Experimental and Theoretical Models to Probe Mechanisms of Biological Charge Flow

Nature is challenged to move charge efficiently over many length scales. From sub-nm to μm distances, electron-transfer proteins orchestrate energy conversion, storage, and release both inside and outside the cell. Uncovering the detailed mechanisms of biological electron-transfer reactions, which are often coupled to bond-breaking and bond-making events, is essential to designing durable, artificial energy conversion systems that mimic the specificity and efficiency of their natural counterparts. Here, we use theoretical modeling of long-distance charge hopping (Chapter 3), synthetic donor-bridge-acceptor molecules (Chapters 4, 5, and 6), and de novo protein design (Chapters 5 and 6) to investigate general principles that govern light-driven and electrochemically driven electron-transfer reactions in biology. We show that fast, μm-distance charge hopping along bacterial nanowires requires closely packed charge carriers with low reorganization energies (Chapter 3); singlet excited-state electronic polarization of supermolecular electron donors can attenuate intersystem crossing yields to lower-energy, oppositely polarized, donor triplet states (Chapter 4); the effective static dielectric constant of a small (~100 residue) de novo designed 4-helical protein bundle can change upon phototriggering an electron transfer event in the protein interior, providing a means to slow the charge-recombination reaction (Chapter 5); and a tightly-packed de novo designed 4-helix protein bundle can drastically alter charge-transfer driving forces of photo-induced amino acid radical formation in the bundle interior, effectively turning off a light-driven oxidation reaction that occurs in organic solvent (Chapter 6). This work leverages unique insights gleaned from proteins designed from scratch that bind synthetic donor-bridge-acceptor molecules that can also be studied in organic solvents, opening new avenues of exploration into the factors critical for protein control of charge flow in biology.

Fossil associations from the middle and upper Eocene strata of the Pamplona Basin and surrounding areas (Navarre, western Pyrenees)

Fossil associations from the middle and upper Eocene (Bartonian and Priabonian) sedimentary succession of the Pamplona Basin are described. This succession was accumulated in the western part of the South Pyrenean peripheral foreland basin and extends from deep-marine turbiditic (Ezkaba Sandstone Formation) to deltaic (Pamplona Marl, Ardanatz Sandstone and Ilundain Marl formations) and marginal marine deposits (Gendulain Formation). The micropalaeontological content is high. It is dominated by foraminifera, and common ostracods and other microfossils are also present. The fossil ichnoasssemblages include at least 23 ichnogenera and 28 ichnospecies indicative of Nereites, Cruziana, Glossifungites and ?Scoyenia-Mermia ichnofacies. Body macrofossils of 78 taxa corresponding to macroforaminifera, sponges, corals, bryozoans, brachiopods, annelids, molluscs, arthropods, echinoderms and vertebrates have been identified. Both the number of ichnotaxa and of species (e. g. bryozoans, molluscs and condrichthyans) may be considerably higher. Body fossil assemblages are comparable to those from the Eocene of the Nord Pyrenean area (Basque Coast), and also to those from the Eocene of the west-central and eastern part of South Pyrenean area (Aragon and Catalonia). At the European scale, the molluscs assemblages seem endemic from the Pyrenean area, although several Tethyan (Italy and Alps) and Northern elements (Paris basin and Normandy) have been recorded. Palaeontological data of studied sedimentary units fit well with the shallowing process that throughout the middle and late Eocene occurs in the area, according to the sedimentological and stratigraphical data.

Evaluation of strontium-site-deficient Sr2Fe1.4Co0.1Mo0.5O6-δ-based perovskite oxides as intermediate temperature solid oxide fuel cell cathodes

