Supercapacitors (or electric double-layer capacitors) are high power energy storage devices that store charge by the non-faradaic adsorption of ions at the interface between porous carbon electrodes and an electrolyte solution. The development of new electrode materials and electrolytes with improved performances is an active area of research today, yet there are relatively few studies of the molecular mechanisms of the charge storage process. In this work, nuclear magnetic resonance (NMR) spectroscopy is developed for the study of the charge storage mechanisms of supercapacitors. Importantly, NMR experiments show that electrolyte ions adsorbed inside the pores of the carbon electrodes can be resolved from those in bulk electrolyte for a range of supercapacitor electrode materials. Chemical shift calculations show that the adsorbed species are subject to ring current effects, whereby the delocalised electrons in the carbon shield the nearby nuclei. The calculated effects depend on the local carbon structure, helping to rationalise the variations observed when different porous carbons are studied experimentally, and allowing structural information to be extracted from the spectra. NMR experiments performed on electrodes extracted from ionic liquid-based supercapacitors with different applied voltages allow the numbers of adsorbed ions to be measured upon charging. It is shown that supercapacitor charging involves the migration of both anions and cations in and out of the carbon pores in each electrode, with the anions dominating the charge storage process. When combined with lineshape measurements, which offer information about the diffusion of adsorbed ions, the power performances of supercapacitor devices with different electrolytes are rationalised. In situ NMR methods are then developed to allow mechanistic studies of working supercapacitors as they are charged and discharged inside the NMR magnet. The experiments reveal that the charge storage mechanism depends on both the electrolyte and the electrode material studied. During charging, reversible chemical shift changes are also observed, arising from the introduction of paratropic ring currents. Finally, cross polarisation experiments allow the selective observation of the adsorbed electrolyte species, and show that their motion slows down during supercapacitor charging. Overall, the NMR approach offers unique insights into the molecular mechanisms of the supercapacitance phenomenon.

This thesis is concerned with the design of numerical methods for quantum simulation and the development of improved models for quantum relaxation. Analysis is presented for the treatment of quantum systems using the density matrix formalism. This approach has been developed from the early days of quantum mechanics as a tool to describe from a statistical point of view a large number of identical quantum ensembles. Traditional methods are well established and reliable, but they perform poorly for practical simulation as the system size is scaled up. Ad hoc schemes for nuclear spin dynamics appearing in the literature can be shown to fail in certain situations. The challenge is therefore to identify efficient reduction methods for the quantum system which are also based on a rigorous foundation. The method presented in the thesis, for the time–independent Hamiltonian case, combines a quantum density matrix formalism with a procedure based on Chebyshev polynomials; application of the method to Nuclear Magnetic Resonance (NMR) spectroscopy is considered, and it is shown that the new technique outperforms existing alternatives in term of computational costs. The case of a time–dependent Hamiltonian in NMR simulation is studied as well and some splitting methods are presented. To the author’s knowledge this is the first time such methods have been applied within the NMR framework, and the numerical results show a better error–to–cost rate than traditional methods. In a separate strand of research, formulations for open quantum systems are studied and new dynamical systems approaches are considered for this problem. Motivations This thesis work is mainly focused on nuclear spin dynamics. Nuclear spin dynamics constitutes the basis for NMR, which is a very powerful spectroscopy technique that exploits the interaction between nuclear spins and magnetic fields. The same technique is used to reveal the presence of hydrogen atoms in the blood for Magnetic Resonance Imaging (MRI). Within this framework the role of simulations is extremely important, as it provides a benchmark for studies of new materials, and the development of new magnetic fields. The main computational issue is that with current software for NMR simulation it is extremely expensive to deal with systems made of more than few (7–10) spins. There is therefore a strong need to develop new algorithms capable of simulating larger systems. In recent years NMR simulations have been found to be one of the most favorable candidates for quantum computing. There are two reasons for this: nuclear quantum states maintain extremely long coherences, and it is possible to attain a very strong control on the quantum state via the application of sequences of pulses. In order to develop a proper quantum computer it is fundamental to understand how the entangled states lose coherence and relax back to equilibrium by means of external interactions. This process is described as relaxation in an open quantum system. The theory for such systems has been available for 50 years but there are still substantial limitations in the two main approaches. There are also relatively few numerical approaches for the simulation of such systems, for this reason it is important to develop numerical alternatives for the description of open quantum systems. Thesis Outline The thesis is organized as follow: the first two chapters provide background material to familiarize the reader with fundamental concepts of both quantum mechanics and nuclear spin dynamics; in this part of the thesis no new results are presented. The first chapter introduces the concept of quantum systems and the mathematical environment with which we describe those systems. We also present the main equations we need to solve to determine the dynamics of a quantum system in a statistical framework. In the second chapter we introduce the nuclear spin system, that is the physical system that has been the main reference frame in this work, for both tests and practical applications of the new algorithms. We describe how nuclear spin systems are at the basis of very important applications like NMR spectroscopy and MRI. We present in some detail the physical features of the NMR technique and the equations we need to solve to describe the dynamics of a spin system; we also focus on the relevance of numerical simulations for these systems, and consequently which must be the interest in developing new algorithms, and the major obstacles which must be overcome. In the third chapter we investigate the numerical challenges that arise in simulation of quantum systems, we describe some of the methods that have been developed in the literature, focusing on the performances and the computational costs of them, setting the new developments of this thesis in the proper research frame. We discuss one of the major issues: the evaluation of the matrix exponential. We also present the analysis we have done of a recent method called Zero Track Elimination (ZTE) that has been developed specifically for NMR simulations. This analysis shows the limitations of this method but also gives a mathematical explanation of why–and in which cases–it works. In the fourth chapter we present the main result of the thesis, the development of a new method that directly evaluates the expectation values for a quantum simulation via a different application of the well known Chebyshev expansion. We have proved that this new method can provide an excellent boost in terms of performance, with computational costs that can be reduced by a factor ten in common cases. (The results of this chapter and the new method have been presented in international conferences and recently they have been submitted for publication). We also present some attempts we have made in the application of splitting methods for the evolution of the system in a time dependent environment. To our knowledge this is the first time splitting methods have been used for NMR simulations. The results of this approach are as follows: for a particular splitting technique combined with a Lanczos iteration method it is possible to speed up the calculation by a third if compared with a Lanczos type method whilst keeping the error below a critical threshold. This last approach is still a work in progress especially in terms of developing clever ways to split the Hamiltonian. The last chapter of this thesis deals with simulation of quantum systems interacting with an external environment. After presenting the main theoretical approaches for the description of such systems we then survey several the techniques that are currently used for the numerical implementation of such theories. As a work in progress we present a considerably different new approach we have been developing aiming to overcome some of the issues that arise when treating this kind of system within usual frameworks. This is somewhat speculative work that gives rise to some new directions in the development of a numerical description for open quantum systems. We also present some numerical results. (The main core of this chapter has been presented in international conferences).

Throughout biological, chemical, and pharmaceutical research,conformational searches are used to explore the possiblethree-dimensional configurations of molecules. This thesis describesa new systematic method for conformational search, including anapplication of the method to determining the structure of a peptidevia solid-state NMR spectroscopy. A separate portion of the thesis isabout protein-DNA binding, with a three-dimensional macromolecularstructure determined by x-ray crystallography.The search method in this thesis enumerates all conformations of amolecule (at a given level of torsion angle resolution) that satisfy aset of local geometric constraints, such as constraints derived fromNMR experiments. Systematic searches, historically used for smallmolecules, generally now use some form of divide-and-conquer forapplication to larger molecules. Our method can achieve a significantimprovement in runtime by making some major and counter-intuitivemodifications to traditional divide-and-conquer:(1) OmniMerge divides a polymer into many alternative pairs ofsubchains and searches all the pairs, instead of simply cutting inhalf and searching two subchains. Although the extra searches mayappear wasteful, the bottleneck stage of the overall search, which isto re-connect the conformations of the largest subchains, can be greatlyaccelerated by the availability of alternative pairs of sidechains.(2) Propagation of disqualified conformations acrossoverlapping subchains can disqualify infeasible conformations veryrapidly, which further offsets the cost of searching the extrasubchains of OmniMerge.(3) The search may be run in two stages, once at low-resolutionusing a side-effect of OmniMerge to determine an optimalpartitioning of the molecule into efficient subchains; then again athigh-resolution while making use of the precomputed subchains.(4) An A* function prioritizes each subchain based onestimated future search costs. Subchains with sufficiently lowpriority can be omitted from the search, which improves efficiency.A common theme of these four ideas is to make good choices about howto break the large search problem into lower-dimensional subproblems.In addition, the search method uses heuristic local searches withinthe overall systematic framework, to maintain the systematic guaranteewhile providing the empirical efficiency of stochastic search.These novel algorithms were implemented and the effectiveness of eachinnovation is demonstrated on a highly constrained peptide with 40degrees of freedom.

The deposition of amyloid in the central nervous system is associated with prevalent neurological disorders such as Alzheimer's and Parkinson's disease. This thesis studies the mechanisms and prevention of amyloid formation in vitro. We specifically focus on Parkinson's disease associated α-synuclein (α-syn). Using novel labeling methods we introduce NMR observable labels onto lysosomal protein glucocerebrosidase (GCase), a leading cause of Parkinson's disease. By introducing NMR active labels we are able to study GCase dynamics and screen potential drug therapeutics (chapter 3). Furthermore, we analyze the three way interaction between GCase, α-syn and lipids. We conclude that GCase is able to effectively chaperone α-syn under lysosomal conditions, both preventing amyloidogenesis and destabilizing mature amyloid fibrils (chapter 4). Additionally, a model chaperone-aggregate system is investigated to gain insight into the mechanisms of small heat shock protein chaperoning, and how such mechanisms prevent aggregation (chapter 5). Finally, a high resolution crystal structure of RNA editing enzyme Cid1 is presented, whilst not directly linked to aggregation, many of the techniques used in this thesis were first developed on Cid1 (chapter 7). Together, we utilize NMR, X-ray crystallography, electron microscopy and native mass spectrometry to elucidate aspects of protein aggregation mechanisms and prevention.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: In this study the kinetic and mechanistic aspects of the Reversible Addition Fragmentation Chain Transfer (RAFT) process on the copolymerization of acrylonitrile (AN) and vinyl acetate (VAc) are investigated by application of in situ 1H nuclear magnetic resonance (NMR) spectroscopy. The focus is on the early stages of the reaction where the first few monomer (M) additions occur; the change in concentration of the leaving group of RAFT species as a function of time is followed. Cumyl dithiobenzoate (CDB), S-sec propionic acid O-ethyl xanthate (PEX) and O-ethyl cumyl xanthate (ECX) were selected for use in this study. The basis for RAFT agent selection was solely the fact that more activated monomers, e.g. acrylonitrile (AN) are controlled by dithiobenzoates while the less activated monomers, e.g. VAc, are controlled by xanthates. Furthermore, the behaviour of the copolymerization, where the reaction medium is composed of a RAFT agent preferring one monomer in the reaction, is largely unexplored in the literature. First, the homopolymerization of each of these monomers was studied. In accordance with the literature, the AN showed good control when CDB was used as the chain transfer agent, whereas VAc showed good control when using PEX to mediate the polymerization. More emphasis is however placed on the CDB-mediated copolymerization as it still showed some preferential consumption of AN even in the presence of the VAc comonomer, although the reaction was retarded. The copolymerization mixtures comprised the monomer pair, the RAFT agent, and the 2,2’-azobis(isobutyronitrile) (AIBN) in mole ratios as specified for each experiment. When using the total monomer to RAFT to initiator ([M]:[CDB]:[AIBN]) ratio of 5:1:0.2, the AN initialization time was found to be 150 min at 60 °C. Copolymerization of AN with VAc under similar conditions resulted in retardation of the initialization reaction; the initialization period was now about 600 min at fVAc = 0.1. In all the copolymerization reactions undertaken under the conditions described, the VAc monomer conversion was 4–6%. This means that VAc, possibly, retards the copolymerization by binding to the cumyl radicals of the CDB, which it then releases due to weak bonds formed with CDB. The results showed excellent correlation between the experimental and fitted data for the CDB- and PEX-mediated systems, but within a narrow experimental data region for ECX at fAN=0.5, thus for [AN]/[VAc] ratios 0.65–0.93. / AFRIKAANSE OPSOMMING: In hierdie studie word die kinetiese en meganistiese aspekte van die proses van die kopolimerisasie van akrilonitriel (AN) en vinielasetaat (VAs) ondersoek met behulp van in situ 1H KMR. Die fokus is op die vroeë stadiums van die reaksie waar addisie van die eerste paar monomere (M) plaasvind. Die verandering in konsentrasie van die verlatende groep as ‘n funksie van tyd is tydens hierdie stadium gemeet. Kumielditiobensoaat (KDB), S-sek-propielsuur-O-etiel-xantaat (PEX) en O-etiel-kumiel-xantaat (ECX) is vir hierdie studie gekies. Die keuses is gebaseer op die feit dat meer geaktiveerde monomere, bv. AN, deur ditiobensoaat beheer word, terwyl die minder geaktiveerde monomere, bv. VAs, deur xantate beheer word. Daar is nie baie voorbeelde in die literatuur oor die gedrag van die kopolimerisasie waar een van die monomere deur die RAFT-agent bevoordeel word nie. Eerstens is die homopolimerisasie van elk van hierdie monomeerpare (AN en VAs) bestudeer. In ooreenstemming met die literatuur, het die AN goeie beheer getoon wanneer KDB gebruik is as die kettingoordragmiddel, terwyl VAs goeie beheer in die polimerisasie getoon het in die teenwoordigheid van PEX as bemiddelingsagent. Meer klem word egter geplaas op die KDB-bemiddelde kopolimerisasie omdat dit AN by voorkeur gebruik, selfs in die teenwoordigheid van die VAs komonomeer, alhoewel daar ‘n vertraging in die reaksie is. Die reaksiemengsel het bestaan uit die monomeepaar, die RAFT-agent en die afsetter (AIBN), in verhoudings soos uiteengesit vir elke eksperiment. Vir ‘n totale monomeer tot RAFT tot afsetter ([M]:[KDB]:[AIBN]) verhouding van 5:1:0.2 was die afsettingstyd vir AN 150 min by 60 °C. Kopolimerisasie van AN en VAs onder dieselfde omstandighede het tot ‘n vertraging in die afsettingstyd gelei. Die periode was 600 min by fVAs = 0.1. Die omsetting van VAs in al die kopolimerisasiereaksies was 4–6%, wat beteken dat VAs die reaksie vertraag deur aan die kumielradikale van die KDB te bind. Die radikale word weer vrygestel a.g.v. die swak bindings tussen die twee vorms. Tweedens is die reaktiwiteitsverhoudings bepaal deur middel van die nie-lineêre kleinstekwadrate passingsmetode. Die resultate het uitstekende ooreenstemming tussen die eksperimentele en gepaste data vir die KBD- en PEX-bemiddelde sisteme getoon. Dit was egter slegs vir ‘n kort eksperimentele area vir ECX by fAN = 0.5, dus vir [AN]/[VAs] verhoudings 0.65–0.93.

With conventional oil reserves in decline, energy companies are increasingly turning to enhanced oil recovery (EOR) processes to extend the productive life of oilfield wells. Laboratory-scale core floods, in which one fluid displaces another from the pore space of a rock core, are widely used in petroleum research for oilfield evaluation and screening EOR processes. Achieving both macro- and pore-scale understandings of such fluid displacement processes is central to being able to optimise EOR strategies. Many of the mechanisms at play, however, are still poorly understood. In this thesis nuclear magnetic resonance (NMR) has been used for quantitatively, non-invasively and dynamically studying laboratory core floods at reservoir-representative conditions. Spatially-resolved relaxation time measurements (L-T1-T2) have been applied to studying a special core analysis laboratory (SCAL) protocol, used for simulating reservoir oil saturations following initial oil migration (primary drainage) and characterising core samples (capillary pressure curves). Axial heterogeneities in pore filling processes were revealed. It was demonstrated that upon approaching irreducible water saturation, brine saturation was reduced to a continuous water-wetting film throughout the pore space; further hydrocarbon injection resulted in pore pressure rise and wetting film thinning. L-T1-T2 techniques were also applied to a xanthan gum polymer-EOR flood in a sandstone core, providing a continuous measurement of core saturation and pore filling behaviours. A total recovery of 56.1% of the original oil in place (OOIP) was achieved, of which 4.9% was from xanthan. It was demonstrated that deposition of xanthan debris in small pores resulted in small-pore blocking, diverting brine to larger pores, enabling greater oil displacement therein. L-T1-T2, spectral and pulsed field gradient (PFG) approaches were applied to a hydrolysed polyacrylamide (HPAM)-EOR flood in a sandstone core. A total recovery of 62.4% of OOIP was achieved, of which 4.3% was from HPAM. Continued brine injection following conventional recovery (waterflooding) and EOR procedures demonstrated most moveable fluid saturation pertained to brine, with a small fraction to hydrocarbon. Increases in residual oil ganglia size was demonstrated following HPAM-EOR, suggesting HPAM encourages ganglia coalescence, supporting the "oil thread/column stabilisation" mechanism proposed in the literature. NMR relaxometry techniques used for assessing surface interaction strengths (T1/T¬2) were benchmarked against an industry-standard SCAL wettability measurement (Amott-Harvey) on a water-wet sandstone at magnetic field strengths comparable to reservoir well-logging tools (WLTs). At 2 MHz, T1/T2 was demonstrated to be weakly sensitive to the core wettability, although yielded wettability information at premature stages of the Amott-Harvey cycle. This suggests the potential for NMR to deliver faster wettability measurements, in SCAL applications or downhole WLT in situ reservoir characterisation.

