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Parametrization in Computational Materials Science: Force Fields for Physisorption and Density-Functional-based Tight-Binding Method for Electronic Structure
No full textPhysisorption of molecular hydrogen in nano- and micro-porous materials is a promising approach to improve the energy storage in mobile applications. Among all the absorbent materials that have been proposed for hydrogen adsorption, metal-organic frameworks (MOFs) and porous aromatic framework (PAFs) attracted significant attention because of their high surface areas and porosities. However, due to weak van der Waals interactions, physisorption of hydrogen in these adsorbents is only efficient at or near the temperature of liquid nitrogen.
At low temperatures both free and adsorbed hydrogen in a confined pore possess significant quantum effects. State-of-the-art molecular simulation methods---grand canonical Monte Carlo (GCMC) with Feynman-Hibbs correction and quantized liquid density‑functional theory (QLDFT)---have been applied to investigate the role of quantum effects on the H2 adsorption process. Under explicit quantum mechanical treatment, simulations have been performed to explore the correlation between storage capacities and structural properties of porous solids. Adsorption calculations have been further extended to determine D2/H2 selectivity through quantum sieving in a narrow pore metal-organic framework. As required by the adsorption calculations, host-guest interaction potentials were parametrized and carefully validated. The accuracy and applicability of different sets of force fields have been discussed.
Typical high-capacity H2 adsorbent materials have very large unit cells, in which the application of high-level quantum chemistry methods are prohibitively expensive. Some recent studies show that density-functional-based tight-binding (DFTB) method can be used to model large framework materials with sufficient accuracy and an affordable computational cost. Unfortunately, the method cannot be applied in a wide range of systems due to the limited availability of the parameters.
In this work, a semi-automatic parametrization scheme for the electronic part of the DFTB parameters has been developed. Applying the scheme, a large part of the periodic table has been parametrized. The accuracy and transferability of the parameters have been tested for a wide variety of systems and found to give an excellent overall performance
Biogas from marine macoalgal waste
No full textBiogas belongs to the biomass-based renewable energy family and biogas plants are largely operated on terrestrial energy crops. Their growth requires fertile farmland, fresh water and fertilizer and faces direct competition with food crop production. It is hoped that third generation biofuels derived from marine biomass will relieve the pressures of the present situation. At the same time, extensive (macro)algal blooms and hypertrophication are common events reported in coastal regions all over the world, causing harm to the marine ecosystem and impairing local tourism. This biomass presents a potential substrate candidate for use in biogas plants, offering the benefits of both the disposal of algae waste and the provision of alternative biogas substrate. In this study the biomethanation potentials of three types of macroalgae were investigated which represent disposable waste material and material involved in eutrophication events. The degradation studies were carried out in batch and continuous systems. Mild thermo-acidic hydrolysis pretreatment was applied to the biomaterial to increase its degradability and boost the biomethane yield. Acid hydrolysis was successfully triggered at 80°C in technical acid media (HCl) as well as in flue gas condensate, a liquid acid waste accumulating in power plants. Co-digestion of macroalgae with maize silage and comparison of mesophilic to thermophilic anaerobic digestion did not lead to any significant benefits. Continuous anaerobic digestion of the respective single macroalgae were successfully conducted throughout several hydraulic residences in mesophilic and thermophilic mode. The trials showed biochemical stability and the possibility of steady CH4 production. The fermentation residue could serve as biofertilizer but exhibited contrasting abilities regarding macronutrient and trace element concentrations. The pollution of macroalgae digestate with heavy metals was acceptable for all tested biomass. Continuous pilot-scale trials with native Lj demonstrated the feasibility of upscaling the overall process with convergence to industrial process conditions
Ion Transport Through Bacterial Outer Membrane Porins: A Computational Study
No full textIon transport through membrane proteins and nanopores is a process of significant importance which has implications ranging from controlling various biological processes to applications in the field of nanoanalytics and stochastic sensing. Therefore it is imperative to probe the behavior and dynamics of ions in nanoscale confinements provided by membrane proteins. The research work reported in this thesis is aimed at understanding ion transport processes, namely ion selectivity and ion conductance, through bacterial outer membrane porins using molecular dynamics simulations.
