Theory of ultrafast electron transfer from localized quantum states at surfaces .

190 p.The ability of materials to transfer electrons is a basic property controlling the functionality and performance of devices at the nanoscale. Of particular importance is the tranfor of electros at surfaces as a fundamental process in catalytic and photocatalytic applications. This work aims along these lines at a theoretical description of resonant charge injection at surfaces using a combination of density functional theory and Green's functions. A close comparison with available data from core-hole-clock experiments is maintained throughout the work and confirms the validity and predictive power of our first-principles approach. This is demonstrated on the basis of three prototypical systems where we study fundamental aspects of charge transfer, providing additional, often complementary information to the interpretation of the experiments. First, we present a detailed study of the effects of structural fluctuations on elastic charge transfer for isonicotinic acid adsorbed on rutile (110) in relation to photovoltaic applications. Second we explore spin-dependent charge injection from core-excited argon resonances on Co(0001) and Fe(110), with possible implications for spintronics. Third, we examine the directionality of charge transfer from sulfur related resonances at surfaces of layered 1T-TaS2 in the commensurate charge density wave phase.DIPC CSIC CICnanoGune CFM Marie Curie Action

NOVEL CARBON-BASED MATERIALS MIXING DIFFERENT HYBRIDIZATION KINDS

In the last twenty years, carbon-based materials and nanostructures have gained more and more popularity. Driven by the breakthrough-discovery and the synthesis of fullerenes, nanotubes, graphene and carbynes, also the search for new exotic carbon allotropes attracted increasing attention in the scientific community, also in view of applications. This thesis focuses on the construction and the investigation of three novel crystalline allotropes of carbon, all mixing different orbital hybridizations. We have employed state-of-the-art numerical simulations to investigate structural, electronic, and mechanical properties of the three structures. Two of these allotropes, novamene and protomene, combine sp2 and sp3 hybridizations and exhibit a semiconductor character in their lowest-energy Peierls-dimerized configuration. Both structures show transitions towards a metallic state at a relatively small energy cost. The third allotrope, zayedene, mixes sp, in the form of a linear chain, and sp3 providing an enclosing cage. This structure exhibits a clear metallic character due to the dangling bonds inside the cavity. We predict characteristic high-frequency vibrations associated with sp chain stretching modes. We also investigate the thermodynamic stability of zayedene at standard conditions. Finally we suggest how hundreds of different allotropes can be built from the simple ones investigated

Theory of ultrafast electron transfer from localized quantum states at surfaces .

190 p.The ability of materials to transfer electrons is a basic property controlling the functionality and performance of devices at the nanoscale. Of particular importance is the tranfor of electros at surfaces as a fundamental process in catalytic and photocatalytic applications. This work aims along these lines at a theoretical description of resonant charge injection at surfaces using a combination of density functional theory and Green's functions. A close comparison with available data from core-hole-clock experiments is maintained throughout the work and confirms the validity and predictive power of our first-principles approach. This is demonstrated on the basis of three prototypical systems where we study fundamental aspects of charge transfer, providing additional, often complementary information to the interpretation of the experiments. First, we present a detailed study of the effects of structural fluctuations on elastic charge transfer for isonicotinic acid adsorbed on rutile (110) in relation to photovoltaic applications. Second we explore spin-dependent charge injection from core-excited argon resonances on Co(0001) and Fe(110), with possible implications for spintronics. Third, we examine the directionality of charge transfer from sulfur related resonances at surfaces of layered 1T-TaS2 in the commensurate charge density wave phase.DIPC CSIC CICnanoGune CFM Marie Curie Action

Probing of dark energy properties in the Universe using astrophysical observations