No description available.

Οι macro τομείς αποτελούν μία οικογένεια δομών, συντηρημένη εξελικτικά σε πολλά είδη οργανισμών. Ομόλογά τους βρίσκονται σε βακτήρια, αρχαία, ασπόνδυλα, φυτά καθώς και σε θηλαστικά. Η βιολογική τους λειτουργία δεν έχει αποσαφηνιστεί πλήρως αλλά το βασικό βιοχημικό τους χαρακτηριστικό είναι η ύπαρξη μιας θετικά φορτισμένης κοιλότητας η οποία χρησιμεύει ως σημείο πρόσδεσης της διφωσφορικής αδενικής ριβόζης (ADPr). Ο macro τομέας αποτελεί επίσης μέρος των μη δομικών πρωτεϊνών ιών, οι οποίοι φέρουν ως γενετικό υλικό νοηματικό μονόκλωνο RNA. Τέτοιου είδους ιοί είναι και οι άλφα ιοί στους οποίους ανήκει και ο ιός Mayaro. Στην παρούσα εργασία, πραγματοποιείται δομική μελέτη του macro τομέα του ιού Mayaro. Με χρήση της τεχνολογίας του ανασυνδυασμένου DNA, ο πρωτεϊνικός τομέας εκφράστηκε σε μεγάλες ποσότητες και κατέστη δυνατή η μελέτη του με τη χρήση πολυπυρηνικής/πολυδιάστατης φασματοσκοπίας πυρηνικού μαγνητικού συντονισμού. Η NMR δομή του macro τομέα του ιού Mayaro επιλύθηκε σε υψηλή διακριτικότητα (tf=1.03+/-9.7*10e-2, RMSD=0.90+/-0.15 και RMSD=1.44+/-0.14 για τα άτομα της πολυπεπτιδικής αλυσίδας και τα βαρέα άτομα αντίστοιχα) και αποκάλυψε μια αβα σάντουιτς δομή στο κέντρο της οποίας σχηματίζεται μια εκτεταμένη β-πτυχωτή επιφάνεια. Στη συνέχεια πραγματοποιήθηκαν πειράματα αλληλεπίδρασης, τα οποία αποκάλυψαν ότι το ADPr αποτελεί προσδέτη στο macro τομέα του ιού Mayaro. / Macro domains are a family of structures, evolutionarily conserved in many kinds of organisms such as bacteria, archaea, invertebrates, plants and mammals. Their biological function is not fully elucidated but their key biochemical feature seems to be the binding of the Adenosine Diphosphate ribose(ADPr). Macro domain is also found in non-structural proteins of several positive strand RNA viruses like Mayaro virus, a member of the genus of Alphavirus. In the present study, a structural analysis of the macro domain of virus Mayaro is being performed. Using the technology of recombinant DNA, the macro domain was expressed in high yield, making the analysis by multinuclear/multidimensional Nuclear Magnetic Resonance possible. The NMR solution structure of the macro domain od virus Mayaro was determined in high resolution(tf=1.03+/-9.7*10e-2, RMSD=0.90+/-0.15 and RMSD=1.44+/-0.14 for backbone and heavy atoms respectively) and revealed a well folded 3-Layer(aba)Sandwich structure in the center of which, an extended beta sheet is formed. Furthermore, interaction experiments were performed which revealed that the ADPr is a ligand for the macro domain of virus Mayaro.

No description available.

No description available.