The major focus of this thesis is to probe the phosphate selectivity of the OprP porin from the bacterium Pseudomonas aeruginosa. The protein OprP is induced in the outer membrane of bacteria under conditions of phosphate starvation and is responsible for the high-affinity uptake of phosphate ions under such circumstances. Free-energy molecular dynamics simulations revealed atomic details leading to the phosphate selectivity of the channel. To further understand the phosphate selectivity of OprP and underlying structure-function relationships, several important residues of OprP have been mutated. Such studies on the mutant OprP channels have enabled us to probe the relative contributions of the residues and their properties, namely charge, size, the ability to desolvate the permeating ion etc., in assigning the phosphate selectivity to OprP. Moreover, the findings obtained for the phosphate selectivity of OprP were further extended to probe the diphosphate selectivity of OprO, a homologous porin of OprP with a high sequence and structural similarity. In silico double mutants of OprP and OprO demonstrated a trend to interchange the phosphate selectivity of OprP and the diphosphate selectivity of OprO.
The other focus of the thesis is to decipher the ion conductance properties through the OmpF and NanC porins from Escherichia coli. A particular kind of bulky ions, i.e., ionic liquids have been investigated with respect to their temperature-dependent pore conductance properties through OmpF. Such ionic liquids can improve the time-resolution of electrophysiological measurements and may be useful in various biosensing applications. Applied-field simulations revealed the importance of a particular orientation of the permeating ion to be able to pass through the pore. In case of NanC, an asymmetric distribution of charged residues inside the pore was found to be responsible for an asymmetric conductance property and a weak anion selectivity of the porin. In addition, mutants of OmpF and NanC have been generated to modify ion conductance properties of these porins.
The findings presented in this thesis enhance the atomistic and functional understanding of ion transport processes through bacterial outer membrane porins in particular and various other membrane proteins in general. Molecular details obtained from such studies can be further exploited to engineer the ion transport properties through nanopores to achieve diverse possible applications, e.g., the design of ion-specific sieves and sensing of biological agents
Computational Studies on Selective Adsorption and Molecular Sieving in HKUST-1 Metal – Organic Framework
No full textMetal organic frameworks (MOFs) bring new possibilities by their potential use in catalysis, gas storage/separation and drug delivery.[1-8]
HKUST-1 consists of Cu2+ ions-connectors and four organic ligands. Open metal sites present in the structure have tremendous impact on the selective adsorption. Showing this is the scope of the studies presented in this thesis.
The guest molecules were chosen basing on the possible applications of HKUST-1. It might serve as an air and water purifying agent (from small gases, niacin and urea) or molecular sieve (for separation of small hydrocarbons).
The results of our research suggest that the adsorption of small gases should be performed in a dry environment, otherwise the copper centers will be blocked by water. In case of separation of aromatic hydrocarbons or biologically important molecules, this does not take place.
The defects in the framework have also been taken into account. Thus, the additional calculations with the defective models have been performed. Results show stronger binding of the guests to the defective site, than the non-defective ones.
Investigation of the changes in the IR spectrum after adsorption allowed to confirm and distinguish the binding mechanism.
The research were performed with DFT, using B3-LYP functional [9,10] and the TZVP basis set (Turbomole program), and two for Gaussian: 6-311G(d) for the non-defective structures and mixed[11] (for the defective ones).
1 Lee et al., Chem. Soc. Rev., 2009, 38, 1450
2 Murray et al., Chem. Soc. Rev., 2009, 38, 1294
3 Li et al., Chem. Soc. Rev.,2009, 38, 1477
4 Bonino et al., Chem. Mater., 2008, 20, 4957
5 Britt et al., P. Natl. Acac. Sci. USA, 2008, 105, 11623
6 Dietzel et al., Chem. Commun., 2008, 5125
7 Caskey et al., J. Am. Chem. Soc., 2008, 130, 10870
8 Valenzano et al., J. Phys. Chem. C, 2010, 114, 11185
9 Becke, Phys. Rev. A , 1988, 38, 3098
10 Lee et al., Phys. Rev. B, 1988, 37, 785
11 Roy et al., J. Chem. Theory. Comput., 2008, 4, 102
Let's Play it Safe! Entertainment-Education in the Digital Age : Developing and Testing a Digital Entertainment-Education Game about HIV/AIDS Protection for Female Adolescents
No full textEntertainment-education (E-E) is a method to educate people through entertainment media products. Research has shown that E-E can have positive effects on people’s behavior, attitudes, knowledge, and interpersonal (peer) communication, and that it works with various media (products) such as radio, TV soap operas, comics etc. These have been non-interactive E-E programs; many theories explain their success on the basis of engaging narratives. The question is whether this strategy also works for interactive media like digital games. To test this, a digital E-E game called Supergöre was created. The game's educational topic was HIV/AIDS, and it was designed according to E-E guidelines. The game was developed in accordance with gender-related digital game research and evaluated within a comprehensive qualitative pilot study. To test its effects as an education product, 75 female adolescents aged 13 to 18 took part in the main study. It was hypothesized that girls who play the game Supergöre would reach significantly higher scores on the knowledge, interest, and follow-up communication posttests than girls in the control group. Additionally, perceived self-efficacy and personal risk perception concerning HIV/AIDS as well as involvement while playing the game were included as moderator/mediator variables. Data were collected via questionnaires. The independent variable (playing or not playing the game) was varied within a Solomon four-group design so as to avoid any influence of pretest sensitization on the results. Supergöre led to a significant increase in knowledge about HIV/AIDS. Involvement had an influence to some extent; highly involved participants reported significantly higher interest in the topic of HIV/AIDS than marginally involved participants. Overall, the present results imply that the digital game Supergöre was successful in informing the participating girls about HIV/AIDS, and that involvement seems to be an important mediator variable
Drug export and nutrient import: Insights from the bacterial model organisms Erwinia amylovora and Pseudomonas aeruginosa
No full textThe emergence of multidrug resistant bacteria is a serious medical and economical problem with global impact. Bacteria have evolved energy-dependent multidrug efflux pumps to prevent intracellular accumulation of toxic compounds and to survive in different ecological niches. On the other hand, the uptake of essential nutrients, while at the same time preventing the internalization of toxic molecules, are accompanying circumstances that cause an enormous selection pressure on bacterial populations.
In the first part of this thesis, three resistance-nodulation-cell division (RND)-type multidrug efflux pumps, AcrD, MdtABC, and MdtUVW, from the plant pathogen Erwinia amylovora were characterized in terms of their substrate specificity, induction upon exposure to various stressors, and pathogenesis on apple and pear. Results of this study show that AcrD is an efflux pump conferring resistance to a limited number of amphiphilic compounds. MdtABC and MdtUVW were found to contribute to disease development in apple rootstocks. Moreover, we identified global and local regulators in E. amylovora and found that the BaeSR two-component system is involved in the activation of the RND-type efflux pumps AcrD and MdtABC.
In the second part, the dipeptide uptake ABC transporter, DppBCDF, and its associated substrate-binding proteins, DppA1-A5, from Pseudomonas aeruginosa were characterized by a high-throughput method. We were able to determine the substrate specificity of this uptake transporter using the Biolog phenotype MicroArray technology
Synthesis, Characterization and Properties of 3d Transition Metal-Substituted Polyoxotungstates and Polyoxo-noble-metalates
No full textPolyoxometalates (POMs) are a large class of discrete, polynuclear metal-oxo anions with an enormous structural and compositional diversity and interesting properties such as thermal and oxidative stability, tunable acidity, redox and magnetic properties, and tunable solubility in aqueous and organic media. The research performed here deals with the synthesis and structural characterization of novel POMs and the investigation of their physicochemical properties, e.g. catalytic, magnetic, electrochemical, medicinal, spectroscopic. Besides 3d transition metal-substituted POMs also the very novel class of polyoxo-noble-metalates was investigated. In the former project, lacunary heteropolytungstate precursors were reacted with different 3d transition metal ions under various reaction conditions. In the latter project, the focus was on noble metal ions with d8 configuration (e.g. Pd2+, Au3+) as addenda. Overall, this work has resulted in the discovery of 16 novel compounds.
This thesis comprises five chapters:
Chapter I provides a comprehensive introduction to the field of POM chemistry, including isopolyanions and heteropolyanions, the classic plenary, lacunary and transition metal-substituted polyanions, and the very novel class of polyoxo-noble-metalates.
Chapter II describes the synthetic procedures for the different POM precursors which were used in this work, and also presents the various analytical techniques used to characterize the products.
Chapter III discusses eight novel 3d transition metal-substituted POMs, which were synthesized and characterized during the course of this work. We have obtained three NiII-substituted POMs, the Ni7-containing, dimeric, sandwich-type [Ni7O6(H2O)6(P2W15O56)2]22- (1), the Ni14-containing, tetrameric [Ni14(OH)6(H2O)10(HPO4)4(P2W15O56)4]34- (2), and the Ni5-containing, dimeric, asymmetric, sandwich-type [Ni5(OH)4(H2O)4(β-GeW9O34){β-GeW8O30(OH)}]13- (3), Polyanion 2 contains the largest nickel-oxo aggregate known in polyoxotungstate chemistry. The 14-FeIII-containing [Fe14O6(OH)13{P2W15O56}4]31- (4) and the 18-FeIII-containing [Fe18O12(OH)8(H2O)3W2O8(CH3COO)2(P2W15O56)4]32- (5) are composed of four trilacunary Wells-Dawson type {P2W15} fragments stabilizing fourteen and eighteen, respectively, iron(III)-oxo units in a tetrahedral fashion. The magnetic properties of 1 - 5 have also been investigated. Three Keggin-type polyanions functionalized by 4,4’-bipyridine were also prepared, [(4,4’-C10H8N2)(ZnSiW11O39)]6- (6), [(C10H8N2)(ZnSiW11O39)2]12- (7), and [(4,4’-C10H8N2)(CoSiW11O39)2]12- (8).
Chapter IV presents the synthesis and structural characterization of eight novel polyoxo-noble-metalates. This includes the 3d transition metal-centered polyoxopalladate(II) cages [(ScO8)Pd12As8O32]13- (9), [(CoO8)Pd12As8O32]14- (10), and [(CuO8)Pd12As8O32]14- (11), the alkaline earth metal-centered polyoxopalladates(II) [SrPd12O6(OH)3(C6H5AsO3)6(CH3COO)3]4- (12) and [BaPd15O10(C6H5AsO3)10]8- (13), the two silver-capped polyoxopalladates(II) {Ag4[Pd13As8O40]}10- (14) and {Ag2[Pd13As8O40]}12- (15) containing heterometallic Ag-Pd interactions, as well as the polyoxoaurate(III) [Au4O4(SeO3)4]4- (16).
All compounds described above were characterized in the solid state by IR spectroscopy, single-crystal X-ray diffraction and thermogravimetric analysis. The solution stability of the diamagnetic compounds was confirmed by multinuclear NMR spectroscopy (e.g. 1H, 13C, 45Sc, 77Se, 183W).
Chapter V describes studies on the above compounds performed by our collaborators, including electrochemistry, magnetism, and mass spectrometry. Several of the above compounds were also investigated by chemical industry partners for catalytic applications
Impact of Local Magnetic Moments on the Anderson Metal-Insulator Transition
No full textThis thesis considers the impact of local magnetic moments on the Anderson transition, which is a disorder-induced quantum phase transition from a metallic to an insulating phase. In certain doped semiconductors like phosphorus-doped silicon (Si:P), a metal-insulator transition (MIT) is observed which is driven not only by disorder, but also by interaction. The latter gives rise to a MIT by itself, the Mott-Hubbard transition. Furthermore, local magnetic moments have been found in Si:P, which persist deep into the metallic regime. The formulation of an acceptable theoretical description of the MIT in such materials is still pending.
We approach the problem within an effective model, using the well-known Anderson model to describe the dynamics of the electrons inside the impurity band formed by the donor states. The presence of a finite concentration of local magnetic moments is approximated by an exchange coupling to classical magnetic impurities. The effects of Heisenberg impurities are compared with those of Ising impurities. The results are obtained numerically, based on a finite-size scaling analysis of the typical density of states, which is the geometric average of the local density of states. The latter is calculated by means of the kernel polynomial method, which allows for an efficient estimation of spectral quantities.
