Position-Selected Molecular Ruler

The molecular ruler method allows the precise control of the gap between a parent gold structure and a deposited daughter structure using a conveniently grown self-assembled molecular multilayer as a lithographic mask. However, we cannot choose a position where the gap should be placed, since the ruler attaches to all exposed gold surfaces. In this work, a convenient method of selecting the position of nanogaps by further patterning the molecular multilayer using low-energy electron beam irradiation and piranha etchant is described

Improved Electrodes and Electrolytes for Dye-Based Solar Cells

The most important factor in limiting the stability of dye-sensitized solar cells is the use of volatile liquid solvents in the electrolytes, which causes leakage during extended operation especially at elevated temperatures. This, together with the necessary complex sealing of the cells, seriously hampers the industrial-scale manufacturing and commercialization feasibilities of DSSCs. The objective of this program was to bring about a significant improvement in the performance and longevity of dye-based solar cells leading to commercialization. This had been studied in two ways first through development of low volatility solid, gel or liquid electrolytes, second through design and fabrication of TiO2 sculptured thin film electrodes

Positive definite metric spaces

Magnitude is a numerical invariant of finite metric spaces, recently introduced by T. Leinster, which is analogous in precise senses to the cardinality of finite sets or the Euler characteristic of topological spaces. It has been extended to infinite metric spaces in several a priori distinct ways. This paper develops the theory of a class of metric spaces, positive definite metric spaces, for which magnitude is more tractable than in general. Positive definiteness is a generalization of the classical property of negative type for a metric space, which is known to hold for many interesting classes of spaces. It is proved that all the proposed definitions of magnitude coincide for compact positive definite metric spaces and further results are proved about the behavior of magnitude as a function of such spaces. Finally, some facts about the magnitude of compact subsets of l_p^n for p \le 2 are proved, generalizing results of Leinster for p=1,2, using properties of these spaces which are somewhat stronger than positive definiteness.Comment: v5: Corrected some misstatements in the last few paragraphs. Updated reference

Blending of nanoscale and microscale in uniform large-area sculptured thin-film architectures

The combination of large thickness ($>3$ $\mu$m), large--area uniformity (75 mm diameter), high growth rate (up to 0.4 $\mu$m/min) in assemblies of complex--shaped nanowires on lithographically defined patterns has been achieved for the first time. The nanoscale and the microscale have thus been blended together in sculptured thin films with transverse architectures. SiO$_x$ ($x\approx 2$) nanowires were grown by electron--beam evaporation onto silicon substrates both with and without photoresist lines (1--D arrays) and checkerboard (2--D arrays) patterns. Atomic self--shadowing due to oblique--angle deposition enables the nanowires to grow continuously, to change direction abruptly, and to maintain constant cross--sectional diameter. The selective growth of nanowire assemblies on the top surfaces of both 1--D and 2--D arrays can be understood and predicted using simple geometrical shadowing equations.Comment: 17 pages, 9 figure

A Parametrization of Bipartite Systems Based on SU(4) Euler Angles

In this paper we give an explicit parametrization for all two qubit density matrices. This is important for calculations involving entanglement and many other types of quantum information processing. To accomplish this we present a generalized Euler angle parametrization for SU(4) and all possible two qubit density matrices. The important group-theoretical properties of such a description are then manifest. We thus obtain the correct Haar (Hurwitz) measure and volume element for SU(4) which follows from this parametrization. In addition, we study the role of this parametrization in the Peres-Horodecki criteria for separability and its corresponding usefulness in calculating entangled two qubit states as represented through the parametrization.Comment: 23 pages, no figures; changed title and abstract and rewrote certain areas in line with referee comments. To be published in J. Phys. A: Math. and Ge

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (KD). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.Department of HE and Training approved lis

Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study

Background Little is known about the persistence of antibodies after the first year following SARS-CoV-2 infection. We aimed to determine the proportion of individuals that maintain detectable levels of SARS-CoV-2 antibodies over an 18-month period following infection. Methods Population-based prospective study of 20 000 UK Biobank participants and their adult relatives recruited in May 2020. The proportion of SARS-CoV-2 cases testing positive for immunoglobulin G (IgG) antibodies against the spike protein (IgG-S), and the nucleocapsid protein (IgG-N), was calculated at varying intervals following infection. Results Overall, 20 195 participants were recruited. Their median age was 56 years (IQR 39–68), 56% were female and 88% were of white ethnicity. The proportion of SARS-CoV-2 cases with IgG-S antibodies following infection remained high (92%, 95% CI 90%–93%) at 6 months after infection. Levels of IgG-N antibodies following infection gradually decreased from 92% (95% CI 88%–95%) at 3 months to 72% (95% CI 70%–75%) at 18 months. There was no strong evidence of heterogeneity in antibody persistence by age, sex, ethnicity or socioeconomic deprivation. Conclusion This study adds to the limited evidence on the long-term persistence of antibodies following SARS-CoV-2 infection, with likely implications for waning immunity following infection and the use of IgG-N in population surveys

Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs

Livestock diseases caused by Trypanosoma congolense, T. vivax and T. brucei, collectively known as nagana, are responsible for billions of dollars in lost food production annually. There is an urgent need for novel therapeutics. Encouragingly, promising antitrypanosomal benzoxaboroles are under veterinary development. Here, we show that the most efficacious subclass of these compounds are prodrugs activated by trypanosome serine carboxypeptidases (CBPs). Drug-resistance to a development candidate, AN11736, emerged readily in T. brucei, due to partial deletion within the locus containing three tandem copies of the CBP genes. T. congolense parasites, which possess a larger array of related CBPs, also developed resistance to AN11736 through deletion within the locus. A genome-scale screen in T. brucei confirmed CBP loss-of-function as the primary mechanism of resistance and CRISPR-Cas9 editing proved that partial deletion within the locus was sufficient to confer resistance. CBP re-expression in either T. brucei or T. congolense AN11736-resistant lines restored drug-susceptibility. CBPs act by cleaving the benzoxaborole AN11736 to a carboxylic acid derivative, revealing a prodrug activation mechanism. Loss of CBP activity results in massive reduction in net uptake of AN11736, indicating that entry is facilitated by the concentration gradient created by prodrug metabolism.</p