Simplex solid states of SU(N) quantum antiferromagnets

I define a set of wavefunctions for SU(N) lattice antiferromagnets, analogous to the valence bond solid states of Affleck, Kennedy, Lieb, and Tasaki (AKLT), in which the singlets are extended over N-site simplices. As with the valence bond solids, the new simplex solid (SS) states are extinguished by certain local projection operators, allowing us to construct Hamiltonians with local interactions which render the SS states exact ground states. Using a coherent state representation, we show that the quantum correlations in each SS state are calculable as the finite temperature correlations of an associated classical model, with N-spin interactions, on the same lattice. In three and higher dimensions, the SS states can spontaneously break SU(N) and exhibit N-sublattice long-ranged order, as a function of a discrete parameter which fixes the local representation of SU(N). I analyze this transition using a classical mean field approach. For N>2 the ordered state is selected via an "order by disorder" mechanism. As in the AKLT case, the bulk representations fractionalize at an edge, and the ground state entropy is proportional to the volume of the boundary.Comment: 14 pages, 8 figures, minor typos correcte

The glucose-6-phosphate dehydrogenase encoding genes from Aspergillus niger and Aspergillus nidulans

Glucose-6-phosphate (G6P) is a central metabolite, that can either be metabolised via the glycolytic and tricarboxylic acid cycle to generate ATP, or converted into storage molecules or can be directed to the pentose phosphate pathway to yield NADPH and various pentoses. This thesis focuses on one of these G6P consuming reactions, catalysed by glucose-6-phosphate dehydrogenase (G6PD), in which G6P is oxidised and NADP +acts as electron acceptor. The central theme of this thesis is the role of glucose-6- phosphate dehydrogenase (G6PD) enzyme activity in the generation of the cytosolic NADPH pool. This cytosolic NADPH pool serves as the reducing agent in a large number of biosynthetic reactions, in the protection against oxidation damage and in the utilisation of nitrate and certain pentoses. Only a limited number of catabolic reactions generate NADPH of which the one catalysed by G6PD is usually considered to be the most important.If G6PD were the major producer of NADPH, one would expect 1) G6PD enzyme activity to respond to changes in NADPH demand and 2) G6PD mutations to be extremely deleterious or even lethal. According to these criteria, examples can be found in the scientific literature, where G6PD appears to be either vital for cytosolic NADPH production or appears to be completely superfluous. Aspergillus nidulans and Aspergillus niger were chosen as model systems because of their ability to metabolise a great variety of carbon- and nitrogen sources and their well developed genetics. These characteristics would allow us to use nitrogen- and carbon sources that influence NADPH consumption and to employ molecular biological techniques to study and manipulate the regulation of G6PD expression.The biochemical characteristics of the purified G6PD enzymes from A. nidulans and A. niger suggest the involvement of these G6PD enzymes in NADPH production. For both pure enzyme preparations, the main modulator of G6PD enzyme activity is the redox potential as is reflected by its stimulation by NADP +and its competitive inhibition by NADPH. Additionally, these observations show that at least part of the regulation of G6PD activity in A. nidulans and A. niger is exerted at the enzyme level. In their biochemical characteristics, their primary and secondary structure the G6PDs from A. nidulans and A. niger are virtually identical. Both fungal G6PD enzymes bind their substrates G6P and NADP +in a random order and exhibit a strict specificity towards them. Whether the presence of two proteins in both pure Aspergillus G6PD preparations, has any physiological significance or is just an artefact due to proteolytic degradation of the native G6PD during the purification procedure, remains to be determined. However, the cloning of the G6PD encoding genes does provide a clue to the origin of the two G6PD proteins. In A. nidulans both G6PD proteins should be derived from the gsd A gene, since only a single G6PD encoding gene could be detected on genomic Southern blots. For the two A. niger G6PD proteins, the situation is less clear because genomic Southern blots revealed the presence of additional DNA bands that cross-hybridised strongly to the gsd A gene and which could represent a second G6PD encoding gene.The gsd A genes from A. nidulans and A. niger have an identical structure; both contain nine introns, which are located at exactly equivalent positions with respect to the coding region. Furthermore, both genes exhibit strong DNA sequence homology in the coding region, but in the introns, 5'- and 3'-flanking sequences, this homology drops significantly. Alignment of the deduced gsd A amino acid sequences with other eukaryotic G6PDs reveals strong homology at the amino acid level and allows localisation of important domains like the putative catalytic site and NADP +bindings sites. The cloning of the gsd A genes a] lows us to manipulate the G6PD activity directly. The increase of G6PD activity by the introduction of multiple copies of the gsd A gene results in A. niger in grossly disturbed growth especially on media containing reduced nitrogen sources. The degree of growth inhibition and the increase in G6PD activity are directly related to the number of functionally integrated gsd A genes. This observation suggests the reduced growth is a direct consequence of the increased G6PD activity. One can explain these phenomena by assuming that increased G6PD activity results in overproduction of NADPH. If for this excess of NADPH no acceptor is available (e.g. nitrate), the redox potential is disturbed and growth is inhibited. A similar experiment with the A. nidulans gene resulted in cotransformants with a single additional