Single-particle Green's function method is a direct way of calculating electron binding energy, which relies on expanding the Fock subspace in a finite single-particle basis. However, these methods suffer from slow asymptotic decay of basis set incompleteness error. An energy-dependent explicitly correlated (F12) formalism for Green's function is presented that achieves faster convergence to the basis set limit. The renormalized second-order Green's function method (NR2-F12) scales as iterative N^5 where N is the system size. These methods are tested on a set of small (O21) and medium-sized (OAM24) organic molecules. The basis set incompleteness error in ionization potential (IP) obtained from the NR2-F12 method and aug-cc-pVDZ basis for OAM24 is 0.033 eV compared to 0.067 eV for NR2 method and aug-cc-pVQZ basis. Hence, accurate electron binding energies can be calculated at a lower cost using NR2-F12 method. For aug-cc-pVDZ basis, the electron binding energies obtained from NR2-F12 are comparable to EOM-IP-CCSD method that uses a CCSD reference and scales as iterative N^6. / Master of Science / Solving the non-relativistic time-independent Schrödinger equation is a central problem in quantum chemistry with the primary goal of finding the exact electronic wave function. Like all many-body problems, the applications of highly accurate electronic structure methods are limited to small molecules since they are computationally expensive. With scalable algorithms and parallel implementation of computer programs, the chemistry of large molecular systems can be investigated. Electron binding energies give an insight into the orbital picture of a molecule, which is manifested in chemical structure and properties of a molecule. Green’s function provides an alternative to wave function based methods to calculate ionization potential and electron affinity directly rather than solving for the wave function itself. For accurate electron binding energies, the wave function needs to be represented by large number of basis functions, which make these methods computationally expensive. Explicitly correlated electronic structure methods are designed to produce accurate results at a smaller basis set. This work investigates the use of explicitly correlated Green’s function methods to calculate electron binding energies of small and medium sized organic molecules. These results are compared to coupled cluster methods, which are known to provide accurate benchmarks in quantum chemistry.

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Three novel, synthetic biarylheterocycles bearing imidazole terminal groups had previously been discovered with high cytotoxicity (IC₅₀ 16-640 nM) against a number of human tumour cell lines. Notably, this biological activity was independent of duplex DNA binding affinity. The compounds were tested in the NCI 60-cell line panel and COMPARE analysis suggests they have a novel mechanism of action, targeting the product of a 'gene-like sequence' of unidentified function. The identity of likely protein targets was explored using a chemical proteomic strategy. Bespoke affinity matrices for chromatography were prepared in which test compounds were attached to a solid support through a biotin tag. A synthetic route to hit compounds containing a biotin moiety in place of one of the imidazole sidechains was developed. Chemosensitivity studies confirmed that the biotinylated compounds retained their activity showing IC₅₀ = 6.25 μM in a susceptible cell line, compared with > 100 μM for an insensitive cell line. The biotinylated ligands were complexed to a streptavidin-activated affinity column and exposed to cell lysates from the susceptible cell lines. Bound proteins were eluted from the column and separated using SDS-PAGE. Proteins were characterised by MALDI MS and MS/MS and identified using Mascot database searches. Heterogeneous nuclear ribonuclear protein A2/B1 was found to selectively bind to the affinity probes.

Protein engineering and in vitro selection systems are powerful methods to generate binding proteins. In nature, antibodies are the primary affinity proteins and their usefulness has led to a widespread use both in basic and applied research. By means of combinatorial protein engineering and protein library technology, smaller antibody fragments or alternative non-immunoglobulin protein scaffolds can be engineered for various functions based on molecular recognition. In this thesis, a 46 amino acid small albumin-binding domain derived from streptococcal protein G was evaluated as a scaffold for the generation of affinity proteins. Using protein engineering, the albumin binding has been complemented with a new binding interface localized to the opposite surface of this three-helical bundle domain. By using in vitro selection from a combinatorial library, bispecific protein domains with ability to recognize several different target proteins were generated. In paper I, a bispecific albumin-binding domain was selected by phage display and utilized as a purification tag for highly efficient affinity purification of fusion proteins. The results in paper II show how protein engineering, in vitro display and multi-parameter fluorescence-activated cell sorting can be used to accomplish the challenging task of incorporating two high affinity binding-sites, for albumin and tumor necrosis factor-alpha, into this new bispecific protein scaffold. Moreover, the native ability of this domain to bind serum albumin provides a useful characteristic that can be used to extend the plasma half-lives of proteins fused to it or potentially of the domain itself. When combined with a second targeting ability, a new molecular format with potential use in therapeutic applications is provided. The engineered binding proteins generated against the epidermal growth factor receptors 2 and 3 in papers III and IV are aimed in this direction. Over-expression of these receptors is associated with the development and progression of various cancers, and both are well-validated targets for therapy. Small bispecific binding proteins based on the albumin-binding domain could potentially contribute to this field. The new alternative protein scaffold described in this thesis is one of the smallest structured affinity proteins reported. The bispecific nature, with an inherent ability of the same domain to bind to serum albumin, is unique for this scaffold. These non-immunoglobulin binding proteins may provide several advantages as compared to antibodies in several applications, particularly when a small size and an extended half-life are of key importance. / <p>QC 20121122</p>

Pontificia Univ. Gregoriana, Diss.--Roma, 2006. / Contains bibliography (p. 535- 565), bibl. references, notes and index. Thesis.

No description available.

One major area of forensic science is to provide identifications of previously unidentifiable individuals. Many of these techniques rely on the accurate interpretation of the morphology of the facial form. An individual's facial form is the result of a complex interaction of their genetic ancestry and the many environmental factors they are exposed to throughout their lives. Facial studies to date have primarily focused on single populations, or on comparing different populations residing in different areas. Very few have looked at the relationships between the facial forms of different populations living in the same area of individuals of mixed population ancestry. In this study the facial morphology of 431 West Australian young adults was analysed, and the relationship between their self reported population affinity and their facial form investigated. The impact of factors such as sexual dimorphism and body mass on facial form were also considered. The relationship between the facial morphology of individuals of mixed population heritage and their parent populations was studied, as was the effect that migration can have on facial form. Strong relationships between self-reported population affinity and facial form were demonstrated over the range of populations in the study. Sex and body mass were seen to have an impact on the morphology of the face; but they did not eclipse the influence of the genetic population affinity. Individuals with ancestry derived from more than one population were seen to resemble one population over another in different areas of the face rather than demonstrating an equal combination of both parent populations. A migration effect was seen in the facial forms of even the first generation offspring of migrants.

We have synthesized a new class of photoaffinity analogs, 2',3'-O-(2,4,6-trinitrophenyl)-8-azido-ATP, -ADP and -AMP (TNP- 8N₃ATP, -ADP and -AMP), and their radiolabeled derivatives, and characterized their interaction with the sarcoplasmic reticulum Ca²⁺-ATPase. The TNP-8N₃-nucleotides were synthesized from ATP in three steps involving bromination in the 8-position of the adenine ring followed by displacement with an azido group and then trinitrophenylation of the resulting 8N₃-nucleotide with TNBS. Inclusion of the oxidizing agent, DTNB, in the final reaction was found to be necessary to prevent reduction of the azido group by the released sulfite anion and also elevated the yield of trinitrophenylation to about 80%. Purity was determined spectrophotometrically, as well as by anion exchange TLC and reversed phase HPLC. In the dark, the compounds were found to display most of the features of the parent TNP-nucleotides and interacted with the Ca²⁺-ATPase in a similar way. When activated by illumination, the probes were specifically incorporated into SR vesicles with high efficiency at alkaline pH. The site of labeling was identified as being on the A₁ tryptic fragment.

No description available.

This thesis considers Michel Foucault’s understanding of friendship as a way of life and its relationship to anarchist models of affinity based organizing. I argue that Foucault’s interviews on friendship, his understanding of power structures as simultaneously individualizing and totalizing, and his notion of the care of the self all help us to rethink what friendship means today. Further, friendship can be a guide towards experimental and aesthetic forms of political resistance. Friendship for Foucault is not utopian, however, and I examine its use as a technique of police surveillance and intelligence gathering in the context of the G20 protests in Toronto in 2010. If friendship can play an important role in the regime of what Foucault termed governmentality, it can also be a site of struggle whereby an alternative vision for politics is elaborated. I argue that this has particular resonance with anarchism, and that while friendship has the danger to becoming an invisible form of power, anarchism responds to this by proposing a culture of solidarity. Overall, I argue that Foucault offers an original account of friendship that fundamentally shifts our understanding of the relationship between friendship and politics. / Graduate