Introduction to Atomic Units, Normalization and Orthogonalization (Part 2 of a Series)

Some consequences of using Atomic Units are treated here.

Aromic Units, Why We Need Them and How They Work

Quantum Chemistry is usually carried out using Atomic Units, so a careful discussion of these units is warranted.

Convergent variational calculation of positronium-hydrogen-atom scattering lengths

We present a convergent variational basis-set calculational scheme for elastic scattering of the positronium atom by the hydrogen atom in S wave. Highly correlated trial functions with appropriate symmetry are needed to achieve convergence. We report convergent results for scattering lengths in atomic units for both singlet (= 3.49 +/-0.20) and triplet (= 2.46 +/-0.10) states.

An ontology for risk management of digital collections

Maintaining accessibility to and understanding of digital information over time is a complex challenge that often requires contributions and interventions from a variety of individuals and organizations. The processes of preservation planning and evaluation are fundamentally implicit and share similar complexity. Both demand comprehensive knowledge and understanding of every aspect of to-be-preserved content and the contexts within which preservation is undertaken. Consequently, means are required for the identification, documentation and association of those properties of data, representation and management mechanisms that in combination lend value, facilitate interaction and influence the preservation process. These properties may be almost limitless in terms of diversity, but are integral to the establishment of classes of risk exposure, and the planning and deployment of appropriate preservation strategies. We explore several research objectives within the course of this thesis. Our main objective is the conception of an ontology for risk management of digital collections. Incorporated within this are our aims to survey the contexts within which preservation has been undertaken successfully, the development of an appropriate methodology for risk management, the evaluation of existing preservation evaluation approaches and metrics, the structuring of best practice knowledge and lastly the demonstration of a range of tools that utilise our findings. We describe a mixed methodology that uses interview and survey, extensive content analysis, practical case study and iterative software and ontology development. We build on a robust foundation, the development of the Digital Repository Audit Method Based on Risk Assessment. We summarise the extent of the challenge facing the digital preservation community (and by extension users and creators of digital materials from many disciplines and operational contexts) and present the case for a comprehensive and extensible knowledge base of best practice. These challenges are manifested in the scale of data growth, the increasing complexity and the increasing onus on communities with no formal training to offer assurances of data management and sustainability. These collectively imply a challenge that demands an intuitive and adaptable means of evaluating digital preservation efforts. The need for individuals and organisations to validate the legitimacy of their own efforts is particularly prioritised. We introduce our approach, based on risk management. Risk is an expression of the likelihood of a negative outcome, and an expression of the impact of such an occurrence. We describe how risk management may be considered synonymous with preservation activity, a persistent effort to negate the dangers posed to information availability, usability and sustainability. Risk can be characterised according to associated goals, activities, responsibilities and policies in terms of both their manifestation and mitigation. They have the capacity to be deconstructed into their atomic units and responsibility for their resolution delegated appropriately. We continue to describe how the manifestation of risks typically spans an entire organisational environment, and as the focus of our analysis risk safeguards against omissions that may occur when pursuing functional, departmental or role-based assessment. We discuss the importance of relating risk-factors, through the risks themselves or associated system elements. To do so will yield the preservation best-practice knowledge base that is conspicuously lacking within the international digital preservation community. We present as research outcomes an encapsulation of preservation practice (and explicitly defined best practice) as a series of case studies, in turn distilled into atomic, related information elements. We conduct our analyses in the formal evaluation of memory institutions in the UK, US and continental Europe. Furthermore we showcase a series of applications that use the fruits of this research as their intellectual foundation. Finally we document our results in a range of technical reports and conference and journal articles. We present evidence of preservation approaches and infrastructures from a series of case studies conducted in a range of international preservation environments. We then aggregate this into a linked data structure entitled PORRO, an ontology relating preservation repository, object and risk characteristics, intended to support preservation decision making and evaluation. The methodology leading to this ontology is outlined, and lessons are exposed by revisiting legacy studies and exposing the resource and associated applications to evaluation by the digital preservation community.

Low-density Three-dimensional Foam Using Self-reinforced Hybrid Two-dimensional Atomic Layers.

Low-density nanostructured foams are often limited in applications due to their low mechanical and thermal stabilities. Here we report an approach of building the structural units of three-dimensional (3D) foams using hybrid two-dimensional (2D) atomic layers made of stacked graphene oxide layers reinforced with conformal hexagonal boron nitride (h-BN) platelets. The ultra-low density (1/400 times density of graphite) 3D porous structures are scalably synthesized using solution processing method. A layered 3D foam structure forms due to presence of h-BN and significant improvements in the mechanical properties are observed for the hybrid foam structures, over a range of temperatures, compared with pristine graphene oxide or reduced graphene oxide foams. It is found that domains of h-BN layers on the graphene oxide framework help to reinforce the 2D structural units, providing the observed improvement in mechanical integrity of the 3D foam structure.

