Heterogeneous catalysis is one of the fundamental processes of modern life, being common in industrial refinery and hydrogen vehicles, all the way to the living cell. The dissociation of H2 on Cu... Show moreHeterogeneous catalysis is one of the fundamental processes of modern life, being common in industrial refinery and hydrogen vehicles, all the way to the living cell. The dissociation of H2 on Cu(111) is an important benchmark system for studying heterogeneous catalysis, with a large and varied amount of experimental and theoretical data available.In this thesis I present my recent advances in including the effects of surface temperature on the H2/Cu(111) reaction in not only classical dynamics, but also quantum dynamics. I show how we can include surface temperature effects by treating the surface as static, but distorted, and present how the neglect of energy exchange between the surface and the hydrogen molecule does not appear to affect the dissociation or (ro)vibrationally elastic scattering probabilities of the H2 molecule. Furthermore, I show how treating the hydrogen at a quantum dynamical level has some minor effects on the scattering probabilities when compared to classical dynamics, but in general agrees very well. Finally, I also discuss how including the surface temperature effects improves agreement with the experimentally obtained dissociation curves, but also how smaller features of the experimental results are not reproduced by our models. Show less
Catalysis is of extreme relevance in the production of everyday materials and plays a central role in many aspects of our life. On the industrial level, metal based catalysts are widely used to... Show moreCatalysis is of extreme relevance in the production of everyday materials and plays a central role in many aspects of our life. On the industrial level, metal based catalysts are widely used to produce molecular hydrogen, which can be used as fuel, or nitrogen, one of the building blocks in the fertilizers synthesis, and other fundamental molecules. A better understanding of heterogeneous catalyzed processes would help to design better and more efficient catalysts but it is hard to achieve because of their high level of complexity. Molecular dissociation on metal surfaces is usually a multi-step process which can be best investigated through a joint experimental and theoretical effort. The comparison of molecular beam experiments with molecular dynamics simulations can help to improve over the theoretical method used, called density functional theory (DFT), in order to achieve chemical accuracy (i.e., errors smaller than 1 kcal/mol) for the reaction studied. As we show in the research reported in the thesis, being able to accurately compute the dissociation barriers for methane on metals like nickel and platinum is of great importance in order to make predictions about the most reactive sites on the surface and possibly, in the future, it can help improving over industrial catalysts. Show less
Nolte, T.; Peijnenburg, W.J.G.M.; Hendriks, A.J.; Meent, D. van de 2017
After use and disposal of chemical products, many types of polymer particles end up in the aquatic environment with potential toxic effects to primary producers like green algae. In this study, we... Show moreAfter use and disposal of chemical products, many types of polymer particles end up in the aquatic environment with potential toxic effects to primary producers like green algae. In this study, we have developed Quantitative Structure-Activity Relationships (QSARs) for a set of highly structural diverse polymers which are capable to estimate green algae growth inhibition (EC50). The model (N = 43, R2 = 0.73, RMSE = 0.28) is a regression-based decision tree using one structural descriptor for each of three polymer classes separated based on charge. The QSAR is applicable to linear homo polymers as well as copolymers and does not require information on the size of the polymer particle or underlying core material. Highly branched polymers, non-nitrogen cationic polymers and polymeric surfactants are not included in the model and thus cannot be evaluated. The model works best for cationic and non-ionic polymers for which cellular adsorption, disruption of the cell wall and photosynthesis inhibition were the mechanisms of action. For anionic polymers, specific properties of the polymer and test characteristics need to be known for detailed assessment. The data and QSAR results for anionic polymers, when combined with molecular dynamics simulations indicated that nutrient depletion is likely the dominant mode of toxicity. Nutrient depletion in turn, is determined by the non-linear interplay between polymer charge density and backbone flexibility. Show less
The thesis __The Dynamics of Plasma Surface Interaction__ described the experimental and simulated results involving the interactions of plasma with surfaces. In the first part, we introduced low... Show moreThe thesis __The Dynamics of Plasma Surface Interaction__ described the experimental and simulated results involving the interactions of plasma with surfaces. In the first part, we introduced low energy ion grazing scattering technique to characterize in-situ and real-time the plasma surface interaction. The experimental results demonstrate that low energy ion grazing scattering is a viable tool for in-situ monitoring of the interaction of plasma with surfaces. In order to interpret the scattering experimental data, the MD simulations were performed to investigate the dynamics of Ar grazing scattering from perfect and defective Si (100) surfaces. A new model including electron stopping is developed. The results based on this model are in reasonable with the experiments. In simulations of CF grazing scattering from Si(100) surfaces, the translational energy loss of CF, the redistribution of the gained internal modes and the stereodynamics of surviving molecules are discussed. The second part is to focus on modeling of plasma-surface interactions. The interaction of CF with the clean Si(100)-(2x1) surface at normal incidence and room temperature was investigated using molecular dynamics simulation. Some simulated results are in good agreement with available experimental data. The level of agreement between the simulated and experimental results and the limitation of MD simulation are discussed. MD simulations of the CHB3B interaction with Si (100) show the H/C ratio obtained from the simulations is in good agreement with available experimental data. H atoms preferentially react with Si. SiH is the dominant form of SiHBxB generated. Show less
This thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a... Show moreThis thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a protein that was being unfolded and refolded using our optical tweezers setup. Our measurements clearly showed that in the presence of SecB, an unfolded protein could not refold. Molecular dynamics simulations were used to successfully explain features that were observed in our unfolding experiments. Our approach enables studies on other chaperones, as well. Next, we aimed to study translocation of single proteins through membranes by the E. coli Sec translocase. We modified an often-used model protein for our experiment. Different used experimental strategies are presented. Future experiments should enable measurements on the translocation of a single protein. The last study was on the packaging of double-stranded DNA by a single bacteriophage phi29. We aimed to study the effect of multivalent cations on the negatively-charged, tightly-packed DNA inside the bacteriophage capsid and in that way on the speed of the packaging process. A special DNA molecule was constructed and used in a number of successful packaging experiments. Future experiments should show the effect of cations on the packaging rate. With Summary in Dutch Show less
This thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a... Show moreThis thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a protein that was being unfolded and refolded using our optical tweezers setup. Our measurements clearly showed that in the presence of SecB, an unfolded protein could not refold. Molecular dynamics simulations were used to successfully explain features that were observed in our unfolding experiments. Our approach enables studies on other chaperones, as well. Next, we aimed to study translocation of single proteins through membranes by the E. coli Sec translocase. We modified an often-used model protein for our experiment. Different used experimental strategies are presented. Future experiments should enable measurements on the translocation of a single protein. The last study was on the packaging of double-stranded DNA by a single bacteriophage phi29. We aimed to study the effect of multivalent cations on the negatively-charged, tightly-packed DNA inside the bacteriophage capsid and in that way on the speed of the packaging process. A special DNA molecule was constructed and used in a number of successful packaging experiments. Future experiments should show the effect of cations on the packaging rate. Show less
