Search results for: molecular modeling

Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

Abstract:

Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: Biological molecular networks, essential genes, graph theory, network subgraphs.

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Authors: K. M. Tan, A. Anvar, T.F. Lu

Abstract:

A sophisticated simulator provides a cost-effective measure to carry out preliminary mission testing and diagnostic while reducing potential failures for real life at sea trials. The presented simulation framework covers three key areas: AUV modeling, sensor modeling, and environment modeling. AUV modeling mainly covers the area of AUV dynamics. Sensor modeling deals with physics and mathematical models that govern each sensor installed onto the AUV. Environment model incorporates the hydrostatic, hydrodynamics, and ocean currents that will affect the AUV in a real-time mission. Based on this designed simulation framework, custom scenarios provided by the user can be modeled and its corresponding behaviors can be observed. This paper focuses on the accuracy of the simulated data from AUV model and environmental model derived from a developed AUV test-bed which was jointly upgraded by DSTO and the University of Adelaide. The main contribution of this paper is to experimentally verify the accuracy of the proposed simulation framework.

Keywords: Autonomous Underwater Vehicle (AUV), simulator, framework, robotics, maritime robot, modeling.

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Authors: Aouattou Nabila, Saighi Mohamed, Fekih Malika

Abstract:

The modeling of water transfer in the unsaturated zone uses techniques and methods of the soil physics to solve the Richards-s equation. However, there is a disaccord between the size of the measurements provided by the soil physics and the size of the fields of hydrological modeling problem, to which is added the strong spatial variability of soil hydraulic properties. The objective of this work was to develop a methodology to estimate the hydrodynamic parameters for modeling water transfers at different hydrological scales in the soil-plant atmosphere systems.

Keywords: Hydraulic properties, Modeling, Unsaturated zone, Transfer, Water

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Authors: Jacek Kuraś, Jacek Lembas, Marek Skomorowski

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In this paper, we introduce GODYS-PC software package for modeling, simulating and analyzing dynamic systems. To illustrate the use of GODYS-PC we present a few examples which concern modeling and simulating of engineering systems. In order to compare GODYS-PC with widely used in academia and industry Simulink®, the same examples are provided both in GODYS-PC and Simulink®.

Keywords: Modeling, simulating and analyzing dynamicsystems.

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Authors: Himanshu Payal, Sachin Maheshwari, Pushpendra S. Bharti

Abstract:

Electrical discharge machining (EDM), a non-conventional machining process, finds wide applications for shaping difficult-to-cut alloys. Process modeling of EDM is required to exploit the process to the fullest. Process modeling of EDM is a challenging task owing to involvement of so many electrical and non-electrical parameters. This work is an attempt to model the EDM process using artificial neural network (ANN). Experiments were carried out on die-sinking EDM taking Inconel 825 as work material. ANN modeling has been performed using experimental data. The prediction ability of trained network has been verified experimentally. Results indicate that ANN can predict the values of performance measures of EDM satisfactorily.

Keywords: Artificial neural network, EDM, metal removal rate, modeling, surface roughness.

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Authors: I-Ling Chang, Jer-An Chen

Abstract:

The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: Energy minimization, fracture, graphene, molecular mechanics.

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Authors: Ahmad Habibizad Navin, Mehdi Naghian Fesharaki, Mirkamal Mirnia, Mohamad Teshnelab, Ehsan Shahamatnia

Abstract:

In this paper we introduce new data oriented modeling of uniform random variable well-matched with computing systems. Due to this conformity with current computers structure, this modeling will be efficiently used in statistical inference.

Keywords: Uniform random variable, Data oriented modeling, Statistical inference, Prodigraph, Statistically complete tree, Uniformdigital probability digraph, Uniform n-complete probability tree.

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Authors: Radek Němec

Abstract:

Today's business environment requires that companies have access to highly relevant information in a matter of seconds. Modern Business Intelligence tools rely on data structured mostly in traditional dimensional database schemas, typically represented by star schemas. Dimensional modeling is already recognized as a leading industry standard in the field of data warehousing although several drawbacks and pitfalls were reported. This paper focuses on the analysis of another data warehouse modeling technique - the anchor modeling, and its characteristics in context with the standardized dimensional modeling technique from a query performance perspective. The results of the analysis show information about performance of queries executed on database schemas structured according to principles of each database modeling technique.

