TumorML: Concept and requirements of an in silico cancer modelling markup language

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification

Interpretation at the controller's edge: designing graphical user interfaces for the digital publication of the excavations at Gabii (Italy)

This paper discusses the authors’ approach to designing an interface for the Gabii Project’s digital volumes that attempts to fuse elements of traditional synthetic publications and site reports with rich digital datasets. Archaeology, and classical archaeology in particular, has long engaged with questions of the formation and lived experience of towns and cities. Such studies might draw on evidence of local topography, the arrangement of the built environment, and the placement of architectural details, monuments and inscriptions (e.g. Johnson and Millett 2012). Fundamental to the continued development of these studies is the growing body of evidence emerging from new excavations. Digital techniques for recording evidence “on the ground,” notably SFM (structure from motion aka close range photogrammetry) for the creation of detailed 3D models and for scene-level modeling in 3D have advanced rapidly in recent years. These parallel developments have opened the door for approaches to the study of the creation and experience of urban space driven by a combination of scene-level reconstruction models (van Roode et al. 2012, Paliou et al. 2011, Paliou 2013) explicitly combined with detailed SFM or scanning based 3D models representing stratigraphic evidence. It is essential to understand the subtle but crucial impact of the design of the user interface on the interpretation of these models. In this paper we focus on the impact of design choices for the user interface, and make connections between design choices and the broader discourse in archaeological theory surrounding the practice of the creation and consumption of archaeological knowledge. As a case in point we take the prototype interface being developed within the Gabii Project for the publication of the Tincu House. In discussing our own evolving practices in engagement with the archaeological record created at Gabii, we highlight some of the challenges of undertaking theoretically-situated user interface design, and their implications for the publication and study of archaeological materials

Cold cathode gauge experiment (ALSEP)

Cold cathode ionization gages were left on the lunar surface as part of ALSEP (Apollo Lunar Surface Experiment Package) on Apollo missions 12, 14, and 15. An instrument prepared for Apollo 13 did not reach the surface because of the abort of that mission. The gages that reached the lunar surface measured the amounts of gas present in the vicinity of the ALSEP sites. The observed daytime gas concentrations were initially about two orders of magnitude greater than the nighttime observations; this was due to contamination of the landing area by the Apollo operations and equipment, and the daytime measurements showed a decrease with time characterized by a time constant of a few months

Low-energy, planar magnetic defects in BaFe2As2: nanotwins, twins, antiphase and domain boundaries

In BaFe2As2, structural and magnetic planar defects begin to proliferate below the structural phase transition, affecting descriptions of magnetism and superconductivity. We study using density-functional theory the stability and magnetic properties of competing antiphase and domain boundaries, twins and isolated $nano$twins (twin nuclei) - spin excitations proposed and/or observed. These nanoscale defects have very low surface energy ($22$-$210$~$m$Jm$^{-2}$), with twins favorable to the mesoscale. Defects exhibit smaller moments confined near their boundaries -- making a uniform-moment picture inappropriate for long-range magnetic order in real samples. {\it{Nano}}twins explain features in measured pair distribution functions, so should be considered when analyzing scattering data. All these defects can be weakly mobile and/or have fluctuations that lower assessed "ordered" moments from longer spatial and/or time averaging, and should be considered directly.Comment: 6 pages, 6 figures, 1 tabl

Near-wall, three-dimensional turbulence measurements: A challenge for laser velocimetry

A new laser velocimeter approach is presented, which has distinct advantages in near-wall, two- and three-dimensional turbulence measurement applications. The approach does require placing a probe into the flow; but in return, there are some important benefits, such as, the direct measurement of the crossflow velocity, w, at a grazing incidence, and the ability to size optical components for the scale of the flow rather than the size of the facility. Promising resuls were obtained with this approach for a two-dimensional turbulent boundary layer

Haldane fractional statistics in the fractional quantum Hall effect

We have tested Haldane's ``fractional-Pauli-principle'' description of excitations around the $\nu = 1/3$ state in the FQHE, using exact results for small systems of electrons. We find that Haldane's prediction $\beta = \pm 1/m$ for quasiholes and quasiparticles, respectively, describes our results well with the modification $\beta_{qp} = 2-1/3$ rather than $-1/3$. We also find that this approach enables us to better understand the {\it energetics\/} of the ``daughter'' states; in particular, we find good evidence, in terms of the effective interaction between quasiparticles, that the states $\nu = 4/11$ and 4/13 should not be stable.Comment: 9 pages, 3 Postscript figures, RevTex 3.0. (UCF-CM-93-005

Computer code to interchange CDS and wave-drag geometry formats

A computer program has been developed on the PRIME minicomputer to provide an interface for the passage of aircraft configuration geometry data between the Rockwell Configuration Development System (CDS) and a wireframe geometry format used by aerodynamic design and analysis codes. The interface program allows aircraft geometry which has been developed in CDS to be directly converted to the wireframe geometry format for analysis. Geometry which has been modified in the analysis codes can be transformed back to a CDS geometry file and examined for physical viability. Previously created wireframe geometry files may also be converted into CDS geometry files. The program provides a useful link between a geometry creation and manipulation code and analysis codes by providing rapid and accurate geometry conversion

What is a quantum simulator?

Quantum simulators are devices that actively use quantum effects to answer questions about model systems and, through them, real systems. Here we expand on this definition by answering several fundamental questions about the nature and use of quantum simulators. Our answers address two important areas. First, the difference between an operation termed simulation and another termed computation. This distinction is related to the purpose of an operation, as well as our confidence in and expectation of its accuracy. Second, the threshold between quantum and classical simulations. Throughout, we provide a perspective on the achievements and directions of the field of quantum simulation.Comment: 13 pages, 2 figure

Investigation of fiber bridging in double cantilever beam specimens

The possibility to eliminate fiber bridging or at least to reduce it, and to evaluate an alternative approach for determination of in situ mode 7 fracture toughness values of composite matrix materials were investigated. Double cantilever beam (DCB) specimens were made using unidirectional lay-ups of T6C/Hx205 composite material in which the delaminating halves were placed at angles of 0, 1.5, and 3 degrees to each other. The small angles between the delaminating plies were used to avoid fiber nesting without significantly affecting mode I teflon insert. The DCB specimens were fabricated and it was found that: (1) the extent which fiber bridging and interlaminar toughness increase with crack length can be reduced by slight cross ply at the delamination plane to reduce fiber nesting; (2) some fiber bridging may occur even in the absence of fiber nesting; (3) the first values of toughness measured ahead of the thin teflon insert are very close to the toughness of the matrix material with no fiber bridging; (4) thin adhesive bondline of matrix material appears to give toughness values equal to the interlaminar toughness of the composite matrix without fiber bridging