The Conformational Space of a Flexible Amino Acid at Metallic Surfaces

In interfaces between inorganic and biological materials relevant for technological applications, the general challenge of structure determination is exacerbated by the high flexibility of bioorganic components, chemical bonding, and charge rearrangement at the interface. In this paper, we investigate a chemically complex building block, namely, the arginine (Arg) amino-acid interfaced with Cu, Ag and Au (111) surfaces. We investigate how the environment changes the accessible conformational space of this amino acid, by building and analyzing a database of thousands of structures optimized with the PBE functional including screened pairwise van der Waals interactions. When in contact with metallic surfaces, the accessible space for Arg is dramatically reduced, while the one for Arg-H$^+$ is instead increased if compared to the gas-phase. This is explained by the formation of strong bonds between Arg and the surfaces and by their absence and charge screening on Arg-H$^+$ upon adsorption. We also observe protonation-dependent stereoselective binding of the amino acid to the metal surfaces: Arg adsorbs with its chiral C$_\alpha$H center pointing H away from the surfaces while Arg-H$^+$ adsorbs with H pointing toward the surface

Fine Tuning Classical and Quantum Molecular Dynamics using a Generalized Langevin Equation

Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. By developing quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, we show that these analytical results accurately predict the behavior of strongly anharmonic systems. We also show that it is possible to correct, to a significant extent, the effects of the GLE term onto the corresponding microcanonical dynamics, which puts on more solid grounds the use of non-equilibrium Langevin dynamics to approximate quantum nuclear effects and could help improve the prediction of dynamical quantities from techniques that use a Langevin term to stabilize dynamics. Finally we address the use of thermostats in the context of approximate path-integral-based models of quantum nuclear dynamics. We demonstrate that a custom-tailored GLE can alleviate some of the artifacts associated with these techniques, improving the quality of results for the modelling of vibrational dynamics of molecules, liquids and solids

Impact of vibrational entropy on the stability of unsolvated peptide helices with increasing length

Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well studied unsolvated alanine based polypeptides, Ac-Alan-LysH+. By exploring extensively the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n=4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics), but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through \emph{ab initio} molecular dynamics, and generalized by testing different terminations and considering larger helical peptide models

How to remove the spurious resonances from ring polymer molecular dynamics

Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the desirable features of RPMD: thermostatted RPMD (TRPMD) is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD

Flat Slabs with Different Longitudinal Reinforcement Ratios Under Horizontal Cyclic Loading

The following dissertation studies the behavior of flat slabs when subjected to constant vertical loads and cyclic horizontal displacements, as a continuation of previous studies developed at FCT/UNL. The main focus of this research is to study the influence of flexural reinforcement on the seismic response of flat slabs. Therefore, three reinforced concrete flat slabs with varying flexural reinforcement ratio were tested, two having the same top reinforcement ratio of !=0,64% and one with !=1,34%. One of the specimens with lower longitudinal ratio was reinforced with studs as specific punching shear reinforcement. All slabs had overall dimensions of 4,15 × 1,85 × 0,15 m3 and a gravity shear ratio, ratio between the gravity load and the punching shear resistance, approximately equal to 55%. For a more complete analysis the results obtained were compared to two other specimens from previous experimental campaigns also conducted at FCT/UNL. These two slabs were designed with top flexural reinforcement ratio (!=0,96%) that lies between the two tested in this dissertation, one with no shear-reinforcement and the other with headed studs. Results showed that the reduction of flexural reinforcement resulted in a more ductile behavior of the specimens and in a higher drift capacity. The high flexural ratio added to one specimen improved the maximum unbalanced moment capacity but also made the slab fail in a more brittle mode. As expected, the specimen with shear headed studs supported the highest drifts and ended up not failing during this experimental campaign, reaching the test setup upper limit.A presente dissertação estuda o comportamento de lajes fungiformes submetidas a carga vertical constante e carregamento horizontal cíclico, sendo a continuação de trabalhos realizados anteriormente no Departamento de Engenharia Civil da FCT/UNL. O principal objetivo deste trabalho é estudar a influência da variação da taxa de reforço longitudinal na resposta sísmica de lajes fungiformes. Assim, três modelos de lajes fungiformes com variação da taxa de armadura longitudinal foram fabricados e testados, dois com a mesma taxa de !=0,64% e outro com !=1,34%. Um dos modelos com baixa taxa de armadura longitudinal foi reforçado com reforço específico ao punçoamento. Todas as lajes possuíam as mesmas dimensões de 4,15 × 1,85 × 0,15 m3 e razão entre a carga vertical e a resistência ao punçoamento aproximadamente igual a 55%. Para uma análise mais completa, os resultados obtidos foram comparados com outros dois modelos testados anteriormente na FCT/UNL. Estas duas lajes possuíam uma taxa intermédia de reforço longitudinal (!=0,96%), uma sem armadura específica de punçoamento e a outra contendo “shear studs”. Os resultados mostraram que a redução da taxa de armadura longitudinal resultou num comportamento mais dúctil das lajes e numa capacidade maior de deslocamentos horizontais. A utilização da taxa mais elevada de armadura longitudinal laje melhorou a capacidade máxima de momentos não balanceados, mas também fez com que a estrutura tivesse uma rotura mais frágil. Como esperado, o modelo com “studs” suportou os maiores “drifts” e acabou não rompendo durante o ensaio, devido a ter sido atingido o limite do sistema de ensaio

Health and Happiness in Uruguay

This article presents a study of the relationship between self-reported happiness and selfassessed health status at the individual level, using the Religion, Health, and Young Emancipation ISSP survey for Uruguay in 2008. Probit estimates suggest that better selfassessed health status is highly correlated with greater levels of self-reported happiness. In order to control for the observed heterogeneity, models are estimated using matching methods. Results show that individuals who report themselves to be in good health have a probability of being at the highest level of happiness between 18 and 29 percentage points higher than individuals who report worse health.happiness, health, matching methods

Elucidating the NuclearQuantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule: A complex paradigmatic system where the making and breaking of H-bonds in a highly anharmonic potential energy surface requires a quantum mechanical treatment not only of the electrons, but also of the nuclei. We combine density-functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates, but between 100 K and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of $2.19 \times 10^{11} \mathrm{s}^{-1}$ at 150 K and $0.63 \times 10^{11} \mathrm{s}^{-1}$ at 100 K, in good agreement with experiment. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostatted ring-polymer molecular dynamics simulations. The position and lineshape of this peak, centered at around 2600 cm$^{-1}$ and spanning 750 cm$^{-1}$, stems from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to $cis$-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQE) influence properties of these systems. In this work, we explore the impact of NQE on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account conformational entropy and anharmonicities at finite temperatures. We propose that when when adsorption is weak and NQE on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We calculate the contribution of NQE to the free energies, including anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared to harmonic estimates. We also find that the dissociation has a negligible contribution from tunneling, but is dominated by ZPE, which can enhance the rate by three orders of magnitude. Finally we highlight how both temperature and NQE indirectly impact dipoles and the redistribution of electron density, causing work function to changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces