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Solving directly general third order ordinary differential equations using two-point four step block method

Zanariah Abdul Majid, Nurul Asyikin Azmi, Mohamed Suleiman, Zarina Bibi Ibrahaim

Sains Malaysiana, 2012;41:623-632.

Two-point four step direct implicit block method is presented by applying the simple form of Adams- Moulton method for solving directly the general third order ordinary differential equations (ODEs) using variable step size. This method is implemented to get the solutions of initial value problems (IVPs) at two points simultaneously in a block using four backward steps. The numerical results showed that the performance of the developed method is better in terms of maximum error at all tested tolerances and lesser total number of steps as the tolerances getting smaller compared to the existence direct method.

Matched MeSH terms: Computer Simulation
Fulltext Polynomial interpolation in Matlab

Siti Hawa Binti Aziz, Zuliana Bt Abdul Mutalib

Journal of Engineering and Science Research, 2018;2(4):12-19.
MyJurnal

The problem of constructing such a continuous function is called data fitting. Many times, data given only at discrete points. With interpolation, we seek a function that allows us to approximate f(x) such that functional values between the original data set values may be determined. The process of finding such a polynomial is called interpolation and one of the most important approaches used are Lagrange interpolating formula. In this study, researcher determining the polynomial interpolation by using Lagrange interpolating formula. Then, a mathematical modelling was built by using MATLAB programming to determine the polynomial interpolation for a given points using the Lagrange method. The result of the study showed that the manual calculating and the MATLAB mathematical modelling will give the same answer for evaluated x and graph.

Matched MeSH terms: Computer Simulation
Fulltext 5G and IoT Based Reporting and Accident Detection (RAD) System to Deliver First Aid Box Using Unmanned Aerial Vehicle

Alkinani MH, Almazroi AA, Jhanjhi NZ, Khan NA

Sensors (Basel), 2021 Oct 18;21(20).
PMID: 34696118 DOI: 10.3390/s21206905

Internet of Things (IoT) and 5G are enabling intelligent transportation systems (ITSs). ITSs promise to improve road safety in smart cities. Therefore, ITSs are gaining earnest devotion in the industry as well as in academics. Due to the rapid increase in population, vehicle numbers are increasing, resulting in a large number of road accidents. The majority of the time, casualties are not appropriately discovered and reported to hospitals and relatives. This lack of rapid care and first aid might result in life loss in a matter of minutes. To address all of these challenges, an intelligent system is necessary. Although several information communication technologies (ICT)-based solutions for accident detection and rescue operations have been proposed, these solutions are not compatible with all vehicles and are also costly. Therefore, we proposed a reporting and accident detection system (RAD) for a smart city that is compatible with any vehicle and less expensive. Our strategy aims to improve the transportation system at a low cost. In this context, we developed an android application that collects data related to sound, gravitational force, pressure, speed, and location of the accident from the smartphone. The value of speed helps to improve the accident detection accuracy. The collected information is further processed for accident identification. Additionally, a navigation system is designed to inform the relatives, police station, and the nearest hospital. The hospital dispatches UAV (i.e., drone with first aid box) and ambulance to the accident spot. The actual dataset from the Road Safety Open Repository is used for results generation through simulation. The proposed scheme shows promising results in terms of accuracy and response time as compared to existing techniques.

Matched MeSH terms: Computer Simulation
Fulltext Lattice Boltzmann Method of Different BGA Orientations on I-Type Dispensing Method

Abas A, Gan ZL, Ishak MH, Abdullah MZ, Khor SF

PLoS One, 2016;11(7):e0159357.
PMID: 27454872 DOI: 10.1371/journal.pone.0159357

This paper studies the three dimensional (3D) simulation of fluid flows through the ball grid array (BGA) to replicate the real underfill encapsulation process. The effect of different solder bump arrangements of BGA on the flow front, pressure and velocity of the fluid is investigated. The flow front, pressure and velocity for different time intervals are determined and analyzed for potential problems relating to solder bump damage. The simulation results from Lattice Boltzmann Method (LBM) code will be validated with experimental findings as well as the conventional Finite Volume Method (FVM) code to ensure highly accurate simulation setup. Based on the findings, good agreement can be seen between LBM and FVM simulations as well as the experimental observations. It was shown that only LBM is capable of capturing the micro-voids formation. This study also shows an increasing trend in fluid filling time for BGA with perimeter, middle empty and full orientations. The perimeter orientation has a higher pressure fluid at the middle region of BGA surface compared to middle empty and full orientation. This research would shed new light for a highly accurate simulation of encapsulation process using LBM and help to further increase the reliability of the package produced.

