Displaying publications 1 - 20 of 604 in total

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  1. 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*
  2. Optimizing neural network algorithms for submerged membrane bioreactor: A comparative study of OVAT and RSM hyperparameter optimization techniques
    Ibrahim S, Abdul Wahab N
    Water Sci Technol, 2024 Apr;89(7):1701-1724.
    PMID: 38619898 DOI: 10.2166/wst.2024.099
    Hyperparameter tuning is an important process to maximize the performance of any neural network model. This present study proposed the factorial design of experiment for screening and response surface methodology to optimize the hyperparameter of two artificial neural network algorithms. Feed-forward neural network (FFNN) and radial basis function neural network (RBFNN) are applied to predict the permeate flux of palm oil mill effluent. Permeate pump and transmembrane pressure of the submerge membrane bioreactor system are the input variables. Six hyperparameters of the FFNN model including four numerical factors (neuron numbers, learning rate, momentum, and epoch numbers) and two categorical factors (training and activation function) are used in hyperparameter optimization. RBFNN includes two numerical factors such as a number of neurons and spreads. The conventional method (one-variable-at-a-time) is compared in terms of optimization processing time and the accuracy of the model. The result indicates that the optimal hyperparameters obtained by the proposed approach produce good accuracy with a smaller generalization error. The simulation results show an improvement of more than 65% of training performance, with less repetition and processing time. This proposed methodology can be utilized for any type of neural network application to find the optimum levels of different parameters.
    Matched MeSH terms: Computer Simulation
  3. Simulation of Rainfall-Runoff Response in Ecological Swale with On-Line Subsurface Detention Using Infoworks SD
    Ghadim HB, Hin LS
    Water Environ Res, 2017 Sep 01;89(9):862-870.
    PMID: 28855022 DOI: 10.2175/106143017X14902968254764
      The Bio-Ecological Drainage System (BIOECODS) is a sustainable drainage (SUDS) to demonstrate the 'control at source' approaches for urban stormwater management in Malaysia. It is an environmentally friendly drainage system that was designed to increase infiltration, reduce peak flow at outlet, improve water quality, through different BMPs, such as grass swale, retention pond, etc. A special feature of BIOECODS is ecological swale with on-line subsurface detention. This study attempted to create a model of ecological swale with on-line subsurface conveyance system with InfoWorks SD. The new technique has been used Storm Water Management Model (SWMM) model to describe overland flow routing and Soil Conservation Service Method (SCS) used to model infiltration or subsurface flow. The modeling technique has been proven successful, as the predicted and observed closely match each other, with a mean error of 4.58 to 7.32%. The calibrated model then used to determine the ratio of the flow exchange between the surface and subsurface drainage system. Results from the model showed that the runoff ratio exchange between the surface and subsurface is 60 to 90%.
    Matched MeSH terms: Computer Simulation
  4. Estimation of an Instrument-Defined Minimally Important Difference in EQ-5D-5L Index Scores Based on Scoring Algorithms Derived Using the EQ-VT Version 2 Valuation Protocols
    Henry EB, Barry LE, Hobbins AP, McClure NS, O'Neill C
    Value Health, 2020 07;23(7):936-944.
    PMID: 32762996 DOI: 10.1016/j.jval.2020.03.003
    OBJECTIVES: To estimate and compare the minimally important difference (MID) in index score of country-specific EQ-5D-5L scoring algorithms developed using EuroQol Valuation Technology protocol version 2, including algorithms from Germany, Indonesia, Ireland, Malaysia, Poland, Portugal, Taiwan, and the United States.

    METHODS: A simulation-based approach contingent on all single-level transitions defined by the EQ-5D-5L descriptive system was used to estimate the MID for each algorithm.

    RESULTS: The resulting mean (and standard deviation) instrument-defined MID estimates were Germany, 0.083 (0.022); Indonesia, 0.093 (0.012); Ireland, 0.098 (0.023); Malaysia, 0.072 (0.010); Poland, 0.080 (0.030); Portugal, 0.080 (0.018); Taiwan, 0.101 (0.010); and the United States, 0.078 (0.014).

    CONCLUSIONS: These population preference-based MID estimates and accompanying evidence of how such values vary as a function of baseline index score can be used to aid interpretation of index score change. The marked consistency in the relationship between the calculated MID estimate and the range of the EQ-5D-5L index score, represented by a ratio of 1:20, might substantiate a rule of thumb allowing for MID approximation in EQ-5D-5L index score warranting further investigation.

    Matched MeSH terms: Computer Simulation
  5. A computational simulation study on the acoustic pressure generated by a dental endosonic file: effects of intensity, file shape and volume
    Tiong TJ, Price GJ, Kanagasingam S
    Ultrason Sonochem, 2014 Sep;21(5):1858-65.
    PMID: 24735986 DOI: 10.1016/j.ultsonch.2014.03.024
    One of the uses of ultrasound in dentistry is in the field of endodontics (i.e. root canal treatment) in order to enhance cleaning efficiency during the treatment. The acoustic pressures generated by the oscillation of files in narrow channels has been calculated using the COMSOL simulation package. Acoustic pressures in excess of the cavitation threshold can be generated and higher values were found in narrower channels. This parallels experimental observations of sonochemiluminescence. The effect of varying the channel width and length and the dimensions and shape of the file are reported. As well as explaining experimental observations, the work provides a basis for the further development and optimisation of the design of endosonic files.
    Matched MeSH terms: Computer Simulation
  6. A technique for evaluating the oil/heavy-oil viscosity changes under ultrasound in a simulated porous medium
    Hamidi H, Mohammadian E, Junin R, Rafati R, Manan M, Azdarpour A, et al.
    Ultrasonics, 2014 Feb;54(2):655-62.
    PMID: 24075416 DOI: 10.1016/j.ultras.2013.09.006
    Theoretically, Ultrasound method is an economical and environmentally friendly or "green" technology, which has been of interest for more than six decades for the purpose of enhancement of oil/heavy-oil production. However, in spite of many studies, questions about the effective mechanisms causing increase in oil recovery still existed. In addition, the majority of the mechanisms mentioned in the previous studies are theoretical or speculative. One of the changes that could be recognized in the fluid properties is viscosity reduction due to radiation of ultrasound waves. In this study, a technique was developed to investigate directly the effect of ultrasonic waves (different frequencies of 25, 40, 68 kHz and powers of 100, 250, 500 W) on viscosity changes of three types of oil (Paraffin oil, Synthetic oil, and Kerosene) and a Brine sample. The viscosity calculations in the smooth capillary tube were based on the mathematical models developed from the Poiseuille's equation. The experiments were carried out for uncontrolled and controlled temperature conditions. It was observed that the viscosity of all the liquids was decreased under ultrasound in all the experiments. This reduction was more significant for uncontrolled temperature condition cases. However, the reduction in viscosity under ultrasound was higher for lighter liquids compare to heavier ones. Pressure difference was diminished by decreasing in the fluid viscosity in all the cases which increases fluid flow ability, which in turn aids to higher oil recovery in enhanced oil recovery (EOR) operations. Higher ultrasound power showed higher liquid viscosity reduction in all the cases. Higher ultrasound frequency revealed higher and lower viscosity reduction for uncontrolled and controlled temperature condition experiments, respectively. In other words, the reduction in viscosity was inversely proportional to increasing the frequency in temperature controlled experiments. It was concluded that cavitation, heat generation, and viscosity reduction are three of the promising mechanisms causing increase in oil recovery under ultrasound.
    Matched MeSH terms: Computer Simulation
  7. 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*
  8. Fulltext Hypothetical Protein BPSL3393 of Burkholderia pseudomallei is Involved in Ethanolamine Catabolism
    Luan OG, Yam H, Samian R, Wajidi MFF, Mahadi NM, Mohamad S, et al.
    Trop Life Sci Res, 2017 Jul;28(2):57-74.
    PMID: 28890761 MyJurnal DOI: 10.21315/tlsr2017.28.2.5
    Burkholderia pseudomallei is a soil-dwelling bacterium that causes a globally emerging disease called melioidosis. Approximately one third of the in silico annotated genes in its genome are classified as hypothetical genes. This group of genes is difficult to be functionally characterised partly due to the absence of noticeable phenotypes under conventional laboratory settings. A bioinformatic survey of hypothetical genes revealed a gene designated as BPSL3393 that putatively encodes a small protein of 11 kDA with a CoA binding domain. BPSL3393 is conserved in all the B. pseudomallei genomes as well as various in other species within the genus Burkholderia. Taking into consideration that CoA plays a ubiquitous metabolic role in all life forms, characterisation of BPSL3393 may uncover a previously over-looked metabolic feature of B. pseudomallei. The gene was deleted from the genome using a double homologous recombination approach yielding a null mutant. The BPSL3393 mutant showed no difference in growth rate with the wild type under rich and minimal growth conditions. An extensive metabolic phenotyping test was performed involving 95 metabolic substrates. The deletion mutant of BPSL3393 was severely impaired in its ethanolamine metabolism. The growth rate of the mutant was attenuated when ethanolamine was used as the sole carbon source. A transcriptional analysis of the ethanolamine metabolism genes showed that they were down-regulated in the BPSL3393 mutant. This seemed to suggest that BPSL3393 functions as a positive regulator for ethanolamine metabolism.
