Search results for: CAD based simulation

Authors: Marius Mosoarca, Victor Gioncu, Ovidiu Cosma

Abstract:

Historic religious buildings located in seismic areas have developed different failure mechanisms. Simulation of failure modes is done with computer programs through a nonlinear dynamic analysis or simplified using the method of failure blocks. Currently there are simulation methodologies of failure modes based on the failure rigid blocks method only for Roman Catholic churches type. Due to differences of shape in plan, elevation and construction systems between Orthodox churches and Catholic churches, for the first time there were initiated researches in the development of this simulation methodology for Orthodox churches. In this article are presented the first results from the researches. The theoretical results were compared with real failure modes recorded at an Orthodox church from Banat region, severely damaged by earthquakes in 1991. Simulated seismic response, using a computer program based on finite element method was confirmed by cracks after earthquakes. The consolidation of the church was made according to these theoretical results, realizing a rigid floor connecting all the failure blocks.

Keywords: Dinamic analysis, failure mechanism, rigid blocks seismic simulation.

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Authors: Mwafak Shakoor

Abstract:

The purpose of this study was to reduce patient waiting times, improve system throughput and improve resources utilization in radiology department. A discrete event simulation model was developed using Arena simulation software to investigate different alternatives to improve the overall system delivery based on adding resource scenarios due to the linkage between patient waiting times and resource availability. The study revealed that there is no addition investment need to procure additional scanner but hospital management deploy managerial tactics to enhance machine utilization and reduce the long waiting time in the department.

Keywords: Arena, Computed Tomography (CT), Discrete event simulation, Healthcare modeling, Radiology department, Waiting time.

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Authors: Yi Zhang, Quan Zhou, Jun Li, Yanlang Hu

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Scheduling algorithm is a key technology in satellite switching system with input-buffer. In this paper, a new scheduling algorithm and its realization are proposed. Based on Crossbar switching fabric, the algorithm adopts serial scheduling strategy and adjusts the output port arbitrating strategy for the better equity of every port. Consequently, it increases the matching probability. The algorithm can greatly reduce the scheduling delay and cell loss rate. The analysis and simulation results by OPNET show that the proposed algorithm has the better performance than others in average delay and cell loss rate, and has the equivalent complexity. On the basis of these results, the hardware realization and simulation based on FPGA are completed, which validate the feasibility of the new scheduling algorithm.

Keywords: Scheduling algorithm, input-buffer, serial scheduling, hardware design.

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Authors: Marco Intelvi, Apolinar Picado, Joaquín Martínez

Abstract:

In this work, simulation algorithms for contact drying of agitated particulate materials under vacuum and at atmospheric pressure were developed. The implementation of algorithms gives a predictive estimation of drying rate curves and bulk bed temperature during contact drying. The calculations are based on the penetration model to describe the drying process, where all process parameters such as heat and mass transfer coefficients, effective bed properties, gas and liquid phase properties are estimated with proper correlations. Simulation results were compared with experimental data from the literature. In both cases, simulation results were in good agreement with experimental data. Few deviations were identified and the limitations of the predictive capabilities of the models are discussed. The programs give a good insight of the drying behaviour of the analysed powders.

Keywords: Agitated bed, Atmospheric pressure, Penetrationmodel, Vacuum

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Authors: Jiří Barta

Abstract:

The paper deals with simulation programs of spread of harmful substances. Air pollution has a direct impact on the quality of human life and environmental protection is currently a very hot topic. Therefore, the paper focuses on the simulation of release of harmful substances. The first part of article deals with perspectives and possibilities of implementation outputs of simulations programs into the system which is education and of practical training of the management staff during emergency events in the frame of critical infrastructure. The last part shows the practical testing and evaluation of simulation programs. Of the tested simulations software been selected Symos97. The tool offers advanced features for setting leakage. Gradually allows the user to model the terrain, location, and method of escape of harmful substances.

Keywords: Computer Simulation, Symos97, spread, simulation software, harmful substances.