Matched MeSH terms: Computer Simulation
Fulltext Device performances analysis of p-type doped silicene-based field effect transistor using SPICE-compatible model

Chuan MW, Riyadi MA, Hamzah A, Alias NE, Mohamed Sultan S, Lim CS, et al.

PLoS One, 2022;17(3):e0264483.
PMID: 35239699 DOI: 10.1371/journal.pone.0264483

Moore's Law is approaching its end as transistors are scaled down to tens or few atoms per device, researchers are actively seeking for alternative approaches to leverage more-than-Moore nanoelectronics. Substituting the channel material of a field-effect transistors (FET) with silicene is foreseen as a viable approach for future transistor applications. In this study, we proposed a SPICE-compatible model for p-type (Aluminium) uniformly doped silicene FET for digital switching applications. The performance of the proposed device is benchmarked with various low-dimensional FETs in terms of their on-to-off current ratio, subthreshold swing and drain-induced barrier lowering. The results show that the proposed p-type silicene FET is comparable to most of the selected low-dimensional FET models. With its decent performance, the proposed SPICE-compatible model should be extended to the circuit-level simulation and beyond in future work.

Matched MeSH terms: Computer Simulation
Understanding the ideal wound healing mechanistic behavior using in silico modelling perspectives: A review

Abu Bakar N, Mydin RBSMN, Yusop N, Matmin J, Ghazalli NF

J Tissue Viability, 2024 Feb;33(1):104-115.
PMID: 38092620 DOI: 10.1016/j.jtv.2023.11.001

Complexity of the entire body precludes an accurate assessment of the specific contributions of tissues or cells during the healing process, which might be expensive and time consuming. Because of this, controlling the wound's size, depth, and dimensions may be challenging, and there is not yet an efficient and reliable chronic wound model representation. Furthermore, given the inherent challenges associated with conducting non-invasive in vivo investigations, it becomes peremptory to explore alternative methodologies for studying wound healing. In this context, biologically-realistic mathematical and computational models emerge as a valuable framework that can effectively address this need. Therefore, it might improve our approach to understanding the process at its core. This article will examines all facets of wound healing, including the kinds, pathways, and most current developments in wound treatment worldwide, particularly in silico modelling utilizing both mathematical and structure-based modelling techniques. It may be helpful to identify the crucial traits through the feedback loop of computer models and experimental investigations in order to build innovative therapies to cure wounds. Hence the effectiveness of personalised medicine and more targeted therapy in the healing of wounds may be enhanced by this interdisciplinary expertise.

Matched MeSH terms: Computer Simulation
Fulltext Analysis of thin plates with holes by using exact geometrical representation within XFEM

Perumal L, Tso CP, Leng LT

J Adv Res, 2016 May;7(3):445-52.
PMID: 27222749 DOI: 10.1016/j.jare.2016.03.004

This paper presents analysis of thin plates with holes within the context of XFEM. New integration techniques are developed for exact geometrical representation of the holes. Numerical and exact integration techniques are presented, with some limitations for the exact integration technique. Simulation results show that the proposed techniques help to reduce the solution error, due to the exact geometrical representation of the holes and utilization of appropriate quadrature rules. Discussion on minimum order of integration order needed to achieve good accuracy and convergence for the techniques presented in this work is also included.

Matched MeSH terms: Computer Simulation
Fulltext Metamaterial sensor based on rectangular enclosed adjacent triple circle split ring resonator with good quality factor for microwave sensing application

Islam MR, Islam MT, M MS, Bais B, Almalki SHA, Alsaif H, et al.