The astrophysical data of the last two decades have allowed cosmologists to conclude that the present Universe is accelerating. The research carried out to find the origin of this phenomenon has led to the creation of a vast number of dark energy and modified gravity theories, of which the simplest is the ˄CDM model. The latter is, however, plagued with very difficult problems awaiting a solution. The work here presented seeks to contribute to the discussion of the possible explanation for the Cosmos' acceleration and other important questions in modern cosmology using the newest astrophysical observations available. This thesis starts by exploring a dark energy model dubbed thawing quintessence which is characterised by allowing a non constant ratio of pressure to density for dark energy that is however still close to -1 for most of the cosmological evolution, shifting away from this value when the domination of the radiation and matter components fades away. The findings are the most up-to-date constraints for which this model gives a viable theory for dark energy, including a bound on the equation of state at present of w < -0:88. This exact approach was contrasted with the use of an approximate equation-of-state parametrisation for thawing theories. The analysis also includes different parametrisation choices, and comments on the accuracy of the constraints imposed by CMB anisotropies alone. Next, the cosmology of hybrid metric-Palatini gravity is presented. This is a type of Modified Gravity theory in which the Lagrangian density for the gravitational action is a function of the Ricci scalars of both the connection and the metric. The background evolution of two models of this kind is examined explicitly showing the recovery of standard General Relativity at late times. The maximum deviation from the gravitational constant G at early times is constrained using a combination of geometrical data, finding it to be around 1%. A designer scenario, also introduced under the hybrid metric-Palatini formulation, is then used to explore to what extent early modifications of gravity, which become significant after recombination but then decay towards the present, can be constrained by current and future cosmological observations. This model is embedded in the effective field theory description of Horndeski scalar-tensor gravity with an early-time decoupling of the gravitational modification. Applying cosmological data, the constraints on the early-time deviations from General Relativity are obtained. These are dependent on the redshift at which the oscillations in the slip between the gravitational potentials are turned on. For zon = 1000, the deviation from Einstein's theory is ≤ 10-2 with 95% confidence. An explanation of the effect that these divergences have on the CMB power spectrum are discussed, as well as the effect that future 21 cm survey data will have on this study. The last part of this work is a move towards inflation, the early epoch of accelerated expansion undergone by the Universe. Here a parametrisation of the acceleration trajectory is investigated with the aim of measuring the rolling of the inflaton corresponding to the value of the tensor-to-scalar ratio r to be compared with future observations. Considering five ln ε amplitudes and 14 e-foldings, it was found that the posterior distribution of (r,∆Φ) is in very good agreement with Lyth's bound. The analysis included a histogram depiction of the latter result, from which later a minimum constraint on ∆ϕ for each of the bins was found. These outcomes constitute the intermediate step of this project which will be made more accurate by extending it to ~ 50 e-folds, a larger set of cosmological parameters and observational bounds that are restrictive on small scales

Development and Application of a Novel Enhanced Sampling Method and Bayesian Analysis for Characterizing Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are a class of proteins with wide-rangingsignificance in signaling and disease that do not adopt a dominant folded structure asmonomers. Rather, the structures of IDPs in solution are best described as ensembles ofconformational states that may range from being fully random coil to partially ordered.This structural plasticity of IDPs is theorized to facilitate regulation of their interactionwith other species, as in signal transduction or aggregation of IDPs into ordered fibrils.Characterizing the structural ensembles of IDPs in the free, solvated state is key tounderstanding the mechanisms of these interactions, and correspondingly the role an IDPspecies plays in signaling or disease.The rapid interconversion between conformational states, however, complicates theexperimental study of IDPs because most experimental signals report highly averagedinformation. Computational modeling with validation through comparison to experimenthas therefore been a main approach to characterizing IDP structure and dynamics. Thefocus of my dissertation is on the development of new methods for computational study ofIDPs, facilitating better and less expensive de novo generation of IDP structural ensemblesand improving the metrics used to evaluate the degree of agreement between a simulatedensemble and a set of experimental data.Despite vast improvements in computational power and efficiency, moleculardynamics (MD) simulations of IDPs for generating conformational ensembles are stilllimited by the expense of calculations. In Chapter 2 I present the development of a newenhanced sampling method – temperature cool walking (TCW) – and comparison of itsperformance against a standard method – temperature replica exchange (TREx). The TCWmethod accelerates the rate of convergence to the equilibrium conformational ensemblewith increased sampling acceleration relative to TREx at greatly reduced computationalcost.The second major limitation in MD is the accuracy of the force field. Most classicalfixed charge force fields were parameterized using data from folded proteins, and havebeen thought to be biased to overly collapsed and structured conformations. This hasmotivated the development of IDP-tailored force fields that sample greater disorder, at thepotential expense of the ability to model stabilizing interactions between an IDP and itsbinding partners. In Chapter 3, I assess to what degree the shortcomings assigned tostandard force fields may be due to insufficient sampling by characterizing theperformance of standard and newly modified force fields on the Alzheimer’s peptideamyloid-β using both TREx and TCW. We find that with improved sampling, standard andmodified force fields produce similar structural ensembles, suggesting that both areappropriate for simulation of the disordered state. In Chapter 4 I present preliminaryresults building off of this work by characterizing the performance of a polarizable forcefield modeling a synthetic peptide that demonstrates complete loss of helical content withincreasing temperature. Inclusion of polarization effects has been thought to be key foraccurate modeling of such multicomponent systems, especially when there is a shift in theelectrostatic environment as is the case for the unfolding peptide. Our early results, whilelimited by current lack of convergence for tests using the polarizable force field andneeding further confirmation, match that expectation by finding early evidence of greaterresponse to temperature by the polarizable force field than fixed charge comparators.The last work presented here is in the development of new methods for calculatingthe degree of agreement between a simulated IDP ensemble and experimental data. Backcalculationof experimental data from structure can be very imprecise, motivating thedevelopment in Chapter 5 of scoring formalisms that account for variable uncertainties inboth back-calculation and experiment for diverse experimental data types. In summary, themethods described in this dissertation seek to improve computational study of IDPs byfacilitating better, less expensive generation of IDP ensembles and producing moreinformative metrics for evaluating their agreement with experiment