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Authors: Didik Nurhadiyanto , Moch Agus Choiron , Ken Kaminishi , Shigeyuki Haruyama

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At the previous study of new metal gasket, contact width and contact stress were important design parameter for optimizing metal gasket performance. However, the range of contact stress had not been investigated thoroughly. In this study, we conducted a gasket design optimization based on an elastic and plastic contact stress analysis considering forming effect using FEM. The gasket model was simulated by using two simulation stages which is forming and tightening simulation. The optimum design based on an elastic and plastic contact stress was founded. Final evaluation was determined by helium leak quantity to check leakage performance of both type of gaskets. The helium leak test shows that a gasket based on the plastic contact stress design better than based on elastic stress design.

Keywords: Contact stress, metal gasket, plastic, elastic

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Authors: Riza Muhida, Maisarah Ali, Puteri Shireen Jahn Kassim, Muhammad Abu Eusuf, Agus G.E. Sutjipto, Afzeri

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Over recent years, the number of building integrated photovoltaic (BIPV) installations for home systems have been increasing in Malaysia. The paper concerns an analysis - as part of current Research and Development (R&D) efforts - to integrate photovoltaics as an architectural feature of a detached house in the new satellite township of Putrajaya, Malaysia. The analysis was undertaken using calculation and simulation tools to optimize performance of BIPV home system. In this study, a the simulation analysis was undertaken for selected bungalow units based on a long term recorded weather data for city of Kuala Lumpur. The simulation and calculation was done with consideration of a PV panels' tilt and direction, shading effect and economical considerations. A simulation of the performance of a grid connected BIPV house in Kuala Lumpur was undertaken. This case study uses a 60 PV modules with power output of 2.7 kW giving an average of PV electricity output is 255 kWh/month..

Keywords: Building integrated photovoltaic, Malaysia, Simulation, panels' tilt and direction.

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Authors: Wong Poh Lee, Mohd. Azam Osman, Abdullah Zawawi Talib, Ahmad Izani Md. Ismail

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Traffic congestion has become a major problem in many countries. One of the main causes of traffic congestion is due to road merges. Vehicles tend to move slower when they reach the merging point. In this paper, an enhanced algorithm for traffic simulation based on the fluid-dynamic algorithm and kinematic wave theory is proposed. The enhanced algorithm is used to study traffic congestion at a road merge. This paper also describes the development of a dynamic traffic simulation tool which is used as a scenario planning and to forecast traffic congestion level in a certain time based on defined parameter values. The tool incorporates the enhanced algorithm as well as the two original algorithms. Output from the three above mentioned algorithms are measured in terms of traffic queue length, travel time and the total number of vehicles passing through the merging point. This paper also suggests an efficient way of reducing traffic congestion at a road merge by analyzing the traffic queue length and travel time.

Keywords: Dynamic, fluid-dynamic, kinematic wave theory, simulation, traffic congestion.

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Authors: Ainul Akmar Mokhtar, Masdi Muhammad, Hilmi Hussin, Mohd Amin Abdul Majid

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A reliability, availability and maintainability (RAM) model has been built for acid gas removal plant for system analysis that will play an important role in any process modifications, if required, for achieving its optimum performance. Due to the complexity of the plant, the model was based on a Reliability Block Diagram (RBD) with a Monte Carlo simulation engine. The model has been validated against actual plant data as well as local expert opinions, resulting in an acceptable simulation model. The results from the model showed that the operation and maintenance can be further improved, resulting in reduction of the annual production loss.

Keywords: Acid gas removal plant, RAM model, Reliabilityblock diagram

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Authors: Abdulsalam A. Al-Sudairi

Abstract:

Object-oriented simulation is considered one of the most sophisticated techniques that has been widely used in planning, designing, executing and maintaining construction projects. This technique enables the modeler to focus on objects which is extremely important for thorough understanding of a system. Thus, identifying an object is an essential point of building a successful simulation model. In a maintenance process an object is a maintenance work order (MWO). This study demonstrates a maintenance simulation model for the building maintenance division of Saudi Consolidated Electric Company (SCECO) in Dammam, Saudi Arabia. The model focused on both types of maintenance processes namely: (1) preventive maintenance (PM) and (2) corrective maintenance (CM). It is apparent from the findings that object-oriented simulation is a good diagnostic and experimental tool. This is because problems, limitations, bottlenecks and so forth are easily identified. These features are very difficult to obtain when using other tools.