Sci Rep, 2022 Apr 26;12(1):6792.
PMID: 35474227 DOI: 10.1038/s41598-022-10729-4

In this article, a novel shaped metamaterial sensor is presented for the recognition of various oils, fluids, and chemicals using microwave frequency. The performance of the designed sensor structure has been studied both theoretically and experimentally, and it works well. A new sample holder for convenient operation is created and located just behind the designed structure. The results of this study performed better than those of prior liquids sensing studies. Various designs were explored using the Genetic Algorithm (GA), and it is embedded in the Computer Simulation Technology (CST) microwave studio, to optimize the optimal dimensions of the resonator. The suggested metamaterial sensor has a good-quality factor and sensitivity in both frequency shifting and amplitude changing. The resonance frequency shifted to 100 MHz between olive and corn oils, 70 MHz between sunflower and palm oils, 80 MHz between clean and waste brake fluids, and 90 MHz between benzene and carbon-tetrachloride chemicals. The quality factor of the sensor is 135, sensitivity is 0.56, and the figure of merit is 76 which expresses its efficient performance. Furthermore, the proposed sensor can sensitively distinguish different liquids by using the frequency shifting property. The study was carried out in three stages: dielectric constant (DK) measurement with the N1500A dielectric measurement kit, simulation of the structure, and experimental test study with the vector network analyzer. Since the recommended sensor has high sensitivity, good quality factor, and excellent performance, hence it can be used in chemical, oil, and microfluidic industries for detecting various liquid samples.

Matched MeSH terms: Computer Simulation
Fulltext Optimization of a continuous hybrid impeller mixer via computational fluid dynamics

Othman N, Kamarudin SK, Takriff MS, Rosli MI, Engku Chik EM, Meor Adnan MA

ScientificWorldJournal, 2014;2014:619474.
PMID: 25170524 DOI: 10.1155/2014/619474

This paper presents the preliminary steps required for conducting experiments to obtain the optimal operating conditions of a hybrid impeller mixer and to determine the residence time distribution (RTD) using computational fluid dynamics (CFD). In this paper, impeller speed and clearance parameters are examined. The hybrid impeller mixer consists of a single Rushton turbine mounted above a single pitched blade turbine (PBT). Four impeller speeds, 50, 100, 150, and 200 rpm, and four impeller clearances, 25, 50, 75, and 100 mm, were the operation variables used in this study. CFD was utilized to initially screen the parameter ranges to reduce the number of actual experiments needed. Afterward, the residence time distribution (RTD) was determined using the respective parameters. Finally, the Fluent-predicted RTD and the experimentally measured RTD were compared. The CFD investigations revealed that an impeller speed of 50 rpm and an impeller clearance of 25 mm were not viable for experimental investigations and were thus eliminated from further analyses. The determination of RTD using a k-ε turbulence model was performed using CFD techniques. The multiple reference frame (MRF) was implemented and a steady state was initially achieved followed by a transient condition for RTD determination.

Matched MeSH terms: Computer Simulation*
Fulltext Design optimization of pin fin geometry using particle swarm optimization algorithm

Hamadneh N, Khan WA, Sathasivam S, Ong HC

PLoS One, 2013;8(5):e66080.
PMID: 23741525 DOI: 10.1371/journal.pone.0066080

Particle swarm optimization (PSO) is employed to investigate the overall performance of a pin fin.The following study will examine the effect of governing parameters on overall thermal/fluid performance associated with different fin geometries, including, rectangular plate fins as well as square, circular, and elliptical pin fins. The idea of entropy generation minimization, EGM is employed to combine the effects of thermal resistance and pressure drop within the heat sink. A general dimensionless expression for the entropy generation rate is obtained by considering a control volume around the pin fin including base plate and applying the conservations equations for mass and energy with the entropy balance. Selected fin geometries are examined for the heat transfer, fluid friction, and the minimum entropy generation rate corresponding to different parameters including axis ratio, aspect ratio, and Reynolds number. The results clearly indicate that the preferred fin profile is very dependent on these parameters.