Keywords: Data warehousing, anchor modeling, star schema, anchor schema, query performance.

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Authors: Kwa-Sur Tam

Abstract:

This paper reviews various approaches that have been used for the modeling and simulation of large-scale engineering systems and determines their appropriateness in the development of a RICS modeling and simulation tool. Bond graphs, linear graphs, block diagrams, differential and difference equations, modeling languages, cellular automata and agents are reviewed. This tool should be based on linear graph representation and supports symbolic programming, functional programming, the development of noncausal models and the incorporation of decentralized approaches.

Keywords: Interdisciplinary, dynamic, functional programming, object-oriented.

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Authors: Raman Paranjape

Abstract:

We present a new approach to evaluation of Cyber Security in Power Systems using the method of modeling the power systems Infrastructure using software agents. Interfaces between module and the home smart meter are recognized as the primary points of intrusion.

Keywords: Power Systems, Modeling and Simulation, Agent systems.

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Authors: Jihye Jeon

Abstract:

This paper analyzes the conceptual framework of three statistical methods, multiple regression, path analysis, and structural equation models. When establishing research model of the statistical modeling of complex social phenomenon, it is important to know the strengths and limitations of three statistical models. This study explored the character, strength, and limitation of each modeling and suggested some strategies for accurate explaining or predicting the causal relationships among variables. Especially, on the studying of depression or mental health, the common mistakes of research modeling were discussed.

Keywords: Multiple regression, path analysis, structural equation models, statistical modeling, social and psychological phenomenon.

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Authors: A. Ito, S. Okamoto

Abstract:

We constructed an atomic structure model for a PAN-based carbon fiber containing amorphous structures using molecular dynamics methods. It was found that basic physical properties such as crystallinity, Young’s modulus, and thermal conductivity of our model were nearly identical to those of real carbon fibers. We then obtained the tensile strength of a carbon fiber, which has no macro defects. We finally determined that the limitation of the tensile strength was 19 GPa.

Keywords: Amorphous, carbon fiber, molecular dynamics, tensile strength.

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Authors: Guohua Cao, Xu Dong

Abstract:

X-ray Fluorescence Molecular Imaging (XFMI) holds great promise as a low-cost molecular imaging modality for biomedical applications with high chemical sensitivity. However, for in vivo biomedical applications, a key technical bottleneck is the relatively low chemical sensitivity of XFMI, especially at a reasonably low radiation dose. In laboratory x-ray source based XFMI, one of the main factors that limits the chemical sensitivity of XFMI is the scattered x-rays. We will present our latest findings on improving the chemical sensitivity of XFMI using excitation beam spectrum optimization. XFMI imaging experiments on two mouse-sized phantoms were conducted at three different excitation beam spectra. Our results show that the minimum detectable concentration (MDC) of iodine can be readily increased by five times via excitation spectrum optimization. Findings from this investigation could find use for in vivo pre-clinical small-animal XFMI in the future.

Keywords: Molecular imaging, X-ray fluorescence, chemical sensitivity, X-ray scattering.

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Authors: Stefanie Heinke, Carina Pereira, Jan Spillner, Steffen Leonhardt

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Severe heart failure is a common problem that has a significant effect on health expenditures in industrialized countries; moreover it reduces patient-s quality of life. However, current research usually focuses either on detailed modeling of the heart or on detailed modeling of the cardiovascular system. Thus, this paper aims to present a sophisticated model of the heart enhanced with an extensive model of the cardiovascular system. Special interest is on the pressure and flow values close to the heart since these values are critical to accurately diagnose causes of heart failure. The model is implemented in Dymola an object-oriented, physical modeling language. Results achieved with the novel model show overall feasibility of the approach. Moreover, results are illustrated and compared to other models. The novel model shows significant improvements.

Keywords: Cardiovascular system, heart, modeling.

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Authors: Vipin Saxena, Deepa Raj

Abstract:

Unified Modeling language (UML) is one of the important modeling languages used for the visual representation of the research problem. In the present paper, UML model is designed for the Instruction pipeline which is used for the evaluation of the instructions of software programs. The class and sequence diagrams are designed & performance is evaluated for instructions of a sample program through a case study.

Keywords: UML, Instruction Pipeline, Class Diagram &Sequence Diagram.

