Biological Computer Modeling / Biological Computer Simulation
mohamood borzouei; modjtaba emadi-baygi; mohammad mardaani; hasan rabani
Volume 17, Issue 1 , May 2023, , Pages 51-60
Abstract
It is critical for developing treatment strategies to investigate and analyze the growth dynamics and changes of invasive tumors in response to various microenvironmental conditions. When a tumor reaches its maximum amount of non-vascular growth, its cells compete for more food and oxygen sources, triggering ...
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It is critical for developing treatment strategies to investigate and analyze the growth dynamics and changes of invasive tumors in response to various microenvironmental conditions. When a tumor reaches its maximum amount of non-vascular growth, its cells compete for more food and oxygen sources, triggering complex processes in its evolution. Understanding the distribution of oxygen in the tumor environment is critical for unraveling the complexities of cancer progression. Existing physical models for studying oxygen distribution in tumors are based on reaction-diffusion equations, which include factors such as the formation and distribution of the new vascular network. In this study, we presented a computational model to investigate the distribution of oxygen in a hypoxic tumor based on the formation of the vascular network, which has fewer limitations and computational complexity than many common methods and reduces the volume of calculations. When complete with sufficient clinical data, this model can lead to the development of efficient tools in the treatment strategy of some cancers.
Biological Computer Modeling / Biological Computer Simulation
Sajad Shafiekhani; Amin Mashayekhi Shams; Seyed Yashar Banihashem; Nematollah Gheibi; Amir Homayoun Jafari
Volume 14, Issue 1 , May 2020, , Pages 55-67
Abstract
According to cancer’s global statistics, there will be 27.5 million new cases of cancer each year by 2040, therefore, it is crucial to achieve a deeper understanding of the cancer progression mechanisems and immune system functions in response to it. Nowadays, computational models are widely used ...
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According to cancer’s global statistics, there will be 27.5 million new cases of cancer each year by 2040, therefore, it is crucial to achieve a deeper understanding of the cancer progression mechanisems and immune system functions in response to it. Nowadays, computational models are widely used to capture dynamics of the tumor- immune system (TIS). The proposed model on this manuscript is on the basis of the ordinary differential equations which mechanistically models the interactions of tumor cells, CTLs, NKs and MDSCs. CTLs and NK cells are the most important cells of adaptive and innate immune system, respectively that encounter with tumor cells, while MDSCs as immature immune cells suppress the immune responses in the inflammatory environments. Due to the error of the in-vivo/in-vitro experiments, vagueness, imprecise information, incomplete data and natural variability of the tumor-immune system emerges between different individuals, the kinetic parameters of computational models are uncertain that this uncertainty can be captured by fuzzy sets. Hence, we assign fuzzy numbers with triangular membership functions instead of crisp numbers to some kinetic parameters of the tumor–immune system model. In fact, the uncertainty in the kinetic parameters of the ordinary differential equations affects the dynamic of the system species. In this essay, for the first time, a fuzzy number has been used to model the uncertainty of the parameters of the ODE model. Our data reveals that increasing/decreasing the uncertainty region of the model's fuzzy parameters increases/decreases the uncertainty region of dynamics of species. Furtheremore, the simulations of the model in the crisp setting of parameters show that the repition of 5-FU treatment for inhibition of MDSCs dramatically inhibits tumor cells and eradicate tumor.
Biofluid Mechanics / Biofluids
Mohammad Ahmadi Alashti; Bahman Vahidi; Mahtab Ebad
Volume 13, Issue 1 , April 2019, , Pages 1-15
Abstract
The large surface area of the lung with its thin air-blood barrier is exposed to particles in the inhaled air. In this condition, if the inhaled pollutant aerosols are toxic, the particle-lung interaction may cause serious hazards and injuries on human’s health. On the otherhand, these interactions ...
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The large surface area of the lung with its thin air-blood barrier is exposed to particles in the inhaled air. In this condition, if the inhaled pollutant aerosols are toxic, the particle-lung interaction may cause serious hazards and injuries on human’s health. On the otherhand, these interactions are also used for drug delivery to human’s body. In either case, an accurate estimation of dose and sites of deposition in the respiratory tract is fundamental for understanding mechanobiology of these deseases. Obtaining in vivo data of particle transportation in the human lung experimentally is often difficult. But, computational fluid-particle dynamics (CFPD) has provided the possibility to gain aerosol transportion data in realistic airway geometries. Aerosols deposition in the human lung mainly occurs due to combination of inertial impaction, gravitational sedimentation and diffusion. For particles with aerodynamic size of 0.5 to 5 micron and in inhalation state of lung, the main mechanisms of particle deposition in distal parts of human’s respiratory system are sedimentation, due to gravity and convective transfer due to wall movement. In this study, deposition of particles in distal part of human respiratory system, specifically 18th generation, has been modeled for two gravity conditions, normal and absent gravity, by assuming isotropic displacements on the walls and with the rate of 1 (mg/sec) for particle input. By analyzing the results, it was determined that the amount of particle deposition in distal airways reduces a great amount by omitting the effect of gravitational force because, particles smaller than 5 micron can penetrate into that airways. Particles with the diameter of 5 micron deposit under the effect of inertial impact, whereas this mechanism occurs mostly in airways with large and medium diameters and also, by sedimentation which occurs in the distal lung.
Biological Computer Modeling / Biological Computer Simulation
Somayeh Raiesdana
Volume 12, Issue 3 , November 2018, , Pages 249-263
Abstract
Sleep is an essential process to maintain and improve human activities, while many details related to sleep are still not well understood. Decreased or fragmented sleep is a health risk that might result in heart disease or diabetes on one hand and degradation of consciousness and cognition on the other ...
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Sleep is an essential process to maintain and improve human activities, while many details related to sleep are still not well understood. Decreased or fragmented sleep is a health risk that might result in heart disease or diabetes on one hand and degradation of consciousness and cognition on the other hand. Sleep fragmentation is a phenomenon in which an individual's sleep is intermittently disrupted by arousal caused by external factors (noise) or internal factors (apnea) although sleep deprivation does not completely occur. Computational modeling is a suitable framework for understanding complex biological mechanisms. In this paper, the fundamental phenomena underlying the sleep-wake transition was reviewed and simulated. The dynamical behavior of model was then investigated and afterwards the factors that might cause obstructive sleep apnea were implemented and evaluated. The model includes two main neuronal populations: the ascending arousal system in the brain stem that is responsible for awakening and a neuronal population in the hypothalamus, called VLPO, which mediates sleep. These populations have mutual inhibition on each other causing a flip-flop or switching behavior between sleep and wake. The results of modeling in this paper showed hysteresis in the sleep-wake cycle, the size of which is affected by factors causing arousal. In OSA, intermittent and unstable transitions as well as the shrinking of bistable zone is expected. The model could reproduce some experimental results related to obstructive apneas.
Biological Computer Modeling / Biological Computer Simulation
Reza Vosoughi; Armin Allahverdy; Sajjad Shafiekhani; Amir Homayoun Jafari
Volume 11, Issue 4 , February 2018, , Pages 291-301
Abstract
In recent decades, due to the increased prevalence of diabetes and its chronic complications, glucose measurement, modeling of glucose-insulin system and glucose control have been especially important. Since the type I diabetes does not secrete insulin, cells do not absorb glucose, and thus the blood ...
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In recent decades, due to the increased prevalence of diabetes and its chronic complications, glucose measurement, modeling of glucose-insulin system and glucose control have been especially important. Since the type I diabetes does not secrete insulin, cells do not absorb glucose, and thus the blood glucose level increase. In order to control your blood sugar, insulin should besubcutaneously injected into the body under complex, controlled conditions. If the level of insulin increases beyond the natural physiological range, there is a risk of death. There are various treatments for diabetes, the main treatment of which is insulin therapy. Monitoring the patient's blood sugar level continuously during the day and night is a very good treatment strategy, since it controls the patient's blood sugar level in a safe area with the lowest amount of insulin injected at the required times. This mechanism avoid the hyperglycemia (blood glucose levels greater than 120 mg/dl) and hypoglycemia (blood sugar less than 65 mg / dl). To achieve this goal, a two delay model has been developed to model blood glucose levels continuously during time. Some of the parameters of this model are estimated using the genetic algorithm to achieve the best fitness between the dynamics of the model with the experimental data obtained in this study. As a result, the developed model of this study can dynamically obtain blood glucose continuously during time, consequently it can predicts the insulin dynamics required to be injected into the patient to control the amount of blood glucose in the normal range. Therefore this controlling system is capable of preventing hypoglycemia and hyperglycemia.
Biological Computer Modeling / Biological Computer Simulation
Abbas Gholami; Amir Shamloo
Volume 11, Issue 4 , February 2018, , Pages 303-311
Abstract
PASylation is a new and effective way to increase the half-life of pharmaceutical proteins. This method is an alternative of PEGylaion and uses the natural polymers of Proline, Alanine, and Serine (PAS) amino acids in its structure. In this paper, we have studied the pharmacokinetic properties of PASylated ...