In this paper strontium-site-deficient Sr₂Fe_1.4Co_0.1Mo_0.5O_6-δ-based perovskite oxides (S_xFCM) were prepared and evaluated as the cathode materials for intermediate temperature solid oxide fuel cells (IT-SOFCs). All samples exhibited a cubic phase structure and the lattice shrinked with increasing the Sr-deficiency as shown in XRD patterns. XPS results determined that the transition elements (Co/Fe/Mo) in S_xFCM oxides were in a mixed valence state, demonstrating the small polaron hopping conductivity mechanism existed. Among the samples, S_1.950FCM presented the lowest coefficient of thermal expansion of 15.62 × 10^-6 K^-1, the highest conductivity value of 28 S cm^-1 at 500 °C, and the lowest interfacial polarization resistance of 0.093 Ω cm² at 800 °C, respectively. Furthermore, an anode-supported single cell with a S_1.950FCM cathode was prepared, demonstrating a maximum power density of 1.16 W cm^-2 at 800 °C by using wet H₂ (3% H₂O) as the fuel and ambient air as the oxidant. These results indicate that the introduction of Sr-deficiency can dramatically improve the electrochemical performance of Sr₂Fe_1.4Co_0.1Mo_0.5O_6-δ, showing great promise as a novel cathode candidate material for IT-SOFCs.

High-temperature superconductivity in the two-dimensional t-J model: Gutzwiller wavefunction solution

A systematic diagrammatic expansion for Gutzwiller wavefunctions (DE-GWFs) proposed very recently is used for the description of the superconducting (SC) ground state in the two-dimensional square-lattice t-J model with the hopping electron amplitudes t (and t') between nearest (and next-nearest) neighbors. For the example of the SC state analysis we provide a detailed comparison of the method's results with those of other approaches. Namely, (i) the truncated DE-GWF method reproduces the variational Monte Carlo (VMC) results and (ii) in the lowest (zeroth) order of the expansion the method can reproduce the analytical results of the standard Gutzwiller approximation (GA), as well as of the recently proposed 'grand-canonical Gutzwiller approximation' (called either GCGA or SGA). We obtain important features of the SC state. First, the SC gap at the Fermi surface resembles a d(x2-y2) wave only for optimally and overdoped systems, being diminished in the antinodal regions for the underdoped case in a qualitative agreement with experiment. Corrections to the gap structure are shown to arise from the longer range of the real-space pairing. Second, the nodal Fermi velocity is almost constant as a function of doping and agrees semi-quantitatively with experimental results. Third, we compare the

Múltiplas antenas como alternativa para aumentar a taxa de extração de chaves secretas em redes veiculares com desvanecimento lento

The communication in vehicular ad hoc networks (VANETs) is commonly divided in two scenarios, namely vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I). Aiming at establishing secure communication against eavesdroppers, recent works have proposed the exchange of secret keys based on the variation in received signal strength (RSS). However, the performance of such scheme depends on the channel variation rate, being more appropriate for scenarios where the channel varies rapidly, as is usually the case with V2V communication. In the communication V2I, the channel commonly undergoes slow fading. In this work we propose the use of multiple antennas in order to artificially generate a fast fading channel so that the extraction of secret keys out of the RSS becomes feasible in a V2I scenario. Numerical analysis shows that the proposed model can outperform, in terms of secret bit extraction rate, a frequency hopping-based method proposed in the literature.

Neural Modulation of Leg Stiffness in Response to Neuromuscular Fatigue

The spring-mass model is able to accurately represent hopping spring-like behavior (leg and joint stiffness), and leg and joint stiffness changes can reveal overall motor control responses to neural and muscular contributors of neuromuscular fatigue. By understanding leg stiffness modulation, we can determine which variables the nervous system targets to maintain motor performance and stability. The purpose of this study was to determine how neuromuscular fatigue affects hopping behavior by examining leg and joint stiffness before and after a single-leg calf raise fatiguing protocol. Post-fatigue, leg stiffness decreased for the exercised leg, but not for the non-exercised leg. Ankle and knee joint stiffness did not significantly change for either leg. This indicates that leg stiffness decreases primarily from muscular fatigue, but was not explained by ankle and knee joint stiffness. The decrease in leg stiffness may be an attempt to soften landing impact, while at the same time maintaining performance.

