A nested Petri net framework for modeling and analyzing multi-agent systems

In the past two decades, multi-agent systems (MAS) have emerged as a new paradigm for conceptualizing large and complex distributed software systems. A multi-agent system view provides a natural abstraction for both the structure and the behavior of modern-day software systems. Although there were many conceptual frameworks for using multi-agent systems, there was no well established and widely accepted method for modeling multi-agent systems. This dissertation research addressed the representation and analysis of multi-agent systems based on model-oriented formal methods. The objective was to provide a systematic approach for studying MAS at an early stage of system development to ensure the quality of design. ^ Given that there was no well-defined formal model directly supporting agent-oriented modeling, this study was centered on three main topics: (1) adapting a well-known formal model, predicate transition nets (PrT nets), to support MAS modeling; (2) formulating a modeling methodology to ease the construction of formal MAS models; and (3) developing a technique to support machine analysis of formal MAS models using model checking technology. PrT nets were extended to include the notions of dynamic structure, agent communication and coordination to support agent-oriented modeling. An aspect-oriented technique was developed to address the modularity of agent models and compositionality of incremental analysis. A set of translation rules were defined to systematically translate formal MAS models to concrete models that can be verified through the model checker SPIN (Simple Promela Interpreter). ^ This dissertation presents the framework developed for modeling and analyzing MAS, including a well-defined process model based on nested PrT nets, and a comprehensive methodology to guide the construction and analysis of formal MAS models.^

Integrated Ecological Modeling and Decision Analysis Within the Everglades Landscape

Planning for complex ecosystem restoration projects involves integrating ecological modeling with analysis of performance trade-offs among restoration alternatives. The authors used the Everglades Landscape Model and Multi-Criteria Decision Analysis to explore the effect of simulated ecosystem performance, risk preferences, and criteria weights on the ranking of three alternatives to restoring overland sheet flow in the Everglades. The ecological model outputs included both hydrologic and water quality criteria. Results were scored in the decision analysis framework, highlighting the trade-offs between hydrologic restoration and water quality constraints. Given equal weighting of performance measures, the alternative with more homogenous sheet flow was preferred over other alternatives, despite evidence of some localized eutrophication risk.

Control of MNC environmental performance and the challenges of subsidiary network dimensions

The trend of green consumerism and increased standardization of environmental regulations has driven multinational corporations (MNCs) to seek standardization of environmental practices or at least seek to be associated with such behavior. In fact, many firms are seeking to free ride on this global green movement, without having the actual ecological footprint to substantiate their environmental claims. While scholars have articulated the benefits from such optimization of uniform global green operations, the challenges for MNCs to control and implement such operations are understudied. For firms to translate environmental commitment to actual performance, the obstacles are substantial, particularly for the MNC. This is attributed to headquarters' (HQ) control challenges (1) in managing core elements of the corporate environmental management (CEM) process and specifically matching verbal commitment and policy with ecological performance and by (2) the fact that the MNC operates in multiple markets and the HQ is required to implement policy across complex subsidiary networks consisting of diverse and distant units. Drawing from the literature on HQ challenges of MNC management and control, this study examines (1) how core components of the CEM process impact optimization of global environmental performance (GEP) and then uses network theory to examine how (2) a subsidiary network's dimensions can present challenges to the implementation of green management policies. It presents a framework for CEM which includes (1) MNCs' Verbal environmental commitment, (2) green policy Management which guides standards for operations, (3) actual environmental Performance reflected in a firm's ecological footprint and (4) corporate environmental Reputation (VMPR). Then it explains how an MNC's key subsidiary network dimensions (density, diversity, and dispersion) create challenges that hinder the relationship between green policy management and actual environmental performance. It combines content analysis, multiple regression, and post-hoc hierarchal cluster analysis to study US manufacturing MNCs. The findings support a positive significant effect of verbal environmental commitment and green policy management on actual global environmental performance and environmental reputation, as well as a direct impact of verbal environmental commitment on green policy management. Unexpectedly, network dimensions were not found to moderate the relationship between green management policy and GEP.

Changing Guest Preferences and Marketing Challenges In the Resort Industry

Resorts in the future will be feeling the effect of a number of changes in the industry. Changing demographics, economic conditions and the changing priorities of resort guests will play major roles in the future success of resort properties. The authors stress that future resort marketing should emphasize the expansion of current market segments, the creation of new market segments, and hte expansion of qualirty services.

Tool cutting force modeling and wear estimation of micro -end-milling operations

The applications of micro-end-milling operations have increased recently. A Micro-End-Milling Operation Guide and Research Tool (MOGART) package has been developed for the study and monitoring of micro-end-milling operations. It includes an analytical cutting force model, neural network based data mapping and forecasting processes, and genetic algorithms based optimization routines. MOGART uses neural networks to estimate tool machinability and forecast tool wear from the experimental cutting force data, and genetic algorithms with the analytical model to monitor tool wear, breakage, run-out, cutting conditions from the cutting force profiles. ^ The performance of MOGART has been tested on the experimental data of over 800 experimental cases and very good agreement has been observed between the theoretical and experimental results. The MOGART package has been applied to the micro-end-milling operation study of Engineering Prototype Center of Radio Technology Division of Motorola Inc. ^

Methods for modeling and analyzing concurrent software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.

Positive Effects of Peer Modeling and Positive Reinforcement on Healthy Food Intake in Elementary School Children

The current study aims to discover the effects of “Food Dudes” peer modeling videos and positive reinforcement on vegetable consumption using a delayed multiple baseline design across subjects. Results suggest peer modeling and positive reinforcement as effective means to increase vegetable intake.

Tool cutting force modeling and wear estimation of micro-end-milling operations

The applications of micro-end-milling operations have increased recently. A Micro-End-Milling Operation Guide and Research Tool (MOGART) package has been developed for the study and monitoring of micro-end-milling operations. It includes an analytical cutting force model, neural network based data mapping and forecasting processes, and genetic algorithms based optimization routines. MOGART uses neural networks to estimate tool machinability and forecast tool wear from the experimental cutting force data, and genetic algorithms with the analytical model to monitor tool wear, breakage, run-out, cutting conditions from the cutting force profiles. The performance of MOGART has been tested on the experimental data of over 800 experimental cases and very good agreement has been observed between the theoretical and experimental results. The MOGART package has been applied to the micro-end-milling operation study of Engineering Prototype Center of Radio Technology Division of Motorola Inc.

The Construction and Optimization on an Ion Mobility Spectrometer for the Analysis of Explosives and Drugs

Today, over 15,000 Ion Mobility Spectrometry (IMS) analyzers are employed at worldwide security checkpoints to detect explosives and illicit drugs. Current portal IMS instruments and other electronic nose technologies detect explosives and drugs by analyzing samples containing the headspace air and loose particles residing on a surface. Canines can outperform these systems at sampling and detecting the low vapor pressure explosives and drugs, such as RDX, PETN, cocaine, and MDMA, because these biological detectors target the volatile signature compounds available in the headspace rather than the non-volatile parent compounds of explosives and drugs. In this dissertation research volatile signature compounds available in the headspace over explosive and drug samples were detected using SPME as a headspace sampling tool coupled to an IMS analyzer. A Genetic Algorithm (GA) technique was developed to optimize the operating conditions of a commercial IMS (GE Itemizer 2), leading to the successful detection of plastic explosives (Detasheet, Semtex H, and C-4) and illicit drugs (cocaine, MDMA, and marijuana). Short sampling times (between 10 sec to 5 min) were adequate to extract and preconcentrate sufficient analytes (> 20 ng) representing the volatile signatures in the headspace of a 15 mL glass vial or a quart-sized can containing ≤ 1 g of the bulk explosive or drug. Furthermore, a research grade IMS with flexibility for changing operating conditions and physical configurations was designed and fabricated to accommodate future research into different analytes or physical configurations. The design and construction of the FIU-IMS were facilitated by computer modeling and simulation of ion’s behavior within an IMS. The simulation method developed uses SIMION/SDS and was evaluated with experimental data collected using a commercial IMS (PCP Phemto Chem 110). The FIU-IMS instrument has comparable performance to the GE Itemizer 2 (average resolving power of 14, resolution of 3 between two drugs and two explosives, and LODs range from 0.7 to 9 ng). The results from this dissertation further advance the concept of targeting volatile components to presumptively detect the presence of concealed bulk explosives and drugs by SPME-IMS, and the new FIU-IMS provides a flexible platform for future IMS research projects.

Docking and simulation study of the enantiospecificity of chiral epoxidation reactions catalyzed by chloroperoxidase

Chloroperoxidase (CPO), a 298-residue glycosylated protein from the fungus Caldariomyces fumago, is probably the most versatile heme enzyme yet discovered. Interest in CPO as a catalyst is based on its power to produce enantiomerically enriched products. Recent research has focused its attention on the ability of CPO to epoxidize alkenes in high regioselectivity and enantioselectivity as an efficient and environmentally benign alternative to traditional synthetic routes. There has been little work on the nature of ligand binding, which probably controls the regio- and enantiospecifity of CPO. Consequently it is here that we focus our work. We report docking calculations and computer simulations aimed at predicting the enantiospecificity of CPO-catalyzed epoxidation of three model substrates. On the basis of this work candidate mutations to improve the efficiency of CPO are predicted. In order to accomplish these aims, a simulated annealing and molecular dynamics protocol is developed to sample potentially reactive substrate/CPO complexes.

Theoretical modeling and experimental validation of fluid-loaded micro rectangular plates

This paper presents a theoretical model on the vibration analysis of micro scale fluid-loaded rectangular isotropic plates, based on the Lamb's assumption of fluid-structure interaction and the Rayleigh-Ritz energy method. An analytical solution for this model is proposed, which can be applied to most cases of boundary conditions. The dynamical experimental data of a series of microfabricated silicon plates are obtained using a base-excitation dynamic testing facility. The natural frequencies and mode shapes in the experimental results are in good agreement with the theoretical simulations for the lower order modes. The presented theoretical and experimental investigations on the vibration characteristics of the micro scale plates are of particular interest in the design of microplate based biosensing devices. Copyright © 2009 by ASME.

Advances in Dynamic Modeling and Computation for Count Data

A class of multi-process models is developed for collections of time indexed count data. Autocorrelation in counts is achieved with dynamic models for the natural parameter of the binomial distribution. In addition to modeling binomial time series, the framework includes dynamic models for multinomial and Poisson time series. Markov chain Monte Carlo (MCMC) and Po ́lya-Gamma data augmentation (Polson et al., 2013) are critical for fitting multi-process models of counts. To facilitate computation when the counts are high, a Gaussian approximation to the P ́olya- Gamma random variable is developed.

Three applied analyses are presented to explore the utility and versatility of the framework. The first analysis develops a model for complex dynamic behavior of themes in collections of text documents. Documents are modeled as a “bag of words”, and the multinomial distribution is used to characterize uncertainty in the vocabulary terms appearing in each document. State-space models for the natural parameters of the multinomial distribution induce autocorrelation in themes and their proportional representation in the corpus over time.

The second analysis develops a dynamic mixed membership model for Poisson counts. The model is applied to a collection of time series which record neuron level firing patterns in rhesus monkeys. The monkey is exposed to two sounds simultaneously, and Gaussian processes are used to smoothly model the time-varying rate at which the neuron’s firing pattern fluctuates between features associated with each sound in isolation.

The third analysis presents a switching dynamic generalized linear model for the time-varying home run totals of professional baseball players. The model endows each player with an age specific latent natural ability class and a performance enhancing drug (PED) use indicator. As players age, they randomly transition through a sequence of ability classes in a manner consistent with traditional aging patterns. When the performance of the player significantly deviates from the expected aging pattern, he is identified as a player whose performance is consistent with PED use.

All three models provide a mechanism for sharing information across related series locally in time. The models are fit with variations on the P ́olya-Gamma Gibbs sampler, MCMC convergence diagnostics are developed, and reproducible inference is emphasized throughout the dissertation.

A Molecular-scale Programmable Stochastic Process Based On Resonance Energy Transfer Networks: Modeling And Applications

While molecular and cellular processes are often modeled as stochastic processes, such as Brownian motion, chemical reaction networks and gene regulatory networks, there are few attempts to program a molecular-scale process to physically implement stochastic processes. DNA has been used as a substrate for programming molecular interactions, but its applications are restricted to deterministic functions and unfavorable properties such as slow processing, thermal annealing, aqueous solvents and difficult readout limit them to proof-of-concept purposes. To date, whether there exists a molecular process that can be programmed to implement stochastic processes for practical applications remains unknown.

In this dissertation, a fully specified Resonance Energy Transfer (RET) network between chromophores is accurately fabricated via DNA self-assembly, and the exciton dynamics in the RET network physically implement a stochastic process, specifically a continuous-time Markov chain (CTMC), which has a direct mapping to the physical geometry of the chromophore network. Excited by a light source, a RET network generates random samples in the temporal domain in the form of fluorescence photons which can be detected by a photon detector. The intrinsic sampling distribution of a RET network is derived as a phase-type distribution configured by its CTMC model. The conclusion is that the exciton dynamics in a RET network implement a general and important class of stochastic processes that can be directly and accurately programmed and used for practical applications of photonics and optoelectronics. Different approaches to using RET networks exist with vast potential applications. As an entropy source that can directly generate samples from virtually arbitrary distributions, RET networks can benefit applications that rely on generating random samples such as 1) fluorescent taggants and 2) stochastic computing.

By using RET networks between chromophores to implement fluorescent taggants with temporally coded signatures, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the taggant detection process becomes highly efficient, and the Maximum Likelihood Estimation (MLE) based taggant identification guarantees high accuracy even with only a few hundred detected photons.

Meanwhile, RET-based sampling units (RSU) can be constructed to accelerate probabilistic algorithms for wide applications in machine learning and data analytics. Because probabilistic algorithms often rely on iteratively sampling from parameterized distributions, they can be inefficient in practice on the deterministic hardware traditional computers use, especially for high-dimensional and complex problems. As an efficient universal sampling unit, the proposed RSU can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator to bring substantial speedups and power savings.

Policy mixes for resource efficiency – conceptual issues, design and assessment challenges

Since the 1950s the global consumption of natural resources has skyrocketed, both in magnitude and in the range of resources used. Closely coupled with emissions of greenhouse gases, land consumption, pollution of environmental media, and degradation of ecosystems, as well as with economic development, increasing resource use is a key issue to be addressed in order to keep the planet Earth in a safe and just operating space. This requires thinking about absolute reductions in resource use and associated environmental impacts, and, when put in the context of current re-focusing on economic growth at the European level, absolute decoupling, i.e., maintaining economic development while absolutely reducing resource use and associated environmental impacts. Changing behavioural, institutional and organisational structures that lock-in unsustainable resource use is, thus, a formidable challenge as existing world views, social practices, infrastructures, as well as power structures, make initiating change difficult. Hence, policy mixes are needed that will target different drivers in a systematic way. When designing policy mixes for decoupling, the effect of individual instruments on other drivers and on other instruments in a mix should be considered and potential negative effects be mitigated. This requires smart and time-dynamic policy packaging. This Special Issue investigates the following research questions: What is decoupling and how does it relate to resource efficiency and environmental policy? How can we develop and realize policy mixes for decoupling economic development from resource use and associated environmental impacts? And how can we do this in a systemic way, so that all relevant dimensions and linkages—including across economic and social issues, such as production, consumption, transport, growth and wellbeing­—are taken into account? In addressing these questions, the overarching goals of this Special Issue are to: address the challenges related to more sustainable resource-use; contribute to the development of successful policy tools and practices for sustainable development and resource efficiency (particularly through the exploration of socio-economic, scientific, and integrated aspects of sustainable development); and inform policy debates and policy-making. The Special Issue draws on findings from the EU and other countries to offer lessons of international relevance for policy mixes for more sustainable resource-use, with findings of interest to policy makers in central and local government and NGOs, decision makers in business, academics, researchers, and scientists.