COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Overview on agent-based social modelling and the use of formal languages

Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft

Integration of the Cimosa and high-level coloured Petri net modelling techniques with application in the postal process using hierarchical dispatching rules

Enterprise processes, i.e. business and manufacturing, rely on enterprise modelling and simulation tools to assess the quality of their structure and performance in an unobtrusive and cost-effective way. Each of these processes is a collaboration of inseparable elements such as resources, information, operations, and organization. In order to provide a more complete assessment of enterprise processes, a simulation approach that allows communication and interaction among these elements needs to be provided. The simulation approach requires an analysis of the performance of each element and its influence on other elements in an object-oriented way. It also needs to have the capability to represent the structures and dynamics of the elements mentioned, and to present the performance assessment comprehensively. This will ensure a more holistic simulation modelling task. These simulation requirements have motivated the investigation of the novel integration of two popular enterprise process modelling methods: Cimosa and high-level coloured Petri net. The Cimosa framework is used to formalize the enterprise modelling procedure in the aspects of representing process elements, structure, behaviours, and relationships. The high-level coloured Petri nets method provides the mechanism to simulate the dynamics of objects and their characteristics, and also to enable communication among the objects. The approach is applied on a postal process model, which involves elements from manufacturing processes, i.e. machine processing (sorting), inventory (storage), product flow, and resource planning. Simulation studies based on the hierarchical dispatching rules show that the integrated approach is able to present vital information regarding the communication method, resource management, and the effect of interactions among these manufacturing process elements, which are not provided by the current modelling system in the postal company. The current paper has presented a novel mechanism, i.e. Cimosa—HCTSPN modelling approach, to extract information on process elements and their interactions. It has also presented the novel hierarchical dispatching rules and contributed to the extension of information that can be represented for a postal process

Estimating a War of Attrition: The Case of the U.S. Movie Theater Industry

This paper provides a tractable empirical framework to analyze firm behavior in a dynamic oligopoly when demand is declining over time. I modify Fudenberg and Tirole (1986).s model of exit in a duopoly with incomplete information to a model that can be used in an oligopoly, and combine this with an auxiliary entry model to address the initial conditions problem. I estimate this model with panel data on the U.S. movie theater industry from 1949 to 1955, using variations in TV diffusion rates across households, market structure before the exit game starts, and other market characteristics to identify the parameters in the theater’s payoff function and the distribution of unobservable fixed costs. Using the estimated model, I measure strategic delays in the exit process due to oligopolistic competition and incomplete information. The delay in exit that arises from strategic interaction is 2.7 years on average. Out of these years, 3.7% of this delay is accounted for by incomplete information, while the remaining 96.3% is explained by oligopolistic competition

Application of a strong FSI coupling scheme for the numerical simulation of bileaflet mechanical heart valve dynamics: study of wall shear stress on the valve leaflets

One of the major challenges in the design of Bileaflet Mechanical Heart Valves (BMHVs) is reduction of the blood damage generated by non-physiological blood flow. Numerical simulations provide relevant insights into the (fluid) dynamics of the BMHV and are used for design optimisation. In this paper, a strong coupling algorithm for the partitioned Fluid-Structure Interaction (FSI) simulation of a BMHV is presented. The convergence of the coupling iterations between the flow solver and the leaflet motion solver is accelerated by using a numerically calculated Jacobian with the derivatives of the pressure and viscous moments acting on the leaflets with respect to the leaflet accelerations. The developed algorithm is used to simulate the dynamics of a 3D BMHV in three different geometries, allowing an analysis of the solution process. Moreover, the leaflet kinematics and the general flow field are discussed, with special focus on the shear stresses on the valve leaflets

Managing stimulation of regional innovation subjects’ interaction in the digital economy

The reported study was funded by RFBR according to the research project No. 18-01000204_a, No. 16-07-00031_a, No. 18-07-00975_a.Purpose: The article is devoted to solving fundamental scientific problems in the scope of the development of forecasting modeling methods and evaluation of regional company’s innovative development parameters, synthesizing new methods of big data processing and intelligent analysis, as well as methods of knowledge eliciting and forecasting the dynamics of regional innovation developments through benchmarking. Design/Methodology/Approach: For regional economic development, it is required to identify the mechanisms that contribute to (or impede) the innovative economic development of the regions. The synergetic approach to management is based on the fact that there are multiple paths of IS development (scenarios with different probabilities), although it is necessary to reach the required attractor by meeting the management goals. Findings: The present research is focused on obtainment of new knowledge in creating a technique of multi-agent search, collection and processing of data on company’s innovative development indicators, models and methods of intelligent analysis of the collected data. Practical Implications: The author developed recommendations before starting the process of institutional changes in a specific regional innovation system. The article formulates recommendations on the implementation of institutional changes in the region taking into account the sociocultural characteristics of the region’s population. Originality/Value: It is the first time, when a complex of models and methods is based on the use of a convergent model of large data volumes processing is presented.peer-reviewe

MATHEMATICAL SIMULATION FOR ASSESSMENT OF THE SMALL BUSINESS EFFICIENCY: REGIONAL ASPECTS

Mathematical simulation of economic systems and processes are considered. The description of macroeconomic models for assets formation, consumer behaviour, production activity of an enterprise, and market balance is given. The line balance model of diversified economic system is examined