Polycrystalline diamond thin film as wide bandgap material: the optoelectronic behaviour and the relationship with the structure

In this work metal - Microwave Plasma CVD diamond Schottky devices were studied. The current density vs. applied voltage reveals rectification ratios up to 10(4) at \ +/- 2V \. Under illumination an inversion and increase of the rectification is observed. The carrier density is 10(15) cm(-3) and the ideality factors near 1.5. The dark current vs. temperature shows that below 150 K the bulk transport is controlled by a hopping process with a density of defects of 10(16) cm(-3). For higher temperatures an extrinsic ionisation with activation energy of 0.3 eV takes place. The correlation with the polycrystalline nature of the samples is focused.

Topological massive Dirac edge modes and long-range superconducting Hamiltonians

We discover novel topological effects in the one-dimensional Kitaev chain modified by long-range Hamiltonian deformations in the hopping and pairing terms. This class of models display symmetry-protected topological order measured by the Berry/Zak phase of the lower-band eigenvector and the winding number of the Hamiltonians. For exponentially decaying hopping amplitudes, the topological sector can be significantly augmented as the penetration length increases, something experimentally achievable. For power-law decaying superconducting pairings, the massless Majorana modes at the edges get paired together into a massive nonlocal Dirac fermion localized at both edges of the chain: a new topological quasiparticle that we call topological massive Dirac fermion. This topological phase has fractional topological numbers as a consequence of the long-range couplings. Possible applications to current experimental setups and topological quantum computation are also discussed.

Polycrystalline diamond thin film as wide bandgap material: the optoelectronic behaviour and the relationship with the structure

In this work metal - Microwave Plasma CVD diamond Schottky devices were studied. The current density vs. applied voltage reveals rectification ratios up to 10(4) at \ +/- 2V \. Under illumination an inversion and increase of the rectification is observed. The carrier density is 10(15) cm(-3) and the ideality factors near 1.5. The dark current vs. temperature shows that below 150 K the bulk transport is controlled by a hopping process with a density of defects of 10(16) cm(-3). For higher temperatures an extrinsic ionisation with activation energy of 0.3 eV takes place. The correlation with the polycrystalline nature of the samples is focused.

Electronic transport in field-effect transistors of sexithiophene

The electronic conduction of thin-film field-effect-transistors (FETs) of sexithiophene was studied. In most cases the transfer curves deviate from standard FET theory; they are not linear, but follow a power law instead. These results are compared to conduction models of "variable-range hopping" and "multi-trap-and-release". The accompanying IV curves follow a Poole-Frenkel (exponential) dependence on the drain voltage. The results are explained assuming a huge density of traps. Below 200 K, the activation energy for conduction was found to be ca. 0.17 eV. The activation energies of the mobility follow the Meyer-Neldel rule. A sharp transition is seen in the behavior of the devices at around 200 K. The difference in behavior of a micro-FET and a submicron FET is shown. (C) 2004 American Institute of Physics.

Disorder driven transitions in non-equilibrium quantum systems

This thesis presents studies of the role of disorder in non-equilibrium quantum systems. The quantum states relevant to dynamics in these systems are very different from the ground state of the Hamiltonian. Two distinct systems are studied, (i) periodically driven Hamiltonians in two dimensions, and (ii) electrons in a one-dimensional lattice with power-law decaying hopping amplitudes. In the first system, the novel phases that are induced from the interplay of periodic driving, topology and disorder are studied. In the second system, the Anderson transition in all the eigenstates of the Hamiltonian are studied, as a function of the power-law exponent of the hopping amplitude.

In periodically driven systems the study focuses on the effect of disorder in the nature of the topology of the steady states. First, we investigate the robustness to disorder of Floquet topological insulators (FTIs) occurring in semiconductor quantum wells. Such FTIs are generated by resonantly driving a transition between the valence and conduction band. We show that when disorder is added, the topological nature of such FTIs persists as long as there is a gap at the resonant quasienergy. For strong enough disorder, this gap closes and all the states become localized as the system undergoes a transition to a trivial insulator.

Interestingly, the effects of disorder are not necessarily adverse, disorder can also induce a transition from a trivial to a topological system, thereby establishing a Floquet Topological Anderson Insulator (FTAI). Such a state would be a dynamical realization of the topological Anderson insulator. We identify the conditions on the driving field necessary for observing such a transition. We realize such a disorder induced topological Floquet spectrum in the driven honeycomb lattice and quantum well models.

