Modeling Ultrafast Spectroscopy of the NADH Dimer: From UV-VIS to X-rays

Ultrafast pump-probe spectroscopy is a conceptually simple and versatile tool for resolving photoinduced dynamics in molecular systems. Due to the fast development of new experimental setups, such as synchrotron light sources and X-ray free electron lasers (XFEL), new spectral windows are becoming accessible. On the one hand, these sources have enabled scientist to access faster and faster time scales and to reach unprecedent insights into dynamical properties of matter. On the other hand, the complementarity of well-developed and novel techniques allows to study the same physical process from different points of views, integrating the advantages and overcoming the limitations of each approach. In this context, it is highly desirable to reach a clear understanding of which type of spectroscopy is more suited to capture a certain facade of a given photo-induced process, that is, to establish a correlation between the process to be unraveled and the technique to be used. In this thesis, I will show how computational spectroscopy can be a tool to establish such a correlation. I will study a specific process, which is the ultrafast energy transfer in the nicotinamide adenine dinucleotide dimer (NADH). This process will be observed in different spectral windows (from UV-VIS to X-rays), accessing the ability of different spectroscopic techniques to unravel the system evolution by means of state-of-the-art theoretical models and methodologies. The comparison of different spectroscopic simulations will demonstrate their complementarity, eventually allowing to identify the type of spectroscopy that is best suited to resolve the ultrafast energy transfer.

Longitudinal bar buckling behavior

Reinforced concrete columns might fail because of buckling of the longitudinal reinforcing bar when exposed to earthquake motions. Depending on the hoop stiffness and the length-over-diameter ratio, the instability can be local (in between two subsequent hoops) or global (the buckling length comprises several hoop spacings). To get insight into the topic, an extensive literary research of 19 existing models has been carried out including different approaches and assumptions which yield different results. Finite element fiberanalysis was carried out to study the local buckling behavior with varying length-over-diameter and initial imperfection-over-diameter ratios. The comparison of the analytical results with some experimental results shows good agreement before the post buckling behavior undergoes large deformation. Furthermore, different global buckling analysis cases were run considering the influence of different parameters; for certain hoop stiffnesses and length-over-diameter ratios local buckling was encountered. A parametric study yields an adimensional critical stress in function of a stiffness ratio characterized by the reinforcement configuration. Colonne in cemento armato possono collassare per via dell’instabilità dell’armatura longitudinale se sottoposte all’azione di un sisma. In funzione della rigidezza dei ferri trasversali e del rapporto lunghezza d’inflessione-diametro, l’instabilità può essere locale (fra due staffe adiacenti) o globale (la lunghezza d’instabilità comprende alcune staffe). Per introdurre alla materia, è proposta un’esauriente ricerca bibliografica di 19 modelli esistenti che include approcci e ipotesi differenti che portano a risultati distinti. Tramite un’analisi a fibre e elementi finiti si è studiata l’instabilità locale con vari rapporti lunghezza d’inflessione-diametro e imperfezione iniziale-diametro. Il confronto dei risultati analitici con quelli sperimentali mostra una buona coincidenza fino al raggiungimento di grandi spostamenti. Inoltre, il caso d’instabilità globale è stato simulato valutando l’influenza di vari parametri; per certe configurazioni di rigidezza delle staffe e lunghezza d’inflessione-diametro si hanno ottenuto casi di instabilità locale. Uno studio parametrico ha permesso di ottenere un carico critico adimensionale in funzione del rapporto di rigidezza dato dalle caratteristiche dell’armatura.

Gyrokinetic modelling of plasma transport and investigation on test particle dynamics

Turbulent plasmas inside tokamaks are modeled and studied using guiding center theory, applied to charged test particles, in a Hamiltonian framework. The equations of motion for the guiding center dynamics, under the conditions of a constant and uniform magnetic field and turbulent electrostatic field are derived by averaging over the fast gyroangle, for the first and second order in the guiding center potential, using invertible changes of coordinates such as Lie transforms. The equations of motion are then made dimensionless, exploiting temporal and spatial periodicities of the model chosen for the electrostatic potential. They are implemented numerically in Python. Fast Fourier Transform and its inverse are used. Improvements to the original Python scripts are made, notably the introduction of a power-law curve fitting to account for anomalous diffusion, the possibility to integrate the equations in two steps to save computational time by removing trapped trajectories, and the implementation of multicolored stroboscopic plots to distinguish between trapped and untrapped guiding centers. The post-processing of the results is made in MATLAB. The values and ranges of the parameters chosen for the simulations are selected based on numerous simulations used as feedback tools. In particular, a recurring value for the threshold to detect trapped trajectories is evidenced. Effects of the Larmor radius, the amplitude of the guiding center potential and the intensity of its second order term are studied by analyzing their diffusive regimes, their stroboscopic plots and the shape of guiding center potentials. The main result is the identification of cases anomalous diffusion depending on the values of the parameters (mostly the Larmor radius). The transitions between diffusive regimes are identified. The presence of highways for the super-diffusive trajectories are unveiled. The influence of the charge on these transitions from diffusive to ballistic behaviors is analyzed.

Numerical study on viscoelastic behavior of polypropylene fiber reinforced concrete subjected to temperature variations using LDPM theory

This thesis is focused on the viscoelastic behavior of macro-synthetic fiber-reinforced concrete (MSFRC) with polypropylene studied numerically when subjected to temperature variations (-30 oC to +60 oC). LDPM (lattice discrete particle model), a meso-scale model for heterogeneous composites, is used. To reproduce the MSFRC structural behavior, an extended version of LDPM that includes fiber effects through fiber-concrete interface micromechanics, called LDPM-F, is applied. Model calibration is performed based on three-point bending, cube, and cylinder test for plain concrete and MSFRC. This is followed by a comprehensive literature study on the variation of mechanical properties with temperature for individual fibers and plain concrete. This literature study and past experimental test results constitute inputs for final numerical simulations. The numerical response of MSFRC three-point bending test is replicated and compared with the previously conducted experimental test results; finally, the conclusions were drawn. LDPM numerical model is successfully calibrated using experimental responses on plain concrete. Fiber-concrete interface micro-mechanical parameters are subsequently fixed and LDPM-F models are calibrated based on MSFRC three-point bending test at room temperature. Number of fibers contributing crack bridging mechanism is computed and found to be in good agreement with experimental counts. Temperature variations model for individual constituents of MSFRC, fibers and plain concrete, are implemented in LDPM-F. The model is validated for MSFRC three-point bending stress-CMOD (crack mouth opening) response reproduced at -30 oC, -15 oC, 0 oC, +20 oC, +40 oC and +60 oC. It is found that the model can well describe the temperature variation behavior of MSFRC. At positive temperatures, simulated responses are in good agreement. Slight disagreement in negative regimes suggests an in-depth study on fiber-matrix interface bond behavior with varying temperatures.