Matched MeSH terms: Computer Simulation*
Numerical simulation of undular jumps on graveled bed using volume of fluid method

Rostami F, Yazdi SR, Said MA, Shahrokhi M

Water Sci Technol, 2012;66(5):909-17.
PMID: 22797216 DOI: 10.2166/wst.2012.213

Undular hydraulic jumps are characterized by a smooth rise of the free surface, followed by a train of stationary waves. These jumps sometimes occur in natural waterways and rivers. Numerical difficulties are especially distinct when the flow condition is close to the critical value because of the high sensitivity of the near-critical flow field to flow and channel conditions. Furthermore, the free surface has a wavy shape, which may indicate the occurrence of several transitions from supercritical to subcritical states and vice versa (i.e., undular hydraulic jumps). In this study, a flow model is used to predict an undular hydraulic jump in a rectangular open channel. The model is based on the general two-dimensional, Reynolds-averaged, Navier-Stokes flow equations. The resulting set of partial differential equations is solved using the FLOW-3D solver. The results are compared with the experimental data to validate the model. The comparative analysis shows that the proposed model yields good results. Several types of undular hydraulic jumps occurring in different situations are then simulated to prove the potential application of the model.

Matched MeSH terms: Computer Simulation*
A non-dominated sorting Differential Search Algorithm Flux Balance Analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout

Daud KM, Mohamad MS, Zakaria Z, Hassan R, Shah ZA, Deris S, et al.

Comput Biol Med, 2019 10;113:103390.
PMID: 31450056 DOI: 10.1016/j.compbiomed.2019.103390

Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many methods consider growth coupling as the objective function, whereby it searches for mutants that maximise the growth and production rate. However, the final goal is to increase the production rate. Furthermore, they produce one single solution, though in reality, cells do not focus on one objective and they need to consider various different competing objectives. In this work, a method, termed ndsDSAFBA (non-dominated sorting Differential Search Algorithm and Flux Balance Analysis), has been developed to find the reaction knockouts involved in maximising the production rate and growth rate of the mutant, by incorporating Pareto dominance concepts. The proposed ndsDSAFBA method was validated using three genome-scale metabolic models. We obtained a set of non-dominated solutions, with each solution representing a different mutant strain. The results obtained were compared with the single objective optimisation (SOO) and multi-objective optimisation (MOO) methods. The results demonstrate that ndsDSAFBA is better than the other methods in terms of production rate and growth rate.

Matched MeSH terms: Computer Simulation*
Fulltext Ridge regression and its applications in genetic studies

Arashi M, Roozbeh M, Hamzah NA, Gasparini M

PLoS One, 2021;16(4):e0245376.
PMID: 33831027 DOI: 10.1371/journal.pone.0245376

With the advancement of technology, analysis of large-scale data of gene expression is feasible and has become very popular in the era of machine learning. This paper develops an improved ridge approach for the genome regression modeling. When multicollinearity exists in the data set with outliers, we consider a robust ridge estimator, namely the rank ridge regression estimator, for parameter estimation and prediction. On the other hand, the efficiency of the rank ridge regression estimator is highly dependent on the ridge parameter. In general, it is difficult to provide a satisfactory answer about the selection for the ridge parameter. Because of the good properties of generalized cross validation (GCV) and its simplicity, we use it to choose the optimum value of the ridge parameter. The GCV function creates a balance between the precision of the estimators and the bias caused by the ridge estimation. It behaves like an improved estimator of risk and can be used when the number of explanatory variables is larger than the sample size in high-dimensional problems. Finally, some numerical illustrations are given to support our findings.

Matched MeSH terms: Computer Simulation*
Fulltext An improved adaptive memetic differential evolution optimization algorithms for data clustering problems

Mustafa HMJ, Ayob M, Nazri MZA, Kendall G

PLoS One, 2019;14(5):e0216906.
PMID: 31137034 DOI: 10.1371/journal.pone.0216906

The performance of data clustering algorithms is mainly dependent on their ability to balance between the exploration and exploitation of the search process. Although some data clustering algorithms have achieved reasonable quality solutions for some datasets, their performance across real-life datasets could be improved. This paper proposes an adaptive memetic differential evolution optimisation algorithm (AMADE) for addressing data clustering problems. The memetic algorithm (MA) employs an adaptive differential evolution (DE) mutation strategy, which can offer superior mutation performance across many combinatorial and continuous problem domains. By hybridising an adaptive DE mutation operator with the MA, we propose that it can lead to faster convergence and better balance the exploration and exploitation of the search. We would also expect that the performance of AMADE to be better than MA and DE if executed separately. Our experimental results, based on several real-life benchmark datasets, shows that AMADE outperformed other compared clustering algorithms when compared using statistical analysis. We conclude that the hybridisation of MA and the adaptive DE is a suitable approach for addressing data clustering problems and can improve the balance between global exploration and local exploitation of the optimisation algorithm.

Matched MeSH terms: Computer Simulation*
A novel computer-based simulated learning environment in audiology with learning assistance: Preliminary findings

Dzulkarnain AAA, Rahmat S, Ismail AW, Musa R, Badzis M, Tengku Zam Zam TZH

Med J Malaysia, 2019 04;74(2):168-173.
PMID: 31079129

INTRODUCTION: This paper describes the development and the evaluation of a new Two-dimensional (2D) computer-based (CB) Simulated Learning Environment (SLE) software for routine audiology tests that comes with learning assistance for audiology students. The aim of the study was to serve as preliminary evaluation on the effectiveness of the new 2D CB SLE audiology software among audiology students.
MATERIALS AND METHODS: The development process of the new 2D CB SLE includes, (i) the identification of common errors made by students in the audiology clinic, (ii) the development of five case simulations that include four routine audiology tests incorporating learning assistance derived from the errors commonly made by audiology students and, (iii) the development of 2D CB SLE from a technical perspective. A preliminary evaluation of the use of the 2D CB SLE software was conducted among twenty-six second-year undergraduate audiology students.
RESULTS: The pre-analysis evaluation of the new 2D CB SLE showed that the majority of the students perceived the new 2D CB SLE software as realistic and helpful for them in achieving the course learning outcomes and in improving their clinical skills. The mean overall scores among the twenty-six students using the self-reported questionnaire were significantly higher when using the 2D CB SLE software than with the existing software typically used in their SLE training.
CONCLUSIONS: This new 2D CB SLE software has the potential for use by audiology students for enhancing their learning.

Matched MeSH terms: Computer Simulation*
A Kernel Bayesian Adaptive Resonance Theory with A Topological Structure

Masuyama N, Loo CK, Wermter S

Int J Neural Syst, 2019 Jun;29(5):1850052.
PMID: 30764724 DOI: 10.1142/S0129065718500521

This paper attempts to solve the typical problems of self-organizing growing network models, i.e. (a) an influence of the order of input data on the self-organizing ability, (b) an instability to high-dimensional data and an excessive sensitivity to noise, and (c) an expensive computational cost by integrating Kernel Bayes Rule (KBR) and Correntropy-Induced Metric (CIM) into Adaptive Resonance Theory (ART) framework. KBR performs a covariance-free Bayesian computation which is able to maintain a fast and stable computation. CIM is a generalized similarity measurement which can maintain a high-noise reduction ability even in a high-dimensional space. In addition, a Growing Neural Gas (GNG)-based topology construction process is integrated into the ART framework to enhance its self-organizing ability. The simulation experiments with synthetic and real-world datasets show that the proposed model has an outstanding stable self-organizing ability for various test environments.

Matched MeSH terms: Computer Simulation*
A computational framework for the multiphysics simulation of microbubble-mediated sonothrombolysis using a forward-viewing intravascular transducer

Tan ZQ, Ooi EH, Chiew YS, Foo JJ, Ng EYK, Ooi ET

Ultrasonics, 2023 May;131:106961.
PMID: 36812819 DOI: 10.1016/j.ultras.2023.106961

