Qualitative simulation predicts the set of possible behaviors...

Abstract not found

The ability to answer prediction questions is crucial to reasoning about physical systems. A prediction question poses a hypothetical scenario and asks for the resulting behavior of variables of interest. Prediction questions can be answered by simulating a model of the scenario. An appropriate system boundary, which separates aspects of the scenario that must be modeled from those that can be ignored, is critical to achieving a simple yet adequate model. This paper presents an efficient algorithm for system boundary selection, it shows the important role played by the model's time scale, and it provides a separate algorithm for selecting this time scale. Both algorithms have been implemented in a compositional modeling program called tripel and evaluated in the plant physiology domain.

Abstract. The endocytic itineraries of lipid raft markers, such as glycosyl phosphatidylinositol (GPI)anchored proteins and glycosphingolipids, are incompletely understood. Here we show that different GPI-anchored proteins have different intracellular distributions; some (such as the folate receptor) accumulate in transferrin-containing compartments, others (such as CD59 and GPI-linked green fluorescent protein [GFP]) accumulate in the Golgi apparatus. Selective photobleaching shows that the Golgi pool of both GPI-GFP and CD59-GFP constantly and rapidly exchanges with the pool of these proteins found on the plasma membrane (PM). We visualized intermediates carrying GPI-GFP from the Golgi apparatus to the PM and separate structures delivering GPI-GFP to the Golgi apparatus. GPI-GFP does not accumulate within endocytic compartments containing transferrin, although it is detected in intracellular structures which are endosomes by the criteria of accessibility to a fluid phase marker and to cholera and shiga toxin B subunits (CTxB and STxB, which are also found in rafts). GPI-GFP and a proportion of the total CTxB and STxB taken up into cells are endocytosed independently of clathrin-associated machinery and are delivered to the Golgi complex via indistinguishable mechanisms. Hence, they enter the Golgi complex in the same intermediates, get there independently of both clathrin and rab5 function, and are excluded from it at 20�C and under conditions of cholesterol sequestration. The PM–Golgi cycling pathway followed by GPI-GFP could serve to regulate lipid raft distribution and function within cells.

When we build simulation models and construct dynamical models for physical systems, we often do not do so using a clear overall framework that organizes our geometry, dynamics and models. How do geometry and dynamics intertwine to effect system change over multiple abstraction levels? We present a methodology, called object-oriented physical modeling (OOPM), which builds on the currently accepted computer science approach in object-oriented program design. This type of modeling injects a way of incorporating geometry and dynamics into general object-oriented design. Moreover, we present an approach to dynamical modeling that mirrors major categories of computer programming languages, thereby achieving a definition of system modeling that reinforces the relation of model to program.

Qualitative simulation is a useful method for predicting the possible qualitatively distinct behaviors of an incompletely known mechanism described by a system of qualitative differential equations (QDEs). Under some circumstances, sparse information about the derivatives of variables can lead to intractable branching (or "chatter") representing uninteresting or even spurious distinctions among qualitative behaviors. The problem of chatter stands in the way of real applications such as qualitative simulation of models in the design or diagnosis of engineered systems. One solution to this problem is to exploit information about higherorder derivatives of the variables. We demonstrate automatic methods for identification of chattering variables, algebraic derivation of expressions for second-order derivatives, and evaluation and application of the sign of second- and third-order derivatives of variables, resulting in tractable simulation of important qualitative models. Caution is requir...

Recent trends in software engineering, especially within the object-oriented community, reflect a clear trend toward systems engineering methods. Object oriented designs, meant for programming design, often take on the distinct appearance of system models of physical networks and devices. It is not immediately apparent how the areas of "modeling" and "programming" relate to one another, and why the convergence is taking place. To explore the convergence in depth, we discuss common concepts between models and programs, and discuss future trends in computer science which are forging a steady convergence between models and programs. The convergence is spawned by increased emphasis on object oriented design, distributed systems, complex systems, new forms of analog computation, and abstraction methodology. We close with a discussion of MOOSE, which provides a comprehensive modeling environment for both programmers and modelers.

We present a new modeling taxonomy for computer simulation. The importance of this work centers on a cohesive approach to modeling that attempts to unify heretofore disparate modeling techniques. For example, while there exists a taxonomy for discrete event simulation, this taxonomy does not incorporate models whose execution is via continuous time increment. The modeling taxonomy has a similar structure to computer language categories: declarative, functional and constraint. The multimodeling model type permits the creation of a multi-level heterogeneous model that can integrate different model types, rather than displacing them in favor of a singular modeling method. Instead of advocating the removal of existing modeling techniques, our focus has been on organizing modeling techniques from different disciplines to yield unification. A TAXONOMY FOR SIMULATION MODELING BASED ON PROGRAMMING LANGUAGE PRINCIPLES PAUL A. FISHWICK Dept. of Computer & Information Science and Engineering U...

We present a design approach for structuring multimodels in an object-oriented framework for physical modeling. This approach is termed object-oriented physical modeling (OOPM). Multimodels have played a key role in permitting a model designer to construct large-scale dynamical models. We have built upon earlier work in multimodeling by specifying how multimodels are defined for object-oriented model designs. The object-oriented approach permits class reusability and a more efficient method for designing multimodels. By using basic physical categories, such as point-mass and many-particle system as metaphors, we explain the use of this new approach to modeling. 1 Introduction Models exist to allow humans to communicate about the dynamics and geometry of real world objects. Our definition of modeling is described at a level where models are translated into executable programs and formal specifications. Object-oriented methodology in simulation has a long history, as with the introducti...

Positive linear systems are frequently used as mathematical models in research areas like biology and economics. The problem to classify all minimal realizations of these systems is treated in this paper. Extensive use is made of the theory of polyhedral cones. Sufficient and necessary conditions for the existence of a positive realization are given, but the problem of minimality leads to the factorization problem of positive matrices. Ideas and results are given to come towards a solution of this factorization problem. AMS Subject Classification (1991): 93B15, 15A48. Keywords and Phrases: Positive Realization, Positive Matrices, Polyhedral Cones. Note: This paper has been accepted for publication in Linear Algebra and its Applications. 1.