for which there is experimental data to relate to, we applied this method to dielectric relaxation, and successfully reproduced the Debye, and non-Debye behaviors in the frequency domain, as well as corresponding non-exponential behaviors in the time domain. The proposed approach will likely provide an adequate mathematical framework for such disparate phenomena as recombination of photodissociable molecules, distribution of income in large populations of humans, and non-exponential decay of fluorescence in systems with multiple, hierarchically organized energetic levels. This in turn could help, develop correct approaches for analyzing FRET measurements in the time domain, which currently pose many challenges

    Topical meeting on Condensed-matter Chemistry on Actinides: The Kumatori meeting 2021

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    Topical meeting on Condensed-matter Chemistry on Actinides : The Kumatori meeting 2021, Feb. 10th, 2021@ZoomThis report is published to preserve the discussions of“the Kumatori 2021”conference held on Feb. 10, 2021.Chapter 1 Program [1]Chapter 2 Opening Remarks [4]Chapter 3 Presentation Materials [8]3.1 H. Yamagami(Kyoto Sangyo Univ.), Objectives of this meeting [9]3.2 Y. Haga(ASRC, JAEA), Uranium-based inter metallics with layered structure: characterization and magnetism [11]3.3 K. Ishida(Dept. Phys., Kyoto Univ.), Superconducting Spin Susceptibility of UTe₂ [13]3.4 T. Yaita(SPring-8, JAEA), Recent activities of Actinide Chemistries in the Materials Sciences Rsearch Center of JAEA [17]3.5 N. Ishikawa(Dept. Chem., Osaka Univ.), Observation of interaction between 5f electronic system and photo-excited cyclic π system [21]3.6 T. Suzuki(Nagaoka Univ. Tech.), Fundamental Study for Precise Analysis of Actinides in Hardly Soluble Substances Containing Uranium Oxides [25]3.7 K. Washiyama(Fukushima Medical University), Current status and prospects of domestic supply of alpha-emitting radionuclides [29]3.8 Y. Kawabata(KURNS, Kyoto Univ.), Current status and future plans of our institute [34]3.9 T. Yamamura(KURNS, Kyoto Univ.), Actinide researches using KUR hot-lab [35]3.10 M. Suzuki(KURNS, Kyoto Univ.), The Future of Cyclotron-Based BNCR Research [38]3.11 T. Kitazawa(Dept. Chem., Toho Univ.), Synthesis and Crystal Structures of Three New Complexes Constructed with Uranyl(VI)-acetylacetonate and Uranyl(VI)-nitrate [43]3.12 T. Yoshimura(IRS, Osaka Univ.), Preparation of guidelines for evaluation to ensure safety in the use of short-lived unsealed radioisotopes [50]3.13 H. Amitsuka(Hokkaido Univ.), Odd Parity Multipole Ordering in Uranium Compounds [52]3.14 T. Yanagisawa(Hokkaido Univ.), Electric Quadrupolar Contributions in the Magnetic Phases of UNi₄B [56]3.15 M. Manjum(Dept. Appl. Chem., Keio Univ.), Electrochemical Formation of Samarium and Samarium-Cobalt Nanoparticles in a Pyrrolidinium-based Ionic Liquid [60]3.16 T. Nomoto(Tokyo Inst. Tech.), Drug delivery using functional polymer-conjugates [63]3.17 A. P. Goncalves(Universidade Lisboa, Portugal), On the U-Fe-Ge system and its compounds [65]3.18 A. S. P. Gomes(Universite de Lille, France), Electronic structure of actinide systems from relativistic correlated and quantum embedding approaches [72]3.19 R. Caciuffo(EU JRC, Karlsruhe, Germany), Radioisotopes for medical applications [77]Chapter 4 Break Session [81]4.1 Break Session 1 [83]4.1.1 H. Shishido(Tohoku Univ.), Proposals for the advanced nuclear fuel cycle by introducing a fusion reactor [83]4.1.2 M. Nakase(Tokyo Inst. Tech.), Development and characterization of phthalocyanine derivatized ligands for recognition and complexation of light Actinide elements [87]4.1.3 H. Nakai(Kindai Univ.), Development of ligands for new actinide complexes [89]4.1.4 C. Tabata(Kyoto Univ.), Crystal structure and magnetic property of uranium phthalocyanine complexes [93]4.1.5 Y. Kasamatsu(Osaka Univ.), Co-precipitation experiment of group 2 elements with barium hydrosulfate toward chemical study of No [98]4.1.6 K. Shirasaki(Tohoku Univ.), Extraction of strontium from aqueous solutions intoHFCusing dicyclohexano-18-crown-6 and perfluorinated polyethylene glycol derivative [102]4.1.7 Y. Sekiguchi(CRIEPI), Thermodynamic estimation of vaporization of CsI dissolved in LiFNaF-KF molten salt [104]4.1.8 F. Kon(Hokkaido Univ.), Observation of Antiferromagnetic Order in the Heavy-Fermion Compound UIr₂Ge₂ - Resonant X-ray Scat-tering [109]4.1.9 A. Sato(Tokyo Met. Univ.), Theoretical study on isotope fractionation in uraninite [112]4.1.10 Y. Kitawaki(Kyoto Sangyo Univ.), Orbital magnetization in many-electron systems described by spin-orbital-polarized coupled Dirac equation [116]4.2 Break Session 2 [119]4.2.1 T. Fukuda(JAEA), Present status of the study on energy conversion using actinides in radioactive wastes [119]4.2.2 T. Oda(Kyoto Univ.), Slow dynamics study by neutron resonance spin echo spectromete [121]4.2.3 A. Sunaga(Kyoto Univ.), Theoretical study of the linearity of uranyl molecule based on relativistic correlation method [125]4.2.4 M. Nogami(Kindai Univ.), Change in precipitation ability of treated cyclic urea compounds for selective precipitation of U(VI) species [128]4.2.5 Y. Homma(Tohoku Univ.), Mossbaure spectroscopy of the Eu-based skyrmion compounds EuPtSi and EuAl₄ [134]4.2.6 K. Nagata(Osaka Univ.), Synthesis of Actinium Complex with a Macrocycle Having Pyridine Phosphonate Pendant Arms [138]4.2.7 T. Yamane(Nagaoka Univ. Tech.), Electrochemical method of minor actinide recovery from nitric acid solution using Ga liquid electrode and ionic liquid [140]4.2.8 M. Yokota(Kindai Univ.), Adsorptivity of monoamide polymer adsorbent impregnated with PPTPT to metal ions in neutral aqueous solutions for recovery of uranium in seawater [144]4.2.9 K. Mori(Kyoto Univ.), Introduction of Versatile Compact Neutron Diffractometer (VCND) at B-3 Beam Port of KUR [147]4.2.10 T. Kobayashi(SPring-8, JAEA), XAFS study on the the aged deterioration of a simulated fuel debris [148]Chapter 5 Concluding Remarks [152]5.1 S. Kambe(ASRC, JAEA), Concluding Remarks 1 [152]5.2 H. Yamagami(Kyoto Sangyo Univ.), Concluding Remarks 2 [154]Chapter 6 Summary of Discussion [155]Chapter 7 List of Participants [156]Chapter 8 Photos of the workshop [158