    Matched MeSH terms: Computer Simulation
  9. Fulltext Modelling the effect of temperature change on the extrinsic incubation period and reproductive number of Plasmodium falciparum in Malaysia
    Chua TH
    Trop Biomed, 2012 Mar;29(1):121-8.
    PMID: 22543612 MyJurnal
    According to the report of the Intergovernmental Panel on Climate Change (IPCC), Malaysia will experience an increase of 3-5°C in the future. As the development of the malaria parasite, Plasmodium falciparum, is sensitive to temperature, we investigated, using computer models, the effect of increase of 3º and 5ºC on the possible changes in the epidemiology of malaria transmission of P. falciparum in Malaysia. Four environmentally different locations were selected: Kuala Lumpur (KL), Cameron Highlands (CH), Kota Kinabalu (KK) and Kinabalu Park (KP). The extrinsic incubation period (EIP) was estimated using hourly temperatures and the mean daily temperatures. The EIP values estimated using the mean daily temperature were lower than those computed from hourly temperatures in warmer areas (KL, KK), but higher in the cooler areas (CH, KP). The computer simulations also indicated that the EIP will be decreased if the temperature was raised by 3º or 5ºC, with the effect more pronounced for the greater temperature increase, and for the cooler places. The vector cohort that is still alive at a time to transmit malaria (s(EIP)) also increased when the temperature was raised, with the increase more pronounced in the cooler areas. This study indicates an increase in temperature will have more significant effect in shortening the EIP in a cooler place (eg CH, KP), resulting in a greater s(EIP), and consequently increasing the transmission intensity and malaria risk. A temperature increase arising from the global climate change will likely affect the epidemiology of malaria in Malaysia, especially in the cooler areas.
    Matched MeSH terms: Computer Simulation
  10. Fulltext A novel alternative method for 3D visualisation in Parasitology: the construction of a 3D model of a parasite from 2D illustrations
    Teo BG, Sarinder KK, Lim LH
    Trop Biomed, 2010 Aug;27(2):254-64.
    PMID: 20962723 MyJurnal
    Three-dimensional (3D) models of the marginal hooks, dorsal and ventral anchors, bars and haptoral reservoirs of a parasite, Sundatrema langkawiense Lim & Gibson, 2009 (Monogenea) were developed using the polygonal modelling method in Autodesk 3ds Max (Version 9) based on two-dimensional (2D) illustrations. Maxscripts were written to rotate the modelled 3D structures. Appropriately orientated 3D haptoral hard-parts were then selected and positioned within the transparent 3D outline of the haptor and grouped together to form a complete 3D haptoral entity. This technique is an inexpensive tool for constructing 3D models from 2D illustrations for 3D visualisation of the spatial relationships between the different structural parts within organisms.
    Matched MeSH terms: Computer Simulation
  11. Discovery of small molecule inhibitors against the NS3/4A serine protease of Hepatitis C virus genotype 3 via highthroughput virtual screening and in vitro evaluations
    Sakhor W, Teoh TC, Yusof R, Lim SK, Razif MFM
    Trop Biomed, 2020 Sep 01;37(3):609-625.
    PMID: 33612776 DOI: 10.47665/tb.37.3.609
    The hepatitis C virus (HCV) consists of eight genotypes and 90 subtypes, with genotype (GT) 3 being the second most common globally and is linked to higher incidences of steatosis and rapid development of fibrosis and cirrhosis. The NS3/4A serine protease, a heterodimer complex of two HCV non-structural proteins, is an effective target for pharmaceutical intervention due to its essential roles in processing HCV polyproteins and inhibiting innate immunity. This study combines structure-based virtual screening (SBVS) of predefined compound libraries, pharmacokinetic prediction (ADME/T) and in vitro evaluation to identify potential low molecular weight (<500 Dalton) inhibitors of the NS3/4A serine protease (GT3). In silico screening of ZINC and PubChem libraries yielded five selected compounds as potential candidates. Dose-dependent inhibition of the NS3/4A serine protease and HCV replication in HuH-7.5 cells revealed that compound A (PubChem ID No. 16672637) exhibited inhibition towards HCV GT3 with an IC50 of 106.7µM and EC50 of 25.8µM, respectively. Thus, compound A may be developed as a potent, low molecular weight drug against the HCV NS3/4A serine protease of GT3.