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Authors: Shankar Kambhampaty, Venkata Srinivas Modali

Abstract:

When architecting an application, key nonfunctional requirements such as performance, scalability, availability and security, which influence the architecture of the system, are some times not adequately addressed. Performance of the application may not be looked at until there is a concern. There are several problems with this reactive approach. If the system does not meet its performance objectives, the application is unlikely to be accepted by the stakeholders. This paper suggests an approach for performance modeling for web based J2EE and .Net applications to address performance issues early in the development life cycle. It also includes a Performance Modeling Case Study, with Proof-of-Concept (PoC) and implementation details for .NET and J2EE platforms.

Keywords: Performance Measures, Performance Modeling, Performance Testing, Resource Utilization, Response Time, Throughput.

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Authors: C. Patrascioiu

Abstract:

The paper describes the modeling and simulation of the heat pumps domain processes. The main objective of the study is the use of the heat pump in propene–propane distillation processes. The modeling and simulation instrument is the Unisim^® Design simulator. The paper is structured in three parts: An overview of the compressing gases, the modeling and simulation of the freezing systems, and the modeling and simulation of the heat pumps. For each of these systems, there are presented the Unisim^® Design simulation diagrams, the input–output system structure and the numerical results. Future studies will consider modeling and simulation of the propene–propane distillation process with heat pump.

Keywords: Distillation, heat pump, simulation, Unisim Design.

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Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: Christina G. Siontorou

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This paper presents an integrated knowledge-based approach to multi-scale modeling of aquatic systems, with a view to enhancing predictive power and aiding environmental management and policy-making. The basic phases of this approach have been exemplified in the case of a bay in Saronicos Gulf (Attiki, Greece). The results showed a significant problem with rising phytoplankton blooms linked to excessive microbial growth, arisen mostly due to increased nitrogen inflows; therefore, the nitrification/denitrification processes of the benthic and water column sub-systems have provided the quality variables to be monitored for assessing environmental status. It is thereby demonstrated that the proposed approach facilitates modeling choices and implementation option decisions, while it provides substantial support for knowledge and experience capitalization in long-term water management.

Keywords: Aquatic ecosystem, integrated modeling, multi-scale modeling, ontological platform.

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Authors: Salem El-tohami Ashoor

Abstract:

A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH₂)₃NAr)}^2-((ηⁿ-Cp)Cp)} (Ar = 2,6-Prⁱ₂C₆H₃)(Cp = C₅H₅ and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions.

The optimised of [V(ArN(CH₂)₃NAr)₂Cl(η⁵-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH₂)₃NAr)₂Cl(η¹-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Vanadium(IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO.

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Authors: Ibrahim A. Aref, Tarek A. El-Mihoub

Abstract:

This paper shows how we can integrate communication modeling into the design modeling at early stages of the design flow. We consider effect of incorporating noise such as impulsive noise on system stability. We show that with change of the system model and investigate the system performance under the different communication effects. We modeled a unmanned aerial vehicle (UAV) as a demonstration using SystemC methodology. Moreover the system is modeled by joining the capabilities of UML and SystemC to operate at system level.

Keywords: Modelling, SoC, SystemC, UAV, Simulation, SoC.

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Authors: Sina Babadi, K. M. Ebrahimi

Abstract:

The aim of this paper is to determine the stress levels at the end of a long slender shaft such as a drilling assembly used in the oil or gas industry using a mathematical model in real-time. The torsional deflection experienced by this type of drilling shaft (about 4 KM length and 20 cm diameter hollow shaft with a thickness of 1 cm) can only be determined using a distributed modeling technique. The main objective of this project is to calculate angular velocity and torque at the end of the shaft by TLM method and also analyzing of the behavior of the system by transient response. The obtained result is compared with lumped modeling technique the importance of these results will be evident only after the mentioned comparison. Two systems have different transient responses and in this project because of the length of the shaft transient response is very important.

Keywords: Distributed Lumped modeling, Lumped modeling, Drill string, Angular Velocity, Torque.

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Authors: I. D. Arroyo

Abstract:

This article seeks to integrate different concepts from contemporary software engineering with an agile development approach. We seek to clarify some definitions and uses, we make a difference between the Systems Development Life Cycle (SDLC) and the methodologies, we differentiate the types of frameworks such as methodological, philosophical and behavioral, standards and documentation. We define relationships based on the documentation of the development process through formal and ad hoc models, and we define the usefulness of using DevOps and Agile Modeling as integrative methodologies of principles and best practices.

Keywords: Methodologies, SDLC, modeling languages, agile modeling, DevOps, UML, agile software development.

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Authors: Ahmed Helal, Sherif Zain Elabideen, Ahmed Lotfy

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In this paper the modeling and analysis of Space Vector Pulse Width Modulation (SVPWM) based Dynamic Voltage Restorer (DVR) using PSCAD/EMTDC software will be presented in details. The simulation includes full modeling of the SVPWM technique used to control the DVR inverter. A test power system composed of three phase voltage source, sag generator, DVR and three phase resistive load is used to demonstrate restoration capability of the DVR. The simulation results of the presented DVR proved excellent voltage sag mitigation to protect sensitive loads.

Keywords: Dynamic voltage restorer, power quality, simulationand modeling, voltage sag.

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Authors: J. Fernandez de Canete

Abstract:

Object-oriented modeling is spreading in current simulation of physiological systems through the use of the individual components of the model and its interconnections to define the underlying dynamic equations. In this paper we describe the use of both the SIMSCAPE and MODELICA simulation environments in the object-oriented modeling of the closed loop cardiovascular system. The performance of the controlled system was analyzed by simulation in light of the existing hypothesis and validation tests previously performed with physiological data. The described approach represents a valuable tool in the teaching of physiology for graduate medical students.

Keywords: Object-Oriented Modeling, SIMSCAPE Simulation Language, MODELICA Simulation Language, Cardiovascular System.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: R. Mkahl, A. Nait-Sidi-Moh, M. Wack

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Batteries of electric vehicles (BEV) are becoming more attractive with the advancement of new battery technologies and promotion of electric vehicles. BEV batteries are recharged on board vehicles using either the grid (G2V for Grid to Vehicle) or renewable energies in a stand-alone application (H2V for Home to Vehicle). This paper deals with the modeling, sizing and control of a photovoltaic stand-alone application that can charge the BEV at home. The modeling approach and developed mathematical models describing the system components are detailed. Simulation and experimental results are presented and commented.

Keywords: Electric vehicles, photovoltaic energy, lead-acid batteries, charging process, modeling, simulation, experimental tests.

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Authors: S. Kulsri, M. Jaroensutasinee, K. Jaroensutasinee

Abstract:

We developed a method based on quasi-molecular modelling to simulate the fall of water drops on horizontally smooth and rough surfaces. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. When a falling water droplet was simulated at low impact velocity on both smooth and rough surfaces, the droplets moved periodically (i.e. the droplets moved up and down for a certain period, finally they stopped moving and reached a steady state), spreading and recoiling without splash or break-up. Spreading rates of falling water droplets increased rapidly as time increased until the spreading rate reached its steady state at time t ~ 0.25 s for rough surface and t ~ 0.40 s for smooth surface. The droplet height above both surfaces decreased as time increased, remained constant after the droplet diameter attained a maximum value and reached its steady state at time t ~ 0.4 s. However, rough surface had higher spreading rates of falling water droplets and lower height on the surface than smooth one.

Keywords: Quasi-molecular modelling, particle modelling, molecular aggregate approach.

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Authors: Ola A. Younis, Said Ghoul

Abstract:

Systems running these days are huge, complex and exist in many versions. Controlling these versions and tracking their changes became a very hard process as some versions are created using meaningless names or specifications. Many versions of a system are created with no clear difference between them. This leads to mismatching between a user’s request and the version he gets. In this paper, we present a system versions meta-modeling approach that produces versions based on system’s features. This model reduced the number of steps needed to configure a release and gave each version its unique specifications. This approach is applicable for systems that use features in its specification.

Keywords: Features, Meta-modeling, Semantic Modeling, SPL, VCS, Versioning.

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Authors: Nguyen Van Tuong, Premysl Pokorny

Abstract:

This paper describes a computer-aided design for design of the concave globoidal cam with cylindrical rollers and swinging follower. Four models with different modeling methods are made from the same input data. The input data are angular input and output displacements of the cam and the follower and some other geometrical parameters of the globoidal cam mechanism. The best cam model is the cam which has no interference with the rollers when their motions are simulated in assembly conditions. The angular output displacement of the follower for the best cam is also compared with that of in the input data to check errors. In this study, Pro/ENGINEER® Wildfire 2.0 is used for modeling the cam, simulating motions and checking interference and errors of the system.

Keywords: Globoidal cam, sweep, pitch surface, modeling.

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