Keywords: Object oriented, simulation, maintenance, process, work orders

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Authors: A. Khafaji, R. Saadane, J. El Abbadi, M. Belkasmi

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The main objectif of this paper is to present a tool that we have developed subject to characterize and modelling indoor radio channel propagation at millimetric wave. The tool is based on the ray tracing technique (RTT). As, in realistic environment we cannot neglect the significant impact of Human Body Shadowing and other objects in motion on indoor 60 GHz propagation channel. Hence, our proposed model allows a simulation of propagation in a dynamic indoor environment. First, we describe a model of human body. Second, RTT with this model is used to simulate the propagation of millimeter waves in the presence of persons in motion. Results of the simulation show that this tool gives results in agreement with those reported in the literature. Specially, the effects of people motion on temporal channel properties.

Keywords: Simulation. 60 GHz band, Ray Tracing Technique, Indoor channel, Propagation, Human Body Model, Level crossing rate,

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Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari

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The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

Keywords: DNA computing, PCR, POA, simulation software

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Authors: Ziraguen O. Williams, Shield B. Lin, Fouad N. Matari, Leslie J. Quiocho

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Simulation for seated row exercise was a continued task to assist NASA in analyzing a one-dimensional vibration isolation and stabilization system for astronaut’s exercise platform. Feedback delay and signal noise were added to the simulation model. Simulation runs for this study were conducted in two software simulation tools, Trick and MBDyn, software simulation environments developed at the NASA Johnson Space Center. The exciter force in the simulation was calculated from motion capture of an exerciser during a seated aerobic row exercise. The simulation runs include passive control, active control using a Proportional, Integral, Derivative (PID) controller, and active control using a Piecewise Linear Integral Derivative (PWLID) controller. Output parameters include displacements of the exercise platform, the exerciser, and the counterweight; transmitted force to the wall of spacecraft; and actuator force to the platform. The simulation results showed excellent force reduction in the active controlled system compared to the passive controlled system, which showed less force reduction.

Keywords: Simulation, counterweight, exercise, vibration.

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Authors: Rahib Hidayat Abiyev

Abstract:

This paper presents the development of recurrent neural network based fuzzy inference system for identification and control of dynamic nonlinear plant. The structure and algorithms of fuzzy system based on recurrent neural network are described. To train unknown parameters of the system the supervised learning algorithm is used. As a result of learning, the rules of neuro-fuzzy system are formed. The neuro-fuzzy system is used for the identification and control of nonlinear dynamic plant. The simulation results of identification and control systems based on recurrent neuro-fuzzy network are compared with the simulation results of other neural systems. It is found that the recurrent neuro-fuzzy based system has better performance than the others.

Keywords: Fuzzy logic, neural network, neuro-fuzzy system, control system.

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Authors: H.-H. Doh, J.-M. Yu, Y.-J. Kwon, J.-H. Shin, H.-W. Kim, S.-H. Nam, D.-H. Lee

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This paper suggests a decision tree based approach for flexible job shop scheduling with multiple process plans, i.e. each job can be processed through alternative operations, each of which can be processed on alternative machines. The main decision variables are: (a) selecting operation/machine pair; and (b) sequencing the jobs assigned to each machine. As an extension of the priority scheduling approach that selects the best priority rule combination after many simulation runs, this study suggests a decision tree based approach in which a decision tree is used to select a priority rule combination adequate for a specific system state and hence the burdens required for developing simulation models and carrying out simulation runs can be eliminated. The decision tree based scheduling approach consists of construction and scheduling modules. In the construction module, a decision tree is constructed using a four-stage algorithm, and in the scheduling module, a priority rule combination is selected using the decision tree. To show the performance of the decision tree based approach suggested in this study, a case study was done on a flexible job shop with reconfigurable manufacturing cells and a conventional job shop, and the results are reported by comparing it with individual priority rule combinations for the objectives of minimizing total flow time and total tardiness.

Keywords: Flexible job shop scheduling, Decision tree, Priority rules, Case study.

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Authors: Maziar Ahmad Sharbafi, Caro Lucas, Abolfazel Toroghi Haghighat, Omid AmirGhiasvand, Omid Aghazade

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RoboCup Rescue simulation as a large-scale Multi agent system (MAS) is one of the challenging environments for keeping coordination between agents to achieve the objectives despite sensing and communication limitations. The dynamicity of the environment and intensive dependency between actions of different kinds of agents make the problem more complex. This point encouraged us to use learning-based methods to adapt our decision making to different situations. Our approach is utilizing reinforcement leaning. Using learning in rescue simulation is one of the current ways which has been the subject of several researches in recent years. In this paper we present an innovative learning method implemented for Police Force (PF) Agent. This method can cope with the main difficulties that exist in other learning approaches. Different methods used in the literature have been examined. Their drawbacks and possible improvements have led us to the method proposed in this paper which is fast and accurate. The Brain Emotional Learning Based Intelligent Controller (BELBIC) is our solution for learning in this environment. BELBIC is a physiologically motivated approach based on a computational model of amygdale and limbic system. The paper presents the results obtained by the proposed approach, showing the power of BELBIC as a decision making tool in complex and dynamic situation.

Keywords: Emotional learning, rescue, simulation environment, RoboCup, multi-agent system.

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Authors: Hiroyuki Nishida, Taku Nonomura, Takashi Abe

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Wall-surface jet induced by the dielectric barrier discharge (DBD) has been proposed as an actuator for active flow control in aerodynamic applications. Discharge plasma evolution of the DBD plasma actuator was simulated based on a simple fluid model, in which the electron, one type of positive ion and negative ion were taken into account. Two-dimensional simulation was conducted, and the results are in agreement with the insights obtained from experimental studies. The simulation results indicate that the discharge mode changes depending on applied voltage slope; when the applied voltage is positive-going with high applied voltage slope, the corona-type discharge mode turns into the streamer-type discharge mode and the threshold voltage slope is around 300 kV/ms in this simulation. The characteristics of the electrohydrodynamic (EHD) force, which is the source of the wall-surface jet, also change depending on the discharge mode; the tentative peak value of the EHD force during the positive-going voltage phase is saturated by the periodical formation of the streamer-type discharge.

Keywords: Dielectric barrier discharge, Plasma actuator, Fluid simulation.

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Authors: Doseong Eom, Jeongmin Kim, Kwang Ryel Ryu

Abstract:

Large exhibition halls require a lot of energy to maintain comfortable atmosphere for the visitors viewing inside. One way of reducing the energy cost is to have thermal energy storage systems installed so that the thermal energy can be stored in the middle of night when the energy price is low and then used later when the price is high. To minimize the overall energy cost, however, we should be able to decide how much energy to save during which time period exactly. If we can foresee future energy load and the corresponding cost, we will be able to make such decisions reasonably. In this paper, we use machine learning technique to obtain models for predicting weather conditions and the number of visitors on hourly basis for the next day. Based on the energy load thus predicted, we build a cost-optimal daily operation plan for the thermal energy storage systems and cooling and heating facilities through simulation-based optimization.

Keywords: Building energy management, machine learning, simulation-based optimization, operation planning.

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Authors: Muhammad T. Alam, Zheng Da Wu

Abstract:

In this research, we propose a weighted class based queuing (WCBQ) mechanism to provide class differentiation and to reduce the load for the IMS (IP Multimedia Subsystem) presence server (PS). The tasks of admission controller for the PS are demonstrated. Analysis and simulation models are developed to quantify the performance of WCBQ scheme. An optimized dropping time frame has been developed based on which some of the preexisting messages are dropped from the PS-buffer. Cost functions are developed and simulation comparison has been performed with FCFS (First Come First Served) scheme. The results show that the PS benefits significantly from the proposed queuing and dropping algorithm (WCBQ) during heavy traffic.

Keywords: Admission control, presence, queuing.

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Authors: U. Tancredi, D. Accardo, M. Grassi, G. Fasano, A. E. Tirri, A. Vitale, N. Genito, F. Montemari, L. Garbarino

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The development of guidance, navigation and control algorithms and avionic procedures requires the disposability of suitable analysis and verification tools, such as simulation environments, which support the design process and allow detecting potential problems prior to the flight test, in order to make new technologies available at reduced cost, time and risk. This paper presents a simulation environment for avionic software development and qualification, especially aimed at equipment for general aviation aircrafts and unmanned aerial systems. The simulation environment includes models for short and medium-range radio-navigation aids, flight assistance systems, and ground control stations. All the software modules are able to simulate the modeled systems both in fast-time and real-time tests, and were implemented following component oriented modeling techniques and requirement based approach. The paper describes the specific models features, the architectures of the implemented software systems and its validation process. Performed validation tests highlighted the capability of the simulation environment to guarantee in real-time the required functionalities and performance of the simulated avionics systems, as well as to reproduce the interaction between these systems, thus permitting a realistic and reliable simulation of a complete mission scenario.