    Matched MeSH terms: Computer Simulation
  12. In silico approaches for probiotic-derived bioactives
    Tan PL, Liong MT
    Trends Biotechnol, 2014 Dec;32(12):599-601.
    PMID: 25457386 DOI: 10.1016/j.tibtech.2014.09.011
    Matched MeSH terms: Computer Simulation
  13. New method for distance-based close following safety indicator
    Sharizli AA, Rahizar R, Karim MR, Saifizul AA
    Traffic Inj Prev, 2015;16(2):190-5.
    PMID: 24827899 DOI: 10.1080/15389588.2014.921913
    The increase in the number of fatalities caused by road accidents involving heavy vehicles every year has raised the level of concern and awareness on road safety in developing countries like Malaysia. Changes in the vehicle dynamic characteristics such as gross vehicle weight, travel speed, and vehicle classification will affect a heavy vehicle's braking performance and its ability to stop safely in emergency situations. As such, the aim of this study is to establish a more realistic new distance-based safety indicator called the minimum safe distance gap (MSDG), which incorporates vehicle classification (VC), speed, and gross vehicle weight (GVW).
    Matched MeSH terms: Computer Simulation*
  14. Motorcyclist rear brake simple perception-response times in rear-end collision situations
    Davoodi SR, Hamid H, Arintono S, Muniandy R, Faezi SF
    Traffic Inj Prev, 2011 Apr;12(2):174-9.
    PMID: 21469025 DOI: 10.1080/15389588.2010.533314
    The purpose of this study was to determine the baseline motorcycle riders' perception-response times (PRTs) in an expected object braking task and to determine the significant difference between PRTs of older and younger riders.
    Matched MeSH terms: Computer Simulation
  15. Cost-effectiveness analysis of pharmacogenetic-guided warfarin dosing in Thailand
    Chong HY, Saokaew S, Dumrongprat K, Permsuwan U, Wu DB, Sritara P, et al.
    Thromb Res, 2014 Dec;134(6):1278-84.
    PMID: 25456732 DOI: 10.1016/j.thromres.2014.10.006
    Pharmacogenetic (PGx) test is a useful tool for guiding physician on an initiation of an optimal warfarin dose. To implement of such strategy, the evidence on the economic value is needed. This study aimed to determine the cost-effectiveness of PGx-guided warfarin dosing compared with usual care (UC).
    Matched MeSH terms: Computer Simulation
  16. Fulltext Investigation of micro- and nanosized particle erosion in a 90° pipe bend using a two-phase discrete phase model
    Safaei MR, Mahian O, Garoosi F, Hooman K, Karimipour A, Kazi SN, et al.
    ScientificWorldJournal, 2014;2014:740578.
    PMID: 25379542 DOI: 10.1155/2014/740578
    This paper addresses erosion prediction in 3-D, 90° elbow for two-phase (solid and liquid) turbulent flow with low volume fraction of copper. For a range of particle sizes from 10 nm to 100 microns and particle volume fractions from 0.00 to 0.04, the simulations were performed for the velocity range of 5-20 m/s. The 3-D governing differential equations were discretized using finite volume method. The influences of size and concentration of micro- and nanoparticles, shear forces, and turbulence on erosion behavior of fluid flow were studied. The model predictions are compared with the earlier studies and a good agreement is found. The results indicate that the erosion rate is directly dependent on particles' size and volume fraction as well as flow velocity. It has been observed that the maximum pressure has direct relationship with the particle volume fraction and velocity but has a reverse relationship with the particle diameter. It also has been noted that there is a threshold velocity as well as a threshold particle size, beyond which significant erosion effects kick in. The average friction factor is independent of the particle size and volume fraction at a given fluid velocity but increases with the increase of inlet velocities.
    Matched MeSH terms: Computer Simulation
  17. Fulltext An adaptive handover prediction scheme for seamless mobility based wireless networks
    Sadiq AS, Fisal NB, Ghafoor KZ, Lloret J
    ScientificWorldJournal, 2014;2014:610652.
