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Struktura a dynamika peptidů a proteinů v roztoku:aplikace Ramanovy optické aktivity / Structure and dynamics of peptides and proteins in solution: application of Raman optical activityProfant, Václav January 2017 (has links)
The thesis inquires the specific and advantageous applications of Raman optical activity (ROA) in wide range of diverse structural and conformational studies of biomolecules and other biologically important molecules. Our investigation was focused on several interconnected topics covering the fields of methodology, basic and applied research. The combination of experimental and theoretical approaches facilitated deeper understanding of studied phenomena, and allowed for the effects of solute-solvent interactions. High-quality spectra of model molecules in the C-H stretching region, acquired as a result of successful extension of ROA measurements to the whole region of fundamental molecular vibrations, enabled verification and further development of methods for ROA spectra simulations encompassing anharmonic corrections. Utilizing spirodilactams with highly nonplanar amide groups, we have traced the specific ROA spectral manifestations of amide nonplanarity. In case of antimicrobial peptide lasiocepsine, we have successfully simulated ROA signals of S-S stretching vibrations which contrary to current belief do not seem to reflect sense of the S-S group torsion. In larger molecular systems, we have better understood the process of the formation of stable polyproline II conformation and proved that ROA may...
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UNDERSTANDING THE DECOMPOSITION PROCESSES OF HIGH-ENERGY DENSITY MATERIALSMichael N Sakano (11173161) 23 July 2021 (has links)
<div>For decades, the response of high-energy (HE) density materials at extreme conditions of pressure and temperature from strong insults like burning or impact have been studied in depth by the shock community. Shock physicists aim to develop a fundamental understanding for coupled chemical and physical processes across orders of magnitude spatial and temporal regimes. In order to succeed, this requires extensive collaboration between experiments and simulations, ranging from the electronic to the engineering scales. The end goals would be to develop predictive multiscale models capable of explaining ignition and initiation of HE systems and composites. The collected works in this thesis detail my contributions to the field of HE materials, specifically addressing the chemical reactivity at the atomistic level using reactive molecular dynamics (MD) simulations.</div><div><div>Through this endeavor, we aim to develop a critical understanding for the decomposition processes of HE materials. We begin with a validation the reactive force field, ReaxFF, by addressing the very strong anisotropic shock sensitivity in 2,2-Bis[(nitrooxy)methyl]propane-1,3-diyl dinitrate (PETN) through direct comparison of time-evolved spectra between experiments and simulations. Such strong orientation dependence is thought to relate to the initial decomposition events. Therefore we compare spectra at three different shock pressures, where we observe similar timescales for the disappearance of the NO2 symmetric and antisymmetric stretch modes. A more detailed chemical species analysis indicates that the NO2 molecular species could be considered the primary intermediate which initiates the decomposition process. Furthermore, these results suggest that the combination of explicit MD simulations and ultrafast spectroscopy will be key to the development of a detailed understanding of chemistry at extreme conditions.</div></div><div><div>Following the validation study, we further our understanding of reactivity in HE systems by investigating the differences in kinetics between an ordered and disordered system. It has been shown that shocked material is often severely strained, causing a loss in crystalline order. This in turn results in the disordered materials, such as amorphous solids, having</div><div>faster reactivity due to their higher internal energy and/or lower thermal conductivity. Our results indicate that extra energy is required to break the long-range order in bulk crystalline systems, thus resulting in slower decomposition rates. Further analyses of thermal hotspots point towards slightly faster chemical propagation in the amorphous samples due to lower thermal conductivity. These results provide an understanding for how molecular disorder can be attributed to increased reactivity.</div></div><div><div>After developing an understanding for the initial decomposition processes of HE materials, we turn our attention to a growing interest in the community which is the developing reduced order chemistry models for use in multiscale efforts. Many schemes report mechanisms that are obtained from experiments, which can have large error bars depending on the apparatus and/or extraction technique, or from gas phase simulations, which may not be relevant at shock conditions. To circumvent these issues, we develop a coarse-grained chemical kinetics model from all-atom reactive MD simulations by taking advantage of an unsupervised dimensionality reduction machine learning technique called non-negative matrix factorization. Doing so allows us to represent the overall decomposition chemistry as latent concentrations akin to reactants, intermediates, and products, which we then use to extract kinetics parameters and heats of reaction. These values are implemented into a continuum model, where we could simulate the criticality of thermal hotspots at regimes beyond the reach of MD, as well as verify how uncertainties in the parameters vary as a function of hotspot sizes.</div></div><div><div>Finally, we close with significant progress made towards on-going and future work, where we address two of the most challenging ideas in the field of HE materials: 1) developing definitive chemistry models at extreme conditions, and 2) improving coarse-grained descriptions for multiscale modeling.</div></div>
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