Keywords: ADS-B, avionics, NAVAIDs, real time simulation, TCAS, UAS ground control station.

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Authors: Ajoy Kumar Das, Prasenjit Dey

Abstract:

Heat transfer due to forced convection of copper water based nanofluid has been predicted by Artificial Neural network (ANN). The present nanofluid is formed by mixing copper nanoparticles in water and the volume fractions are considered here are 0% to 15% and the Reynolds number are kept constant at 100. The back propagation algorithm is used to train the network. The present ANN is trained by the input and output data which has been obtained from the numerical simulation, performed in finite volume based Computational Fluid Dynamics (CFD) commercial software Ansys Fluent. The numerical simulation based results are compared with the back propagation based ANN results. It is found that the forced convection heat transfer of water based nanofluid can be predicted correctly by ANN. It is also observed that the back propagation ANN can predict the heat transfer characteristics of nanofluid very quickly compared to standard CFD method.

Keywords: Forced convection, Square cylinder, nanofluid, neural network.

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Authors: Jiří Barta, Josef Krahulec, Jiří F. Urbánek

Abstract:

Education and practical training crisis management members are a topical issue nowadays. The paper deals with the perspectives and possibilities of "smart solutions" to education for crisis management staff. Currently, there is a large number of simulation tools, which notes that they are suitable for practical training of crisis management staff. The first part of the paper is focused on the introduction of the technology simulation tools. The simulators aim is to create a realistic environment for the practical training of extending units of crisis staff. The second part of the paper concerns the possibilities of using the simulation technology to the education process. The aim of this section is to introduce the practical capabilities and potential of the simulation programs for practical training of crisis management staff.

Keywords: Crisis management staff, computer simulation, software, technological education.

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Authors: S. MacDonald, A. Manuel, R. Law, N. Bandruak, A. Dubrowski, V. Curran, J. Smith-Young, K. Simmons, A. Warren

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High fidelity human patient simulation has been used for many years by health sciences education programs to foster critical thinking, engage learners, improve confidence, improve communication, and enhance psychomotor skills. Unfortunately, there is a paucity of research on the use of high fidelity human patient simulation to foster teamwork among nursing, medicine and pharmacy undergraduate students. This study compared the impact of high fidelity and low fidelity simulation education on teamwork among nursing, medicine and pharmacy students. For the purpose of this study, two innovative teaching scenarios were developed based on the care of an adult patient experiencing acute anaphylaxis: one high fidelity using a human patient simulator and one low fidelity using case based discussions. A within subjects, pretest-posttest, repeated measures design was used with two-treatment levels and random assignment of individual subjects to teams of two or more professions. A convenience sample of twenty-four (n=24) undergraduate students participated, including: nursing (n=11), medicine (n=9), and pharmacy (n=4). The Interprofessional Teamwork Questionnaire was used to assess for changes in students’ perception of their functionality within the team, importance of interprofessional collaboration, comprehension of roles, and confidence in communication and collaboration. Student satisfaction was also assessed. Students reported significant improvements in their understanding of the importance of interprofessional teamwork and of the roles of nursing and medicine on the team after participation in both the high fidelity and the low fidelity simulation. However, only participants in the high fidelity simulation reported a significant improvement in their ability to function effectively as a member of the team. All students reported that both simulations were a meaningful learning experience and all students would recommend both experiences to other students. These findings suggest there is merit in both high fidelity and low fidelity simulation as a teaching and learning approach to foster teamwork among undergraduate nursing, medicine and pharmacy students. However, participation in high fidelity simulation may provide a more realistic opportunity to practice and function as an effective member of the interprofessional health care team.

Keywords: Acute anaphylaxis, high fidelity human patient simulation, low fidelity simulation, interprofessional education.