Finally, we show that two-dimensional periodically driven quantum systems with spatial disorder admit a unique topological phase, which we call the anomalous Floquet-Anderson insulator (AFAI). The AFAI is characterized by a quasienergy spectrum featuring chiral edge modes coexisting with a fully localized bulk. Such a spectrum is impossible for a time-independent, local Hamiltonian. These unique characteristics of the AFAI give rise to a new topologically protected nonequilibrium transport phenomenon: quantized, yet nonadiabatic, charge pumping. We identify the topological invariants that distinguish the AFAI from a trivial, fully localized phase, and show that the two phases are separated by a phase transition.

The thesis also present the study of disordered systems using Wegner's Flow equations. The Flow Equation Method was proposed as a technique for studying excited states in an interacting system in one dimension. We apply this method to a one-dimensional tight binding problem with power-law decaying hoppings. This model presents a transition as a function of the exponent of the decay. It is shown that the the entire phase diagram, i.e. the delocalized, critical and localized phases in these systems can be studied using this technique. Based on this technique, we develop a strong-bond renormalization group that procedure where we solve the Flow Equations iteratively. This renormalization group approach provides a new framework to study the transition in this system.

Change, stability and prediction of gross motor co-ordination in portuguese children

The knowledge about intra- and inter-individual variation can stimulate attempts at description, interpretation and prediction of motor co-ordination (MC). Aim: To analyse change, stability and prediction of motor co-ordination (MC) in children. Subjects and methods: A total of 158 children, 83 boys and 75 girls, aged 6, 7 and 8 years, were evaluated in 2006 and re-evaluated in 2012 at 12, 13 and 14 years of age. MC was assessed through the Kiphard-Schilling’s body co-ordination test and growth, skeletal maturity, physical fitness, fundamental motor skills (FMS), physical activity and socioeconomic status (SES) were measured and/or estimated. Results: Repeated-measures MANOVA indicated that there was a significant effect of group, sex and time on a linear combination of the MC tests. Univariate tests revealed that group 3 (8–14 years) scored significantly better than group 1 (6–12 years) in all MC tests and boys performed better than girls in hopping for height and moving sideways. Scores in MC were also higher at follow-up than at baseline. Inter-age correlations for MC were between 0.15–0.74. Childhood predictors of MC were growth, physical fitness, FMS, physical activity and SES. Biological maturation did not contribute to prediction of MC. Conclusion: MC seemed moderately stable from childhood through adolescence and, additionally, inter-individual predictors at adolescence were growth, FMS, physical fitness, physical activity and SES.

Change, stability and prediction of gross motor co-ordination in portuguese children

The knowledge about intra- and inter-individual variation can stimulate attempts at description, interpretation and prediction of motor co-ordination (MC). Aim: To analyse change, stability and prediction of motor co-ordination (MC) in children. Subjects and methods: A total of 158 children, 83 boys and 75 girls, aged 6, 7 and 8 years, were evaluated in 2006 and re-evaluated in 2012 at 12, 13 and 14 years of age. MC was assessed through the Kiphard-Schilling’s body co-ordination test and growth, skeletal maturity, physical fitness, fundamental motor skills (FMS), physical activity and socioeconomic status (SES) were measured and/or estimated. Results: Repeated-measures MANOVA indicated that there was a significant effect of group, sex and time on a linear combination of the MC tests. Univariate tests revealed that group 3 (8–14 years) scored significantly better than group 1 (6–12 years) in all MC tests and boys performed better than girls in hopping for height and moving sideways. Scores in MC were also higher at follow-up than at baseline. Inter-age correlations for MC were between 0.15–0.74. Childhood predictors of MC were growth, physical fitness, FMS, physical activity and SES. Biological maturation did not contribute to prediction of MC. Conclusion: MC seemed moderately stable from childhood through adolescence and, additionally, inter-individual predictors at adolescence were growth, FMS, physical fitness, physical activity and SES.