gsd A copy, that only slightly overexpressed G6PD end did not exhibit reduced growth.This already shows that despite the similarity in the biochemical characteristics and in primary structure of the enzymes and genes, there are remarkable differences in the regulation of the A. niger and A. nidulansgsd A expression. In A. nidulans , but not in A. niger , G6PD enzyme activity and gsd A transcription respond to the increased NADPH demand during growth on nitrate. These observations indicate that in A. nidulans G6PD does play an important role in NADPH production, whereas in A. niger it probably does not. Further evidence for this statement comes from the observation that in A. niger G6PD enzyme activity and steady state mRNA levels do not change in response to growth on xylose or in response to oxidation stress.The homology in the gsd A 5'-upstream regions is limited to four 11 to 22 bp long sequence blocks, named gsd A-boxes, which in both promoters appear in the same order. Homologues of gsd A-boxes 1, 2 and 4 are also encountered in the same order in the S. cerevisiae zwf l promoter. In both Aspergilli, the gsd A-box region contains all transcription start sites: in the case of A. niger there are four and in A. nidulans there are as much as eight. We did not find any conservation, neither in the number of transcription sites nor the site of initiation. In A. niger all deletions within the region containing the gsd A- boxes, reduce transcription to background level while such a deletion in A. nidulans retains 25% of its original transcription. These observations indicate that despite the gsd A-box homology, these regions still differ functionally.From the deletion study of the A. nidulansgsd A promoter, it is clear that the nitrate induced increase in G6PD activity is caused by an increased gsd A transcription. Furthermore, evidence has been obtained that the NIRA transcription factor, which mediates induction of the nitrate utilisation pathway, is also involved in the nitrate stimulation of gsd A transcription in A. nidulans . Furthermore our data show clearly, that NIRA plays an important role in the regulation of gsd A transcription in the absence of nitrate. This phenomenon is probably yet another difference in the regulation of gsd A expression between A. nidulans and A. niger . Since A. nigergsd A expression does not respond to nitrate induction, it is unlikely that the uninduced level of its gsd A transcription is under the control of NIRA. This NIRA dependence of gsd A transcription might also explain the remarkably different behaviour of the two gsd A genes in cotransformation experiments.In A. nidulans , titration of the NIRA protein by the cotransformed gsd A gene might limit the expression of the cotransformed gsd A copies. At the same time cotransformants with multiple copies of gsd A would be lost on the nitrate containing selection medium, since NIRA titration would render them incapable of nitrate utilisation. These two phenomena would explain the low cotransformation frequency of the A. nidulansgsd A gene and low G6PD overproduction observed in A. nidulans cotransformants. Conversely, the absence of NIRA regulation in the gsd A expression in A. niger does not limit overproduction of G6PD in gsd A cotransformants. Furthermore, the absence of NIRA titration in A. niger g sdA cotransformants allows the use of nitrate as an acceptor for the excess NADPH.In contrast to the other members of the nitrate utilisation regulon (e.g. nia D, nii A and crn A) is gsd A expression not subject to nitrogen catabolite repression exerted by the areA gene product. Still, AREA seems to act on the A. nidulansgsd A promoter. The physiological significance of this phenomenon remains to be established.The data presented in this thesis show that although the primary structure and biochemical characteristics of an enzyme from two different organisms are virtually identical, there can be significant differences in the regulation of their expression and hence in their physiological function. Of course our data provide only an outline of the regulation of G6PD activity in two Aspergilli and, unfortunately, raise more questions then they answer.Our data indicate that G6PD does not play a crucial role in the generation of the cytoplasmic NADPH pool in A. niger . What is then the physiological function of G6PD enzyme activity in A. niger? Furthermore, as it is difficult to assign a physiological function to the A. nigergsd A gene, is it reasonable to assume that the fragments that cross-hybridise to the gsd A gene in digests of A. niger genomic DNA could represent a second G6PD encoding gene? Clearly, the construction and characterisation of a gsd A null mutant should provide important clues to these questions. Since G6PD is not the main producer of NADPH in A. niger , a gsd A null mutation should be viable. This of course raises the question which pathway provides the bulk of the cytoplasmic NADPH in A. niger ?In A. nidulans G6PD enzyme activity is clearly involved in the maintenance of a proper cytoplasmic NADP +/NADPH ratio as its expression responds to the increased NADPH consumption during growth on nitrate. From this observation we would predict that a gsd A null mutant, if not lethal, would be either unable to utilise nitrate or would exhibit reduced growth on this nitrogen source. However, the fact that no G6PD mutants have been found among the nitrate non-utilising mutants suggests that such mutations are in fact lethal. How does A. nidulansgsd A expression respond to NADPH consuming processes other than nitrate utilisation? Are these responses also regulated at the transcriptional level and if so which transacting factors are involved? What is the function of the individual gsd A-boxes in A. niger and A. nidulans ? Why do the regions containing the gsd A-boxes differ functionally, despite the obvious homology? Does titration of NIRA rely occur in A. nidulansgsd A cotransformants? In any case these questions demonstrate the necessity for further research

Automated Dynamic Error Analysis Methods for Optimization of Computer Arithmetic Systems

Computer arithmetic is one of the more important topics within computer science and engineering. The earliest implementations of computer systems were designed to perform arithmetic operations and cost if not all digital systems will be required to perform some sort of arithmetic as part of their normal operations. This reliance on the arithmetic operations of computers means the accurate representation of real numbers within digital systems is vital, and an understanding of how these systems are implemented and their possible drawbacks is essential in order to design and implement modern high performance systems. At present the most widely implemented system for computer arithmetic is the IEEE754 Floating Point system, while this system is deemed to the be the best available implementation it has several features that can result in serious errors of computation if not implemented correctly. Lack of understanding of these errors and their effects has led to real world disasters in the past on several occasions. Systems for the detection of these errors are highly important and fast, efficient and easy to use implementations of these detection systems is a high priority. Detection of floating point rounding errors normally requires run-time analysis in order to be effective. Several systems have been proposed for the analysis of floating point arithmetic including Interval Arithmetic, Affine Arithmetic and Monte Carlo Arithmetic. While these systems have been well studied using theoretical and software based approaches, implementation of systems that can be applied to real world situations has been limited due to issues with implementation, performance and scalability. The majority of implementations have been software based and have not taken advantage of the performance gains associated with hardware accelerated computer arithmetic systems. This is especially problematic when it is considered that systems requiring high accuracy will often require high performance. The aim of this thesis and associated research is to increase understanding of error and error analysis methods through the development of easy to use and easy to understand implementations of these techniques

Evaluation of Three Rapid Tests for Diagnosis of P. Falciparum and P. Vivax Malaria in Colombia.

The diagnostic capacity of three malaria rapid diagnostic tests (RDTs), NOW-Malaria-ICT, OptiMAL-IT, and Paracheck-Pf, was evaluated against expert microscopy in Colombia. We tested 896 patients, of whom microscopy confirmed 139 P. falciparum, 279 P. vivax, and 13 mixed P.f/P.v infections and 465 negatives. Paracheck-Pf and NOW-malaria-ICT were more accurate in detecting P. falciparum (sensitivities 90.8% and 90.1%, respectively) in comparison with Optimal-IT (83.6%). NOW showed an acceptable Pf detection rate at low densities (< 500/microL), but resulted in a higher proportion of false positives. For P. vivax diagnosis, Optimal-IT had a higher sensitivity than NOW (91.0% and 81.4%, respectively). The choice between the two Pf/Pv detecting RDTs balances P. falciparum and P. vivax detection rates. Considering some degree of P. falciparum overtreatment and failure to detect all P. vivax cases as more acceptable than missing some cases of P. falciparum, we recommend careful implementation of NOW-malaria-ICT in areas where microscopy is lacking. The price is however still a constraint

Inducing a mental context for associative memory formation with real-time fMRI neurofeedback

Memory, one of the hallmarks of human cognition, can be modified when humans voluntarily modulate neural population activity using neurofeedback. However, it is currently unknown whether neurofeedback can influence the integration of memories, and whether memory is facilitated or impaired after such neural perturbation. In this study, participants memorized objects while we provided them with abstract neurofeedback based on their brain activity patterns in the ventral visual stream. This neurofeedback created an implicit face or house context in the brain while memorizing the objects. The results revealed that participants created associations between each memorized object and its implicit context solely due to the neurofeedback manipulation. Our findings shed light onto how memory formation can be influenced by synthetic memory tags with neurofeedback and advance our understanding of mnemonic processing

Current ethical issues in synthetic biology: Where should we go from here?

Synthetic Biology (SynBio) is an emerging scientific field which has quickly established momentum and visibility. Although no single definition of SynBio prevails, the field broadly encompasses the application of engineering principles to biology; re-designing biological materials and using them as new substrates to create products and entities not otherwise found in nature. This paper first reviews SynBio, highlighting the novel aspects of this technology. It then synthesises ethical issues highlighted in the literature to date and makes some initial claims that research on the ethical aspects of SynBio should: avoid creating a new sub-type of bioethics, concentrate on novel concepts and problems and be situated within a context of cooperative inter-disciplinary investigation. Keywords: Synthetic biology, ethical issues, regulation, creating life.This article was written by Dr Ainsley Newson during the time of her employment with the University of Bristol, UK (2006-2012). Self-archived in the Sydney eScholarship Repository with permission of Bristol University, Sept 2014