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Authors: Seong Do Kim, Woo Young Jung

Abstract:

Recently, damages due to typhoons and strong wind are on the rise. Considering this issue, we evaluated the performance of soundproofing walls based on the strong wind fragility by means of numerical analysis. Among the components of the soundproof wall, aluminum frame was the most vulnerable member, thus we have considered different section of aluminum frame in the determination of wind fragility. Wind load was randomly generated using Monte Carlo Simulation method. Moreover, limit state was based on the test standard of road construction soundproofing wall. In this study, the strong wind fragility was determined by considering the influence factors of wind exposure category, soundproof wall’s installation position, and shape of aluminum frame section. Results of this study could be used to determine the section shape of the frame that has high resistance to the wind during construction of the soundproofing wall.

Keywords: Aluminum frame soundproofing wall, Monte Carlo Simulation, numerical simulation, wind fragility.

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Authors: P. Javid, A. Aeenmehr, J. Taghavifar

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In this paper, supply air pressure of HVAC system has been modeled with second-order transfer function plus dead-time. In HVAC system, the desired input has step changes, and the output of proposed control system should be able to follow the input reference, so the idea of using model based predictive control is proceeded and designed in this paper. The closed loop control system is implemented in MATLAB software and the simulation results are provided. The simulation results show that the model based predictive control is able to control the plant properly.

Keywords: Air conditioning system, GPC, dead time, Air supply control.

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Authors: Said F. Urmancheev, Victor N. Kireev, Svetlana F. Khizbullina

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This paper presents results of numerical simulation of filtration of abnormal thermoviscous fluid on an example of thermo reversible polymer gel.

Keywords: Abnormal thermoviscous fluid, filtration, numerical simulation.

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Authors: Nayera E. El-Gharably, Khaled S. El-Kilany, Aziz E. El-Sayed

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A key element of many distribution systems is the routing and scheduling of vehicles servicing a set of customers. A wide variety of exact and approximate algorithms have been proposed for solving the vehicle routing problems (VRP). Exact algorithms can only solve relatively small problems of VRP, which is classified as NP-Hard. Several approximate algorithms have proven successful in finding a feasible solution not necessarily optimum. Although different parts of the problem are stochastic in nature; yet, limited work relevant to the application of discrete event system simulation has addressed the problem. Presented here is optimization using simulation of VRP; where, a simplified problem has been developed in the ExtendSimTM simulation environment; where, ExtendSimTM evolutionary optimizer is used to minimize the total transportation cost of the problem. Results obtained from the model are very satisfactory. Further complexities of the problem are proposed for consideration in the future.

Keywords: Discrete event system simulation, optimization using simulation, vehicle routing problem.

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Authors: Arash Esmaeili, Omid Ghabouli

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The production and consumption of natural gas is on the rise throughout the world as a result of its wide availability, ease of transportation, use and clean-burning characteristics. The chief use of ethane is in the chemical industry in the production of Ethene (ethylene) by steam cracking. In this simulation, obtained ethane recovery percent based on Gas sub-cooled process (GSP) is 99.9 by mole that is included 32.1% by using de-methanizer column and 67.8% by de-ethanizer tower. The outstanding feature of this process is the novel split-vapor concept that employs to generate reflux for de-methanizer column. Remain amount of ethane in export gas cause rise in gross heating value up to 36.66 MJ/Nm3 in order to use in industrial and household consumptions.

Keywords: Ethane recovery, Hydrocarbon dew point, Simulation, Water dew point

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Authors: S. Sfarni, E. Bellenger, J. Fortin, M. Guessasma

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The use of the mechanical simulation (in particular the finite element analysis) requires the management of assumptions in order to analyse a real complex system. In finite element analysis (FEA), two modeling steps require assumptions to be able to carry out the computations and to obtain some results: the building of the physical model and the building of the simulation model. The simplification assumptions made on the analysed system in these two steps can generate two kinds of errors: the physical modeling errors (mathematical model, domain simplifications, materials properties, boundary conditions and loads) and the mesh discretization errors. This paper proposes a mesh adaptive method based on the use of an h-adaptive scheme in combination with an error estimator in order to choose the mesh of the simulation model. This method allows us to choose the mesh of the simulation model in order to control the cost and the quality of the finite element analysis.

Keywords: Finite element, discretization errors, adaptivity.

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

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A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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