The use of Petri nets for modeling pipelined processors

This paper discusses the use of Petri Nets for modeling and analyzing pipelined processors. Petri Nets are particularly well-suited to modeling the synchronization, buffering, resource contention and delicate timing so common in pipelined processors. Tools for simulating, animating and analyzing the behavior of the models are described. The usefulness of the tools and the analysis methods they support in evaluating the performance and analyzing the detailed timing of pipelined microprocessors is illustrated through an example

Modeling and simulation of data communication networks using SARA

The selection of an appropriate simulation language can have a profound impact on the success of a simulation study. The available options range from domain-specific simulation languages to general-purpose programming languages. These languages are often supported by a collection of tools which form a simulation system. This paper examines UCLA's SARA (Systems ARchitects' Apprentice) system and explores its' usefulness in modeling and simulating a data communications network. Based on experimental use of SARA's tools, the system is evaluated with respect to required expertise, modeling power, as well as measurement and reporting capability

Computer-aided analysis of concurrent systems

The introduction of concurrency into programs has added to the complexity of the software design process. This is most evident in the design of communications protocols where concurrency is inherent to the behavior of the system. The complexity exhibited by such software systems makes more evident the needs for computer-aided tools for automatically analyzing behavior.The Distributed Systems project at UCI has been developing a suite of tools, based on Petri nets, which support the design and evaluation of concurrent software systems. This paper focuses attention on one of the tools: the reachability graph analyzer (RGA). This tool provides mechanisms for proving general system properties (e.g., deadlock-freeness) as well as system-specific properties. The tool is sufficiently general to allow a user to apply complex user-defined analysis algorithms to reachability graphs. The alternating-bit protocol with a bounded channel is used to demonstrate the power of the tool and to point to future extensions

Tools for efficient analysis of concurrent software systems

The ever increasing use of distributed computing as a method of providing added computing power and reliability has sparked interest in methods to model and analyze concurrent hardware/ software systems. Efficient automated analysis tools are needed to aid designers of such systems. The Distributed Systems Project at UCI has been developing a suite of tools (dubbed the P-NUT system) which supports efficient analysis of models of concurrent software. This paper presents the principles which guide the development of P-NUT tools and discusses the development of one of the tools: the Reachability Graph Builder (RGB). The P-NUT approach to tool development has resulted in the production of a highly efficient tool for constructing reachability graphs. The careful design of data structures and associated algorithms has significantly enlarged the class of models which can be analyzed

Performance analysis using timed Petri Nets

Petri Nets have been successfully used to model and evaluate the performance of distributed systems. Several researchers have extended the basic Petri Net model to include time, and have demonstrated that restricted classes of Petri Nets can be analyzed efficiently. Unfortunately, the restrictions prohibit the techniques from being applied to many interesting systems, e.g. communication protocols. This paper proposes a version of timed Petri Nets which accurately models communication protocols, and which can be analyzed using Timed Reachability Graphs. Procedures for constructing and analyzing these graphs are presented. The analysis is shown to be applicable to a larger class of Timed Petri Nets than previously thought. The model and the analysis technique are demonstrated using a simple communication protocol

A guided tour of P-Nut (Release 2.2)

P-NUT is a suite of tools for constructing and analyzing Petri Net models. The tools have been developed at UCI to aid researchers in applying Petri Nets to the design of concurrent hardware/software. The tools support state-space analysis, simulation, performance evaluation and verification. While the tools are useful in their current state, the P-NUT system is just beginning to achieve its overall objective of aiding in the design of complex distributed real-time systems. This report provides a guided tour of the tools for researchers who are interested in exploring P-NUT's capabilities

Stability Criteria for SIS Epidemiological Models under Switching Policies

We study the spread of disease in an SIS model. The model considered is a time-varying, switched model, in which the parameters of the SIS model are subject to abrupt change. We show that the joint spectral radius can be used as a threshold parameter for this model in the spirit of the basic reproduction number for time-invariant models. We also present conditions for persistence and the existence of periodic orbits for the switched model and results for a stochastic switched model

Allosteric Inhibition of Factor XIIIa. Non-Saccharide Glycosaminoglycan Mimetics, but Not Glycosaminoglycans, Exhibit Promising Inhibition Profile

Factor XIIIa (FXIIIa) is a transglutaminase that catalyzes the last step in the coagulation process. Orthostery is the only approach that has been exploited to design FXIIIa inhibitors. Yet, allosteric inhibition of FXIIIa is a paradigm that may offer a key advantage of controlled inhibition over orthosteric inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We reasoned that targeting a collection of basic amino acid residues distant from FXIIIa’s active site by using sulfated glycosaminoglycans (GAGs) or non-saccharide GAG mimetics (NSGMs) would lead to the discovery of the first allosteric FXIIIa inhibitors. We tested a library of 22 variably sulfated GAGs and NSGMs against human FXIIIa to discover promising hits. Interestingly, although some GAGs bound to FXIIIa better than NSGMs, no GAG displayed any inhibition. An undecasulfated quercetin analog was found to inhibit FXIIIa with reasonable potency (efficacy of 98%). Michaelis-Menten kinetic studies revealed an allosteric mechanism of inhibition. Fluorescence studies confirmed close correspondence between binding affinity and inhibition potency, as expected for an allosteric process. The inhibitor was reversible and at least 9-fold- and 26-fold selective over two GAG-binding proteins factor Xa (efficacy of 71%) and thrombin, respectively, and at least 27-fold selective over a cysteine protease papain. The inhibitor also inhibited the FXIIIa-mediated polymerization of fibrin in vitro. Overall, our work presents the proof-of-principle that FXIIIa can be allosterically modulated by sulfated non-saccharide agents much smaller than GAGs, which should enable the design of selective and safe anticoagulants

Stochastic Acceleration in Relativistic Parallel Shocks

(abridged) We present results of test-particle simulations on both the first and the second order Fermi acceleration at relativistic parallel shock waves. We consider two scenarios for particle injection: (i) particles injected at the shock front, then accelerated at the shock by the first order mechanism and subsequently by the stochastic process in the downstream region; and (ii) particles injected uniformly throughout the downstream region to the stochastic process. We show that regardless of the injection scenario, depending on the magnetic field strength, plasma composition, and the employed turbulence model, the stochastic mechanism can have considerable effects on the particle spectrum on temporal and spatial scales too short to be resolved in extragalactic jets. Stochastic acceleration is shown to be able to produce spectra that are significantly flatter than the limiting case of particle energy spectral index -1 of the first order mechanism. Our study also reveals a possibility of re-acceleration of the stochastically accelerated spectrum at the shock, as particles at high energies become more and more mobile as their mean free path increases with energy. Our findings suggest that the role of the second order mechanism in the turbulent downstream of a relativistic shock with respect to the first order mechanism at the shock front has been underestimated in the past, and that the second order mechanism may have significant effects on the form of the particle spectra and its evolution.Comment: 14 pages, 11 figures (9 black/white and 2 color postscripts). To be published in the ApJ (accepted 6 Nov 2004