    Atomistic study of magnetite thin film interfaces and defects for Spintronic applications

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    Fe3O4 is a candidate material for future spintronic device applications due to its predicted half metallicity, high Curie temperature and lattice match with current oxide barrier materials. There have been numerous studies on Fe3O4(001)/MgO(001) heterostructures and devices in recent years which show structural defect formation has a significant influence on the properties of the grown layers and device performance. In this work I seek to advance our understanding of defect formation and heterostructure interfaces of epitaxially grown Fe3O4 layers on a range of substrates. Atomically resolved (S)TEM/EELS has been used as a main experimental techniques to determine the atomic structure of the defects and interfaces in order to model their effect of the functional properties of the thin films magnetite. Firstly we investigate the MBE growth of (111) oriented Fe3O4/MgO thin films. This creates highly ordered, atomically sharp APB defect boundaries rather than the random-like fractal geometry defects which have previously been observed in (001) oriented growth. This has enabled us to undertake atomistic modelling and begin to understand the APBs effect on the magnetic properties of grown films. We show that all APB defects exhibit a high density of high angle Fe-O-Fe bonds with antiferromagnetic coupling. The Fe3O4/MgO structure produces a high density of APB defects, and consequently anomalous properties of the grown films such as negative magnetoresistance and high saturating magnetic fields. In order to avoid crystal symmetry as an origin of APBs we undertook a MBE growth of Fe3O4/MgAl2O4 a spinel-spinel growth system. However, the presence of the APBs was still observed and their formation was discussed in terms of strain and 3D film growth. To reduce the density of defects in Fe3O4 we employed pulsed laser deposition with subsequent film annealing in a CO/CO2 atmosphere. This is shown to produce films with bulk like transport properties after a high temperature annealing process. Residual defects including twins were observed. These defects have a low density and the effect on overall film properties is small. Finally, using the spinel/perovskite model structure of Fe3O4/SrTiO3 we show the ability to produce atomically sharp oxide/oxide interfaces which open up the possibility of performing atomic level engineering to tailor potential oxide-oxide device functionality

    Exploring nanoscale properties of organic solar cells

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    The demand for electrical energy is steadily increasing. Highly efficient organic solar cells based on mixed, strongly absorbing organic molecules convert sunlight into electricity and, thus, have the potential to contribute to the worlds energy production. The continuous development of new materials during the last decades lead to a swift increase of power conversion efficiencies (PCE) of organic solar cells, recently reaching 12%. Despite these breakthroughs, the usage of highly complex organic molecules blended together to form a self-organised absorber layer results in complicated morphologies that are poorly understood. However, the morphology has a tremendous impact on the photon-to-electron conversion, affecting all processes ranging from light absorption to charge carrier extraction. This dissertation studies the role of phase-separation of the self-organised thin film blend layers utilized in organic solar cells. On the molecular scale, we manipulate the phase-separation, using different molecule combinations ranging from the well-known ZnPc:C 60 blend layers to highly efficient oligothiophene:C60 blend layers. On the macroscopic scale, we shape the morphology by depositing the aforementioned blend layers on differently heated substrates (in-vacuo substrate temperature, Tsub). To characterise the manufactured blend layers, we utilize high resolution microscopy techniques such as photoconductive atomic force microscopy, different electron microscopic techniques, X-ray microscopy etc., and various established and newly developed computational simulations to rationalise the experimental findings. This multi-technique, multi-scale approach fulfils the demands of several scientific articles to analyse a wide range of length scales to understand the underlying optoelectronic processes. Varying the mixing ratio of a ZnPc:C60 blend layer from 2:1 to 6:1 at fixed in vacuo substrate temperature results in a continuous increase of surface roughness, decrease of short-circuit current, and decrease of crystallinity. Additionally performed density functional theory calculations and 3D drift-diffusion simulations explain the observed crystalline ZnPc nanorod formation by the presence of C60 in the bulk volume and the in turn lowered recombination at crystalline ZnPc nanorods. Moving to oligothiophene:C60 blend layers used in highly efficient organic solar cells deposited at elevated substrate temperatures, we find an increase of phase-separation, surface roughness, decrease of oligothiophene-C60 contacts, and reduced disorder upon increasing Tsub from RT (PCE=4.5%) to 80 °C (PCE=6.8%). At Tsub =140 °C, we observe the formation of micrometer-sized aggregates on the surface resulting in inhomogeneous light absorption and charge carrier extraction, which in turn massively lowers the power conversion efficiency to 1.9%. Subtly changing the molecular structure of the oligothiophene molecule by attaching two additional methyl side chains affects the thin film growth, which is also dependent on the substrate type. In conclusion, the utilized highly sensitive characterisation methods are suitable to study the impact of the morphology on the device performance of all kinds of organic electronic devices, as we demonstrate for organic blend layers. At the prototypical ZnPc:C60 blend, we discovered a way to grow ZnPc nanorods from the blend layer. These nanorods are highly crystalline and facilitate a lowered charge carrier recombination which is highly desirable in organic solar cells. The obtained results at oligothiophene: C60 blends clearly demonstrate the universality of the multi-technique approach for an in-depth understanding of the fragile interplay between phase-separation and phase-connectivity in efficient organic solar cells. Overall, we can conclude that both molecular structure and external processing parameters affect the morphology in manifold ways and, thus, need to be considered already at the synthesis of new materials

    An investigation of fast and slow mapping

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    Children learn words astonishingly skilfully. Even infants can reliably “fast map” novel category labels to their referents without feedback or supervision (Carey & Bartlett, 1978; Houston-Price, Plunkett, & Harris, 2005). Using both empirical and neural network modelling methods this thesis presents an examination of both the fast and slow mapping phases of children's early word learning in the context of object and action categorisation. A series of empirical experiments investigates the relationship between within-category perceptual variability on two-year-old children’s ability to learn labels for novel categories of objects and actions. Results demonstrate that variability profoundly affects both noun and verb learning. A review paper situates empirical word learning research in the context of recent advances in the application of computational models to developmental research. Data from the noun experiments are then simulated using a Dynamic Neural Field (DNF) model (see Spencer & Schöner, 2009), suggesting that children’s early object categories can emerge dynamically from simple label-referent associations strengthened over time. Novel predictions generated by the model are replicated empirically, providing proofof- concept for the use of DNF models in simulations of word learning, as well emphasising the strong featural basis of early categorisation. The noun data are further explored using a connectionist architecture (Morse, de Greef, Belpaeme & Cangelosi, 2010) in a robotic system, providing the groundwork for future research in cognitive robotics. The implications of these different approaches to cognitive modelling are discussed, situating the current work firmly in the dynamic systems tradition whilst emphasising the value of interdisciplinary research in motivating novel research paradigms

    Astrophysics, Cosmology and Particle Phenomenology at the Energy Frontier

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    This dissertation consists of two parts, treating significantly separated fields. Each part consists on several chapters, each treating a somewhat isolated topic from the rest. In each chapter, I present some of the work developed during my passage through the graduate program, which has mostly been published elsewhere. Part I – Cosmic Rays and Particle Physics Chapter 1: In this chapter we present an introduction to the topic of cosmic ray physics, with an special focus on the so-called ultra high energy cosmic rays: their potential origins, effects during their propagation between their sources and Earth, the different techniques used for their detection, and the use of cosmic rays to explore fundamental physics at energies unattainable at particle accelerators. Chapter 2: In this chapter we expose some contributions to the understanding of the sources that UHECRs come from. In particular, this chapter explores some aspects of the hypothesis that starburst galaxies may be their origins. We explore the effect that interactions with cosmic microwave background photons within the source may have on the energy spectrum produced by such sources. Chapter 3: This chapter presents the influence of photon backgrounds like the solar radiation field, the cosmic microwave background or the extragalactic background light have on the propagation of cosmic rays from their source to the Earth, via nuclear photo- disintegration. In particular, we explore the the application of this effect to test violations of Lorentz invariance, and we point out the impact that inaccuracies in the description of photo-disintegration cross sections have as we try to understand the whole picture of cosmic ray production and propagation. Chapter 4: This chapter introduces another phenomenon that affects cosmic ray propagation, namely galactic magnetic fields. Magnetic fields bend charged cosmic ray trajectories, obscuring the association between individual events and their sources. This chapter explores a method by which cosmic ray acceleration, magnetic deflections and photo- disintegration are put together with the purpose of understanding cosmic ray composition. Besides that, we explore more closely the galactic magnetic field, and to which extent it can be constrained assuming that UHECRs are produced in starburst galaxies. Chapter 5: In this chapter I present my contributions to the understanding of neutrino cosmic rays. Specifically, the work in this chapter studies the spectrum of astrophysical neutrinos and the possibility that it exhibits a change in the slope at about few hundreds TeV, which could point to a transition between different astrophysical neutrino sources. Besides that, the possibility of using IceCube data to probe the neutrino cross sections beyond accelerator energies is also explored. Chapter 6: This chapter treats topics related to collective effects that may occur in the interactions of UHECRs in the atmosphere. More specifically, it is expected that when high enough energy densities are reached in nuclear collisions, a quark-gluon plasma may be formed. This would modify the produced particle spectrum as well as their angular distributions. This chapter deals with the possibility that a modification of the particle spectrum may suffice to explain the defect of muons at ground level that UHECR experiments observe. Chapter 7: This chapter presents explorations on the application of cosmic ray experi- ments to understand the detectability of more exotic systems. In particular, the absence of cosmic rays beyond some energy threshold allows us to set constraints on the properties of hypothetical super-heavy dark matter particles. On a different note, we explore the observability of the so-called macros: macroscopically sized nuggets composed of dark matter. Part II – Cosmology: Tensions & Conjectures Chapter 8: In this chapter, we present a far from exhaustive review of modern cosmology. Instead, we address the major points cosmology is based around nowadays, without offering a strong historical background. I start with the cosmological principle of homogeneity and isotropy, develop the mathematical framework to describe it, and assess what are the main contributions that drive the evolution of the Universe staying always in touch with observational evidence, that is, highlighting the impact of different cosmological effects on experimentally accessible observables such as the cosmic microwave background or the distance-redshift relation for several astrophysical objects. Chapter 9: In this chapter, we explore the cosmological implications of the Salam-Sezgin six-dimensional supergravity model after its compactification to a four-dimensional space. Such process gives rise to the presence of two coupled scalar fields. This is on par with the distance conjecture of Swampland program, by which the evolution of a rolling scalar field would produce a family of fields with masses related to such field. Here, we consider those fields as potential accounts of the dark energy and dark matter in our Universe, and explore the ability of such model to alleviate the Hubble constant tension. Chapter 10: In this chapter, we continue exploring cosmological models under the Swampland program. In particular, we consider general inflationary models mediated by scalar fields respecting S-duality invariance (that is, under φ → −φ field transformations). We study how these models are constrained by the distance and de Sitter swampland conjectures, which establish limits on the evolution of the fields. We study the feasibility of the conjecture-constrained models against measurements of the spectral index and the tensor-to-scalar ratio, parameters which measure the imprint of inflationary phenomenology on the cosmic microwave background. Chapter 11: In this chapter, we dive deeper into the Hubble constant tension. We consider a model in which several dark matter species evolve throughout the cosmological history. These particles can decay, without mixing with the standard model, into a dark radiation field. We implement a Markov chain Monte Carlo bayesian analysis to confront the large number of model parameters with a dataset comprised of multiple measurements of the Hubble parameter for low redshift, obtained as distance vs. redshift data for supernova and galaxies, as well as large scale structure information from baryon acoustic oscillations. Armed with these tools, we explore how the data constrains the number of fields, as well as their abundances and decay rates
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