Phonon dispersion curves and atomic mean square displacement for several fcc and bcc materials

The atomic mean square displacement (MSD) and the phonon dispersion curves (PDC's) of a number of face-centred cubic (fcc) and body-centred cubic (bcc) materials have been calclllated from the quasiharmonic (QH) theory, the lowest order (A2 ) perturbation theory (PT) and a recently proposed Green's function (GF) method by Shukla and Hiibschle. The latter method includes certain anharmonic effects to all orders of anharmonicity. In order to determine the effect of the range of the interatomic interaction upon the anharmonic contributions to the MSD we have carried out our calculations for a Lennard-Jones (L-J) solid in the nearest-neighbour (NN) and next-nearest neighbour (NNN) approximations. These results can be presented in dimensionless units but if the NN and NNN results are to be compared with each other they must be converted to that of a real solid. When this is done for Xe, the QH MSD for the NN and NNN approximations are found to differ from each other by about 2%. For the A2 and GF results this difference amounts to 8% and 7% respectively. For the NN case we have also compared our PT results, which have been calculated exactly, with PT results calculated using a frequency-shift approximation. We conclude that this frequency-shift approximation is a poor approximation. We have calculated the MSD of five alkali metals, five bcc transition metals and seven fcc transition metals. The model potentials we have used include the Morse, modified Morse, and Rydberg potentials. In general the results obtained from the Green's function method are in the best agreement with experiment. However, this improvement is mostly qualitative and the values of MSD calculated from the Green's function method are not in much better agreement with the experimental data than those calculated from the QH theory. We have calculated the phonon dispersion curves (PDC's) of Na and Cu, using the 4 parameter modified Morse potential. In the case of Na, our results for the PDC's are in poor agreement with experiment. In the case of eu, the agreement between the tlleory and experiment is much better and in addition the results for the PDC's calclliated from the GF method are in better agreement with experiment that those obtained from the QH theory.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Toward the Optimization of an e-Tongue System Using Information Visualization: A Case Study with Perylene Tetracarboxylic Derivative Films in the Sensing Units

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Relaxation and tunnelling of structural units within the LTO phase of La2CuO4

The anelastic relaxation (elastic energy loss and Young modulus) of nearly stoichiometric La2CuO4+delta with LTO structure was measured. Extraordinarily intense effects are present below room temperature in the elastic dynamic susceptibility, indicating relaxational dynamics of a relevant fraction of the lattice. The involved degrees of freedom are identified as rotations of the CuO6 octahedra. Two distinct processes are found at frequencies around 1 kKz: one is observed around 150 K and is characterized by a mean activation energy of 2800 K; the second one occurs below 30 K and is governed by atomic tunnelling. Two explanations are proposed for the faster process: i) formation of fluctuating LTT domains on a scale of few atomic cells; ii) the LTO phase is a dynamical Jahn-Teller phase with all the octahedra tunneling between two LTT-like tilts. In both cases there would be important implications regarding the mechanisms giving rise to charge nanophase separation and strong electron-phonon coupling.

In Vitro Analysis of Bacterial Morphology by Atomic Force Microscopy of Low Level Laser Therapy 660, 830 and 904 nm

Objective: The objective of this study was to analyze the bacterial morphology by atomic force microscopy (AFM) after the application of low-level laser therapy (LLLT) in in vitro culture of Staphylococcus aureus ATCC 29213. Background data: Infections caused by S. aureus are among the highest occurring in hospitals and can often colonize pressure ulcers. LLLT is among the methods used to accelerate the healing of ulcers. However, there is no consensus on its effect on bacteria. Materials and methods: After being cultivated and seeded, the cultures were irradiated using wavelengths of 660, 830, and 904 nm at fluences of 0, 1, 2, 3, 4, 5, and 16 J/cm(2). Viable cells of S. aureus strain were counted after 24 h incubation. To analyze the occurrence of morphological changes, the topographical measurement of bacterial cells was analyzed using the AFM. Results: The overall assessment revealed that the laser irradiation reduced the S. aureus growth using 830 and 904 nm wavelengths; the latter with the greatest inhibition of the colony-forming units (CFU/mL) (331.1 +/- 38.19 and 137.38 +/- 21.72). Specifically with 660 nm, the statistical difference occurred only at a fluence of 3 J/cm(2). Topographical analysis showed small changes in morphological conformity of the samples tested. Conclusions: LLLT reduced the growth of S. aureus with 830 and 904 nm wavelengths, particularly with 904 nm at a fluence of 3 J/cm(2), where the greatest topographical changes of the cell structure occurred.

