Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

A theoretical reflection on smart shape modeling

This paper presents, as far as the authors are aware, a complete and extended new taxonomy of shape specification modeling techniques and a characterization of shape design systems, all based on the relationship of users’ knowledge to the modeling system they use to generate shapes. In-depth knowledge of this relationship is not usually revealed in the regular university training courses such as bachelor’s, master’s and continuing education. For this reason, we believe that it is necessary to modify the learning process, offering a more global vision of all the currently existing techniques and extending training in those related to algorithmic modeling techniques. We consider the latter to be the most powerful current techniques for modeling complex shapes that cannot be modeled with the usual techniques known to date. Therefore, the most complete training should include everything from the usual geometry to textual programming. This would take us a step further along the way to more powerful design environments. The proposed taxonomy could serve as a guideline to help improve the learning process of students and designers in a complex environment with increasingly powerful requirements and tools. The term “smart” is widely used nowadays, e.g. smart phones, smart cars, smart homes, smart cities... and similar terms such as “smart shape modeling”. Nowadays, the term smart is applied from a marketing point of view, whenever an innovation is used to solve a complex problem. This is the case for what is currently called smart shape modeling. However, in the future; this concept should mean a much better design environment than today. The smart future requires better trained and skilled engineers, architects, designers or technical students. This means that they must be prepared to be able to contribute to the creation of new knowledge, to the use of innovations to solve complex problems of form, and to the extraction of the relevant pieces of intelligence from the growing volume of knowledge and technologies accessible today. Our taxonomy is presented from the point of view of methods that are possibly furthest away from what is considered today as “intelligent shape modeling” to the limit of what is achievable today and which the authors call “Generic Shape Algorithm”. Finally, we discuss the characteristics that a shape modeling system must have to be truly “intelligent”: it must be “proactive” in applying innovative ideas to achieve a solution to a complex problem

An adaptive fixed-mesh ALE method for free surface flows

In this work we present a Fixed-Mesh ALE method for the numerical simulation of free surface flows capable of using an adaptive finite element mesh covering a background domain. This mesh is successively refined and unrefined at each time step in order to focus the computational effort on the spatial regions where it is required. Some of the main ingredients of the formulation are the use of an Arbitrary-Lagrangian–Eulerian formulation for computing temporal derivatives, the use of stabilization terms for stabilizing convection, stabilizing the lack of compatibility between velocity and pressure interpolation spaces, and stabilizing the ill-conditioning introduced by the cuts on the background finite element mesh, and the coupling of the algorithm with an adaptive mesh refinement procedure suitable for running on distributed memory environments. Algorithmic steps for the projection between meshes are presented together with the algebraic fractional step approach used for improving the condition number of the linear systems to be solved. The method is tested in several numerical examples. The expected convergence rates both in space and time are observed. Smooth solution fields for both velocity and pressure are obtained (as a result of the contribution of the stabilization terms). Finally, a good agreement between the numerical results and the reference experimental data is obtained.Postprint (published version

Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems

Virtual Manipulative Materials in Secondary Mathematics: A Theoretical Discussion

With the increased use of computer manipulatives in teaching there is need for theoretical discussions on the role of manipulatives. This article reviews theoretical rationales for using manipulatives and illustrates how earlier distinctions of manipulative materials must be broadened to include new forms of materials such as virtual manipulatives which are also useful tools in a larger collection of learning tools. applying a theoretical lens to a specific material—polynomial tiles—this article demonstrates the following: (a) a complementary relationships between virtual and concrete manipulatives, (b) two or more theories can appropriately justify the same material, and (c) exploration of a specific manipulative may generate novel theoretical rationales. This exploration has proven to be helpful in the process of designing, selecting, categorizing and evaluating learning tool

Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference