ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors

Empirical exploration of air traffic and human dynamics in terminal airspaces

Air traffic is widely known as a complex, task-critical techno-social system, with numerous interactions between airspace, procedures, aircraft and air traffic controllers. In order to develop and deploy high-level operational concepts and automation systems scientifically and effectively, it is essential to conduct an in-depth investigation on the intrinsic traffic-human dynamics and characteristics, which is not widely seen in the literature. To fill this gap, we propose a multi-layer network to model and analyze air traffic systems. A Route-based Airspace Network (RAN) and Flight Trajectory Network (FTN) encapsulate critical physical and operational characteristics; an Integrated Flow-Driven Network (IFDN) and Interrelated Conflict-Communication Network (ICCN) are formulated to represent air traffic flow transmissions and intervention from air traffic controllers, respectively. Furthermore, a set of analytical metrics including network variables, complex network attributes, controllers' cognitive complexity, and chaotic metrics are introduced and applied in a case study of Guangzhou terminal airspace. Empirical results show the existence of fundamental diagram and macroscopic fundamental diagram at the route, sector and terminal levels. Moreover, the dynamics and underlying mechanisms of "ATCOs-flow" interactions are revealed and interpreted by adaptive meta-cognition strategies based on network analysis of the ICCN. Finally, at the system level, chaos is identified in conflict system and human behavioral system when traffic switch to the semi-stable or congested phase. This study offers analytical tools for understanding the complex human-flow interactions at potentially a broad range of air traffic systems, and underpins future developments and automation of intelligent air traffic management systems.Comment: 30 pages, 28 figures, currently under revie

A modular hybrid simulation framework for complex manufacturing system design

For complex manufacturing systems, the current hybrid Agent-Based Modelling and Discrete Event Simulation (ABM–DES) frameworks are limited to component and system levels of representation and present a degree of static complexity to study optimal resource planning. To address these limitations, a modular hybrid simulation framework for complex manufacturing system design is presented. A manufacturing system with highly regulated and manual handling processes, composed of multiple repeating modules, is considered. In this framework, the concept of modular hybrid ABM–DES technique is introduced to demonstrate a novel simulation method using a dynamic system of parallel multi-agent discrete events. In this context, to create a modular model, the stochastic finite dynamical system is extended to allow the description of discrete event states inside the agent for manufacturing repeating modules (meso level). Moreover, dynamic complexity regarding uncertain processing time and resources is considered. This framework guides the user step-by-step through the system design and modular hybrid model. A real case study in the cell and gene therapy industry is conducted to test the validity of the framework. The simulation results are compared against the data from the studied case; excellent agreement with 1.038% error margin is found in terms of the company performance. The optimal resource planning and the uncertainty of the processing time for manufacturing phases (exo level), in the presence of dynamic complexity is calculated

Intelligent agent simulator in massive crowd

Crowd simulations have many benefits over real-life research such as in computer games, architecture and entertainment. One of the key elements in this study is to include elements of decision-making into the crowd. The aim of this simulator is to simulate the features of an intelligent agent to escape from crowded environments especially in one-way corridor, two-way corridor and four-way intersection. The addition of the graphical user interface enables intuitive and fast handling in all settings and features of the Intelligent Agent Simulator and allows convenient research in the field of intelligent behaviour in massive crowd. This paper describes the development of a simulator by using the Open Graphics Library (OpenGL), starting from the production of training data, the simulation process, until the simulation results. The Social Force Model (SFM) is used to generate the motion of agents and the Support Vector Machine (SVM) is used to predict the next step for intelligent agent