Sonothrombolysis is a technique that utilises ultrasound waves to excite microbubbles surrounding a clot. Clot lysis is achieved through mechanical damage induced by acoustic cavitation and through local clot displacement induced by acoustic radiation force (ARF). Despite the potential of microbubble-mediated sonothrombolysis, the selection of the optimal ultrasound and microbubble parameters remains a challenge. Existing experimental studies are not able to provide a complete picture of how ultrasound and microbubble characteristics influence the outcome of sonothrombolysis. Likewise, computational studies have not been applied in detail in the context of sonothrombolysis. Hence, the effect of interaction between the bubble dynamics and acoustic propagation on the acoustic streaming and clot deformation remains unclear. In the present study, we report for the first time the computational framework that couples the bubble dynamic phenomena with the acoustic propagation in a bubbly medium to simulate microbubble-mediated sonothrombolysis using a forward-viewing transducer. The computational framework was used to investigate the effects of ultrasound properties (pressure and frequency) and microbubble characteristics (radius and concentration) on the outcome of sonothrombolysis. Four major findings were obtained from the simulation results: (i) ultrasound pressure plays the most dominant role over all the other parameters in affecting the bubble dynamics, acoustic attenuation, ARF, acoustic streaming, and clot displacement, (ii) smaller microbubbles could contribute to a more violent oscillation and improve the ARF simultaneously when they are stimulated at higher ultrasound pressure, (iii) higher microbubbles concentration increases the ARF, and (iv) the effect of ultrasound frequency on acoustic attenuation is dependent on the ultrasound pressure. These results may provide fundamental insight that is crucial in bringing sonothrombolysis closer to clinical implementation.

Matched MeSH terms: Computer Simulation*
Fulltext Realistic facial expression of virtual human based on color, sweat, and tears effects

Alkawaz MH, Basori AH, Mohamad D, Mohamed F

ScientificWorldJournal, 2014;2014:367013.
PMID: 25136663 DOI: 10.1155/2014/367013

Generating extreme appearances such as scared awaiting sweating while happy fit for tears (cry) and blushing (anger and happiness) is the key issue in achieving the high quality facial animation. The effects of sweat, tears, and colors are integrated into a single animation model to create realistic facial expressions of 3D avatar. The physical properties of muscles, emotions, or the fluid properties with sweating and tears initiators are incorporated. The action units (AUs) of facial action coding system are merged with autonomous AUs to create expressions including sadness, anger with blushing, happiness with blushing, and fear. Fluid effects such as sweat and tears are simulated using the particle system and smoothed-particle hydrodynamics (SPH) methods which are combined with facial animation technique to produce complex facial expressions. The effects of oxygenation of the facial skin color appearance are measured using the pulse oximeter system and the 3D skin analyzer. The result shows that virtual human facial expression is enhanced by mimicking actual sweating and tears simulations for all extreme expressions. The proposed method has contribution towards the development of facial animation industry and game as well as computer graphics.

Matched MeSH terms: Computer Simulation*
Fulltext Adaptive cuckoo search algorithm for unconstrained optimization

Ong P

ScientificWorldJournal, 2014;2014:943403.
PMID: 25298971 DOI: 10.1155/2014/943403

Modification of the intensification and diversification approaches in the recently developed cuckoo search algorithm (CSA) is performed. The alteration involves the implementation of adaptive step size adjustment strategy, and thus enabling faster convergence to the global optimal solutions. The feasibility of the proposed algorithm is validated against benchmark optimization functions, where the obtained results demonstrate a marked improvement over the standard CSA, in all the cases.

Matched MeSH terms: Computer Simulation*
Understanding the retina: a review of computational models of the retina from the single cell to the network level

Guo T, Tsai D, Bai S, Morley JW, Suaning GJ, Lovell NH, et al.

Crit Rev Biomed Eng, 2014;42(5):419-36.
PMID: 25745804

The vertebrate retina is a clearly organized signal-processing system. It contains more than 60 different types of neurons, arranged in three distinct neural layers. Each cell type is believed to serve unique role(s) in encoding visual information. While we now have a relatively good understanding of the constituent cell types in the retina and some general ideas of their connectivity, with few exceptions, how the retinal circuitry performs computation remains poorly understood. Computational modeling has been commonly used to study the retina from the single cell to the network level. In this article, we begin by reviewing retinal modeling strategies and existing models. We then discuss in detail the significance and limitations of these models, and finally, we provide suggestions for the future development of retinal neural modeling.

Matched MeSH terms: Computer Simulation*

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