    PMID: 25574490 DOI: 10.1155/2014/610652
    We propose an adaptive handover prediction (AHP) scheme for seamless mobility based wireless networks. That is, the AHP scheme incorporates fuzzy logic with AP prediction process in order to lend cognitive capability to handover decision making. Selection metrics, including received signal strength, mobile node relative direction towards the access points in the vicinity, and access point load, are collected and considered inputs of the fuzzy decision making system in order to select the best preferable AP around WLANs. The obtained handover decision which is based on the calculated quality cost using fuzzy inference system is also based on adaptable coefficients instead of fixed coefficients. In other words, the mean and the standard deviation of the normalized network prediction metrics of fuzzy inference system, which are collected from available WLANs are obtained adaptively. Accordingly, they are applied as statistical information to adjust or adapt the coefficients of membership functions. In addition, we propose an adjustable weight vector concept for input metrics in order to cope with the continuous, unpredictable variation in their membership degrees. Furthermore, handover decisions are performed in each MN independently after knowing RSS, direction toward APs, and AP load. Finally, performance evaluation of the proposed scheme shows its superiority compared with representatives of the prediction approaches.
    Matched MeSH terms: Computer Simulation
  18. Fulltext Simulation for supporting scale-up of a fluidized bed reactor for advanced water oxidation
    Tisa F, Raman AA, Daud WM
    ScientificWorldJournal, 2014;2014:348974.
    PMID: 25309949 DOI: 10.1155/2014/348974
    Simulation of fluidized bed reactor (FBR) was accomplished for treating wastewater using Fenton reaction, which is an advanced oxidation process (AOP). The simulation was performed to determine characteristics of FBR performance, concentration profile of the contaminants, and various prominent hydrodynamic properties (e.g., Reynolds number, velocity, and pressure) in the reactor. Simulation was implemented for 2.8 L working volume using hydrodynamic correlations, continuous equation, and simplified kinetic information for phenols degradation as a model. The simulation shows that, by using Fe(3+) and Fe(2+) mixtures as catalyst, TOC degradation up to 45% was achieved for contaminant range of 40-90 mg/L within 60 min. The concentration profiles and hydrodynamic characteristics were also generated. A subsequent scale-up study was also conducted using similitude method. The analysis shows that up to 10 L working volume, the models developed are applicable. The study proves that, using appropriate modeling and simulation, data can be predicted for designing and operating FBR for wastewater treatment.
    Matched MeSH terms: Computer Simulation
  19. Fulltext A modified active appearance model based on an adaptive artificial bee colony
    Abdulameer MH, Sheikh Abdullah SN, Othman ZA
    ScientificWorldJournal, 2014;2014:879031.
    PMID: 25165748 DOI: 10.1155/2014/879031
    Active appearance model (AAM) is one of the most popular model-based approaches that have been extensively used to extract features by highly accurate modeling of human faces under various physical and environmental circumstances. However, in such active appearance model, fitting the model with original image is a challenging task. State of the art shows that optimization method is applicable to resolve this problem. However, another common problem is applying optimization. Hence, in this paper we propose an AAM based face recognition technique, which is capable of resolving the fitting problem of AAM by introducing a new adaptive ABC algorithm. The adaptation increases the efficiency of fitting as against the conventional ABC algorithm. We have used three datasets: CASIA dataset, property 2.5D face dataset, and UBIRIS v1 images dataset in our experiments. The results have revealed that the proposed face recognition technique has performed effectively, in terms of accuracy of face recognition.
    Matched MeSH terms: Computer Simulation
  20. Fulltext Computational fluid dynamics modelling of microfluidic channel for dielectrophoretic BioMEMS application
    Low WS, Kadri NA, Abas WA
    ScientificWorldJournal, 2014;2014:961301.
    PMID: 25136701 DOI: 10.1155/2014/961301
    We propose a strategy for optimizing distribution of flow in a typical benchtop microfluidic chamber for dielectrophoretic application. It is aimed at encouraging uniform flow velocity along the whole analysis chamber in order to ensure DEP force is evenly applied to biological particle. Via the study, we have come up with a constructive strategy in improving the design of microfluidic channel which will greatly facilitate the use of DEP system in laboratory and primarily focus on the relationship between architecture and cell distribution, by resorting to the tubular structure of blood vessels. The design was validated by hydrodynamic flow simulation using COMSOL Multiphysics v4.2a software. Simulations show that the presence of 2-level bifurcation has developed portioning of volumetric flow which produced uniform flow across the channel. However, further bifurcation will reduce the volumetric flow rate, thus causing undesirable deposition of cell suspension around the chamber. Finally, an improvement of microfluidic design with rounded corner is proposed to encourage a uniform cell adhesion within the channel.
    Matched MeSH terms: Computer Simulation
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