The results show that the critical value Wc of the site-diagonal disorder amplitude is a monotonically decreasing function of the exchange coupling strength J in the case of Ising impurities. In the presence of Heisenberg impurities, Wc is first enhanced with increasing J, before it eventually decreases as well. The difference in behavior can be explained by a change of symmetry from orthogonal to unitary, caused by the Heisenberg impurities. The scaling of Wc with J is analyzed and compared to analytical predictions
Transition, Opposition and Engagement in the Contemporary Narratives of Central American Feminist and Revolutionary Women
No full textSecond wave feminism in Central America has been directly connected with the participation of thousands of women in the revolutionary wars of the 1980s in El Salvador, Nicaragua, and Guatemala. After these wars ebbed away, former combatant women’s involvement as radical feminist activists took on new forms sometimes in conflict with previous revolutionary roles and identifications. Seemingly, these women had to re-define their identities going from “combatants” to “feminists” to “NGO activists” in less than ten years. Though it is expected that radical activisms change in post-conflict societies, there is little knowledge concerning how these women “reconstructed” their identities in order to reconcile the conflictual demands of these different roles. The objective of this study is to explore how Central American feminists –and former revolutionaries- from El Salvador, Nicaragua and Guatemala, make sense of their identity by exploring instances of identity transition in their lives, as well as looking at how they “construct” a sense of ‘who they are’ through their personal narratives. On one side, this study aims to look at how these women dealt with identity transition; but also, how these transitions eventually informed ideas of opposition and engagement to the state and their revolutionary organizations. In addition, the study identifies those instances of transition that have yielded identity change. This research draws upon narrative psychology and narrative analysis as a way of looking at the process of change. Though the study is concerned with exploring and analyzing individual stories, it positions itself in the intersection between individual and group meaning creation by identifying ‘inter-subjective meanings’ that emerge from these women’s life story narratives. Methodologically speaking, it relies upon methods used to analyze narratives drawn from narratology, socio-linguistics, philosophy and life course research. These methods yield results that are not frequently seen in studies concerning revolutionary women. One of the most conclusive results of this study is that almost all the women interviewed constructed the feminist life period as a progressive narrative. Another contribution expands on Karen Kampwirth’s idea of “family traditions of dissidence” and looks at how particular family constellations regarding mother-daughter relations may influence a daughter’s decision to join a dissident movement. Finally, another result pertains a connection between feminist activism and psychological resilience. The relevance of this project is that it attempts to shed light in the construction of radical identities in Central America, and in addition, it has implications for peace-building processes as well as the strengthening of women’s leadership in post-conflict societies
Physical Layer Wireless Security in Random Networks
No full textA continuing trend of miniaturization and a growing demand for information are two major responsible drivers of new communication systems, which therefore increasingly rely on embedded technology, as illustrated by the Internet of Things and Cyber-Physical Systems. The embedded nature of future wireless networks implies not only power-limitation of devices, but also a likelihood that a greater share of trac will include highly sensitive and personal information, which together call for new wireless security mechanisms that do not rely on the overhead-heavy and coordination-intense cryptographic protocols of today. Physical layer security is an upcoming research area that makes use of properties of the physical layer and seeks the possibility of achieving perfect secrecy in the wireless channel.
In this thesis, we study the impact of topology and interference onto the physical layer wireless security of random networks. In particular, we derive closed-form expressions for the secrecy rate distribution, average secrecy rate, secrecy outage probability, secrecy
transmission capacity of Poisson Point Process (PPP) based random networks under various fading channels (Rayleigh, Nakagami-m, Shadowing), and colluding eavesdroppers with or without considering correlated channels. We also analyse the impact of interference on the secrecy metrics of corresponding random networks. Specifically, we study the aggregation of interference in random networks and its impact on secrecy, by utilizing results of PPP.
At the end, we perform an analysis of the secrecy outage of random networks under the Matern Hard-core Point Process model, with the objective of shedding light on the security limitations/capabilities inherently encountered in cellular systems