Learning The Differences Between Ontologies and Conceptual Schemas Through Ontology-Driven Information Systems.

In the traditional systems modeling approach, the modeler is required to capture a user\u27s view of some domain in a formal conceptual schema. The designer\u27s conceptualization may or may not match with the user\u27s conceptualization. One of the reasons for these conflicts is the lack of an initial agreement among users and modelers concerning the concepts belonging to the domain. Such an agreement could be facilitated by means of an ontology. If the ontology is previously constructed and formalized so that it can be shared by the modeler and the user in the development process, such conflicts would be less likely to happen. Following up on that, a number of investigators have suggested that those working on information systems should make use of commonly held, formally defined ontologies that would constrain and direct the design, development, and use of information systems - thus avoiding the above mentioned difficulties. Whether ontologies represent a significant advance from the more traditional conceptual schemas has been challenged by some researchers. We review and summarize some major themes of this complex discussion. While recognizing the commonalities and historical continuities between conceptual schemas and ontologies, we think that there is an important emerging distinction that should not be obscured and should guide future developments. In particular, we propose that the notions of conceptual schemas and ontologies be distinguished so as to play essentially different roles for the developers and users of information systems. We first suggest that ontologies and conceptual schemas belong to two different epistemic levels. They have different objects and are created with different objectives. Our proposal is that ontologies should deal with general assumptions concerning the explanatory invariants of a domain - those that provide a framework enabling understanding and explanation of data across all domains inviting explanation and understanding. Conceptual schemas, on the other hand, should address the relation between such general explanatory categories and the facts that exemplify them in a particular domain (e.g., the contents of the database). In contrast to ontologies, conceptual schemas would involve specification of the meaning of the explanatory categories for a particular domain as well as the consequent dimensions of possible variation among the relevant data of a given domain. Accordingly, the conceptual schema makes possible both the intelligibility and the measurement of those facts of a particular domain. The proposed distinction between ontologies and conceptual schemas makes possible a natural decomposition of information systems in terms of two necessary but complementary epistemic functions: identification of an invariant background and measurement of the object along dimensions of possible variation. Recognition of the suggested distinction represents, we think, a natural evolution in the field of modeling, and significant principled guidance for developers and users of information systems

Play as the Way Out of the Newspeak-Tower of Babel Dilemma in Data Modeling

A data modeler, when faced with different interpretations of a given reality within an organization, may opt to create a standard model for the whole company (the Newspeak solution). On the other hand, allowing multiple, and sometimes incompatible, models to coexist may lead to what some researchers call the Tower of Babel problem. The clash between these two possibilities creates a fundamental design problem for IS. We argue that the concept of play in Gadamer can be seen as the “place” where differences and similarities among various perspectives are expressed and discussed. Based on Gadamer’s Truth and Method (1960) and on Heidegger’s Being and Time (1962), we review the concepts of horizon, fusion of horizons, play, application, and the hermeneutic circle, and show some applications to information systems. Following Hirschheim et al. (1995), who consider that “the role of a data models should be seen in a similar light as the role of a theory for a scientific community,” we turn to the debate between objectivism and relativism in philosophy of science in order to discover a way of negotiating the clash between the Newspeak and Tower of Babel possibilities in Information Systems. We introduce an historical example of hermeneutical play—the Popper/Kuhn debate in the philosophy of science—which directly addresses the problems and possibilities associated with communication among people holding incommensurable perspectives. We show how this situation informed their hermeneutic play in the philosophy of science. Finally, we argue that a similar play, in conjunction with the dimension of application, is the way beyond the either/or of the Tower of Babel versus Newspeak dilemma

Self-organized Models of Selectivity in Ca and Na Channels

A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA Ca channels and DEKA Na channels in many ionic solutions of different composition and concentration. Only the side chains are different in the model of the Ca and Na channels. Parameters are the same for both channels in all solutions. 'Pauling' radii are used for ions. No information from crystal structures is used in the model. Side chains are grossly approximated as spheres. The predicted properties of the Na and Ca channels are very different. How can such a simple model give such powerful results when chemical intuition says that selectivity depends on the precise relation of ions and side chains? We use Monte Carlo simulations of this model that determine the most stable-lowest free energy-structure of the ions and side chains. Structure is the computed consequence of the forces in this model. The relationship of ions and side chains vary with ionic solution and are very different in simulations of the Na and Ca channels. Selectivity is a consequence of the 'induced fit' of side chains to ions and depends on the flexibility (entropy) of the side chains as well as their location. The model captures the relation of side chains and ions well enough to account for selectivity of both Na channels and Ca channels in the wide range of conditions measured in experiments. Evidently, the structures in the real Na and Ca channels responsible for selectivity are self-organized, at their free energy minimum. Oversimplified models are enough to account for selectivity if the models calculate the 'most stable' structure as it changes from solution to solution, and mutation to mutation.Comment: Version of http://www.ima.umn.edu/2008-2009/W12.8-12.08/abstracts.html, talk given at the Institute for Mathematics and its Applications, University of Minnesota, November 19, 2008. Abstract published in Biophysical Journal, Volume 96, Issue 3, 253

Generalizing the Quantum Dot Lab Towards Arbitrary Shapes and Compositions

As applications in nanotechnology reach the scale of countable atoms, computer simulation has become a necessity in the understanding of new devices, such as quantum dots. To understand the various optoelectronic properties of these nanoparticles, the Quantum Dot Lab (QDL) has been created and powered by NEMO5 to simulate on multi-scale, multi-physics bases. QDL is easy to use by offering choices of different QD geometries such as shapes and sizes to the users from a predefined menu. The simplicity of use, however, limits the simulation of general QD shapes and compositions. A method to import generic strained crystalline and amorphous dot structures into the QDL has been created here. Users can now analyze electronic structure effects in both effective mass and 10-band sp3d5s* tight-binding models. Implementation has been successful through a restructuring of the user interface as well as the alteration of the primary bodies of Tcl code that interpret input and pass them on to NEMO5 for precision computation. With this new development comes the ability for researchers, educators, and students alike to peer into uncharted areas of quantum technology and gain new insight through a high-level of simulation plasticity

Effect of Seagrass on Current Speed: Importance of Flexibility vs. Shoot Density

Water flow through seagrass beds transports nutrients, affects sediment stability and chemistry, and imposes hydrodynamic forces on shoots that alter canopy configuration. Past studies done under diverse conditions yielded conflicting results about the effects of shoot density on flow through seagrass bed canopies. We used eelgrass, Zostera marina, to study how the density of flexible shoots affect the hydrodynamics of seagrass beds in unidirectional water flow. By exposing randomly-arranged shoots of uniform length to current velocities controlled in a flume, the effects of shoot density and distance downstream from the bed edge could be determined without confounding factors. Comparison of velocity profiles within beds to those upstream of beds showed that flow was slower in the beds. However, shoot density, downstream distance, and current velocity did not affect the percent reduction in flow velocity in a bed. Turbulence enhances mixing of substances carried in the water. Here, turbulence intensity (index of the importance of turbulent velocity fluctuations relative to average current velocity) was lower when ambient flow was faster, but was not affected by shoot density or downstream position, Drag (hydrodynamic force on a shoot that bends it over in the flow direction) provides another measure of how the canopy affects flow experienced by a shoot. Drag was not affected by current velocity, shoot density, or downstream position in the bed. Gaps between shoots can enhance light and flow penetration into the canopy, but when shoots are bent over by flow, they can cover gaps. Faster ambient currents caused greater gap closure, which at each current speed was greater for high shoot densities. Thus, canopy gap closure did not correlate with percent flow reduction in grass beds or with drag on individual shoots, both of which were independent of shoot density and ambient current velocity. Since changing shoot density does not affect the flow in a grass bed exposed to a given ambient current, our results are inconsistent with the hypothesis that the high shoot densities observed in grass beds in habitats exposed to rapid flow are due to a direct, adaptive response of the grass to the flow environment

Textile-to-rigid microstrip transition using permanent magnets

A novel transition between a rigid-substrate and a flexible-substrate microstrip for use in wearable devices is described. The contact force between the conductors of the two microstrips is supplied by a pair of rectangular magnets. A simulation and measurement study carried out on a test jig comprising a back-to-back pair of such transitions demonstrated an insertion loss of better than 0.5 dB/transition can be achieved in the range of 0-3 GHz

Simulating Nanowires and Ultra-Thin Body Transistors using NEMO5 on nanoHUB.org

During the past twenty years, the most important aspects of semiconductor electronics have advanced into the nanometer range, resulting in exponential increases of microprocessor computing performance. As the size of electrical components continues to shrink, the cost of experimental research and industrial fabrication in this field has increased dramatically. Thus, the development of accurate nanoscale model simulations becomes necessary as a measure to decrease the high financial expenses of advancing semiconductor technology. This simulator supports atomistic modeling in order to provide an accurate description of the nanoscale devices, as current electrical components operate in the quantum regime and are affected by atomistic fluctuations in real world devices. Using the fifth edition of the Nanoelectronics Modeling engine, or NEMO5, developed in the iNEMO group of Purdue’s Network for Computational Nanotechnology department, the tool is capable of computing strain, phonon spectra, electronic band structures, and many other properties of semiconductor devices. The simulator utilizes effective mass approximations to calculate a device’s internal quantities, such as charge distribution and current densities. Real-space Schrodinger and Poisson equations are solved self-consistently using a 2-D finite difference grid to provide an electric potential map of the device or material being tested. This user-friendly simulation tool will allow students, teachers, and researchers to explore the properties of nanoscale transistors in a graphical manner. The simulator will be able to provide information such as quantum states, transport characteristics, and self-consistent potential densities in an aesthetic manner so that these concepts can be understood intuitively

Microwave interconnects between textile and rigid substrates using permanent magnets

This paper presents a new approach to the problem of the transition between a textile microwave system and a regular microwave system. A simulated model of a transition between copper conductive line and textile conductive line is presented, with a comparison between simulated and measured results of the same model showing reasonable to good agreement. The work aims to create a full textile remountable and flexible microwave connector

Effects of diets containing linseed oil on fatty acid desaturation and oxidation in hepatocytes and intestinal enterocytes in Atlantic salmon (Salmo salar)

We hypothesized that replacing fish oil with 18:3n-3-rich linseed oil may enable salmon to maintain the levels of tissue n-3HUFA levels through a combination of increased desaturation activity and increased substrate fatty acid provision. To this end we investigated desaturation/elongation of [1-14C18:3n-3 in hepatocytes and intestinal enterocytes, and determined the extent to which 18:3n-3 was oxidized and desaturated by measuring both simultaneously in a combined assay. Salmon smolts were stocked randomly into five seawater pens and fed for 40 weeks on diets in which the fish oil was replaced in a graded manner by linseed oil. At the end of the trial, fatty acyl desaturation/elongation and oxidation activities were determined in isolated hepatocytes and intestinal enterocytes using [1-14C]18:3n-3 as substrate, and samples of liver and intestinal tissue were collected for analysis of lipid and fatty acid composition. The results showed that, despite increased desaturation of [1-14C]18:3n-3 in hepatocytes, provision of dietary 18:3n-3 did not prevent the decrease in tissue n-3HUFA in fish fed linseed oil. Intestinal enterocytes were a site of significant fatty acid desaturation but, in contrast to hepatocytes, the activity was not increased by feeding linseed oil and was generally lower in fish fed linseed oil compared to fish fed only fish oil. In contrast, oxidation of [1-14C]18:3n-3 in enterocytes was generally increased in fish fed linseed oil compared to fish fed the diet containing only fish oil. However, oxidation of [1-14C]18:3n-3 in hepatocytes was 4- to 8-fold lower than in enterocytes and was not affected by diet. Furthermore, oxidation of [1-14C]18:3n-3 in enterocytes exceeded desaturation irrespective of dietary treatment, whereas similar amounts of [1-14C]18:3n-3 were desaturated and oxidized in hepatocytes from fish fed only fish oil and desaturation exceeded oxidation by 3-fold in fish fed the diet containing 100% linseed oil. The molecular mechanisms underpinning these results were discussed