Toward the Optimization of an e-Tongue System Using Information Visualization: A Case Study with Perylene Tetracarboxylic Derivative Films in the Sensing Units

The wide variety of molecular architectures used in sensors and biosensors and the large amount of data generated with some principles of detection have motivated the use of computational methods, such as information visualization techniques, not only to handle the data but also to optimize sensing performance. In this study, we combine projection techniques with micro-Raman scattering and atomic force microscopy (AFM) to address critical issues related to practical applications of electronic tongues (e-tongues) based on impedance spectroscopy. Experimentally, we used sensing units made with thin films of a perylene derivative (AzoPTCD acronym), coating Pt interdigitated electrodes, to detect CuCl(2) (Cu(2+)), methylene blue (MB), and saccharose in aqueous solutions, which were selected due to their distinct molecular sizes and ionic character in solution. The AzoPTCD films were deposited from monolayers to 120 nm via Langmuir-Blodgett (LB) and physical vapor deposition (PVD) techniques. Because the main aspects investigated were how the interdigitated electrodes are coated by thin films (architecture on e-tongue) and the film thickness, we decided to employ the same material for all sensing units. The capacitance data were projected into a 2D plot using the force scheme method, from which we could infer that at low analyte concentrations the electrical response of the units was determined by the film thickness. Concentrations at 10 mu M or higher could be distinguished with thinner films tens of nanometers at most-which could withstand the impedance measurements, and without causing significant changes in the Raman signal for the AzoPTCD film-forming molecules. The sensitivity to the analytes appears to be related to adsorption on the film surface, as inferred from Raman spectroscopy data using MB as analyte and from the multidimensional projections. The analysis of the results presented may serve as a new route to select materials and molecular architectures for novel sensors and biosensors, in addition to suggesting ways to unravel the mechanisms behind the high sensitivity obtained in various sensors.

Cooperative and Noncooperative Assembly of Oligopyrenotides Resolved by Atomic Force Microscopy

The supramolecular assembly of amphiphilic oligopyrenotide building blocks (covalently linked heptapyrene, Py7) is studied by atomic force microscopy (AFM) in combination with optical spectroscopy. The assembly process is triggered in a controlled manner by increasing the ionic strength of the aqueous oligomer solution. Cooperative noncovalent interactions between individual oligomeric units lead to the formation of DNA-like supramolecular polymers. We also show that the terminal attachment of a single cytidine nucleotide to the heptapyrenotide (Py7-C) changes the association process from a cooperative (nucleation−elongation) to a noncooperative (isodesmic) regime, suggesting a structure misfit between the cytidine and the pyrene units. We also demonstrate that AFM enables the identification and characterization of minute concentrations of the supramolecular products, which was not accessible by conventional optical spectroscopy.

Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy.

The inwardly rectifying K+ channel ROMK1 has been implicated as being significant in K+ secretion in the distal nephron. ROMK1 has been shown by immunocytochemistry to be expressed in relevant nephron segments. The development of the atomic force microscope has made possible the production of high resolution images of small particles, including a variety of biological macromolecules. Recently, a fusion protein of glutathione S-transferase (GST) and ROMK1 (ROMK1-GST) has been used to produce a polyclonal antibody for immunolocalization of ROMK1. We have used atomic force microscopy to examine ROMK1-GST and the native ROMK1 polypeptide cleaved from GST. Imaging was conducted with the proteins in physiological solutions attached to mica. ROMK1-GST appears in images as a particle composed of two units of similar size. Analyses of images indicate that the two units have volumes of approximately 118 nm3, which is close to the theoretical volume of a globular protein of approximately 65 kDa (the molecular mass of ROMK1-GST). Native GST exists as a dimer, and the images obtained here are consistent with the ROMK1-GST fusion protein's existence as a heterodimer. In experiments on ROMK1 in aqueous solution, single molecules appear to aggregate, but contact to the mica was maintained. Addition of ATP to the solution produced a change in height of the aggregates. This change (which was reversible) suggests that ATP induces a structural change in the ROMK1 protein. The data show that atomic force microscopy is a useful tool for examination of purified protein molecules under near-physiological conditions, and furthermore, that structural alterations in the proteins may be continuously investigated.