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PASylation is a new and effective way to increase the half-life of pharmaceutical proteins. This method is an alternative of PEGylaion and uses the natural polymers of Proline, Alanine, and Serine (PAS) amino acids in its structure. In this paper, we have studied the pharmacokinetic properties of PASylated Granulocyte-colony stimulating factor (G-CSF) using Molecular Dynamics (MD) simulation for three different PAS strings length 210, 420 and 630. We studied several important mechanical quantities involving in enhancing half-life time of the conjugated protein like root-mean-square distance (RMSD), hydrodynamic volume, protein total energy and its hydrophilicity and we found out volume expansion, increase in hydrophilicity amount and coil structure in PASylation are main mechanical properties influencing half-life time. We also found out that RMSD will be modified by PASylation while energy level shows erratic behavior examining the mentioned residues properties, we have also offered a modified sequence for PAS string according to the importance of different parameters in PAS string’s function.
Biological Computer Modeling / Biological Computer Simulation
Seyed Hojat Sabzpoushan; Fateme Pourhasanzade
Volume 11, Issue 1 , May 2017, , Pages 1-18
Abstract
In this paper, a new method is proposed for slowing down avascular tumor growth. Our method is established on an agent based avascular tumor growth model (ABM). The model is based on biological assumptions with regard to the immune system interactions. The model parameters are fitted in compatability ...
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In this paper, a new method is proposed for slowing down avascular tumor growth. Our method is established on an agent based avascular tumor growth model (ABM). The model is based on biological assumptions with regard to the immune system interactions. The model parameters are fitted in compatability with cancer biology using in vivo expremental data. The immune cells recruitment, which usually occur after that tumor cells are identified, are also considered in ABM model. The results show that the proposed model not only is able to simulate the tumor growth graphically, but also the in vivo tumor growth quantitatively and qualitatively. Besides, the model proposes a new idea for slowing down the tumor growth considering two types of prolaiferative tumor cells, i.e. the tumor will grow slowly if the division probability of the proliferative tumor cells depends on the microenvironmental conditions. The proposed idea has been validated using an in silico simulation.
Biological Computer Modeling / Biological Computer Simulation
Mohammad Reza Khodabakhshi; Amir Hossein Davaie Markazi
Volume 11, Issue 1 , May 2017, , Pages 63-81
Abstract
Nowadays, with technological advancements and increasing computing power, the use of mathematical models to describe the functioning of the brain in normal and abnormal manners, especially the study of the formation causes and methods of controlling and treating some nervous system diseases, such as ...
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Nowadays, with technological advancements and increasing computing power, the use of mathematical models to describe the functioning of the brain in normal and abnormal manners, especially the study of the formation causes and methods of controlling and treating some nervous system diseases, such as epilepsy, have become widespread and many models have been developed to simulate patterns appearing in the brain signals of these patients. One of the most commonly used types of modeling is neural mass models such as the Jansen-Rit model that those can simulate some of the essential brain patterns and rhythms that appear in the brain recorded signals. Therefore, in this paper, we have tried to provide a complete dynamical analysis of the Jansen-Rit model. To analyze this model, first, the equations of the model have been changed so that the output of the model be one of the system states variables. Then, the new equations have been nondimensionalized by defining a biological parameter (proportion of inhibition to excitation in neural populations of the model). In the following, the bifurcation diagram of the dimensionless model has been plotted with respect to nondimensional input and inhibition to excitation proportion parameters (codimension-two bifurcation) and the dynamical behavior of the system, such as bifurcations, periods and frequency of the limit cycles and time responses, have been investigated. Further, we have discussed two significant behaviors in this model, spike-and-wave discharges (SWDs) and alpha rhythms. In the present paper, we have been shown how these models can describe complex disease such as epilepsy and have been mentioned dynamical mechanism underlying transition from a normal state (background activity) to an abnormal situation (epileptic seizures). The innovations of this study one can be the definition of the new meaningful and significant biological parameter in the dimensionless model that all dynamical analysis are based on it. Also, some bifurcations and, consequently, some of the behaviors observed in the model are for the first time reported. Moreover, this new parameter contains two primary model parameters and then the effect of three parameters simultaneously in the system behavior has been investigated.
Biological Computer Modeling / Biological Computer Simulation
Fateme Pourhasan Zade; Seyed Hojat Sabzpoushan; Ali Mohammad Alizade; Ebrahim Esmati
Volume 10, Issue 2 , August 2016, , Pages 99-112
Abstract
Cancer is the third leading cause of death in Iran after cardiac diseases and car accidents. Mathematical and computational models are great help to better understand cancer related phenomena. It may even improve common therapies or introduce new therapies. In this paper, a new multiscale cellular automata ...
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Cancer is the third leading cause of death in Iran after cardiac diseases and car accidents. Mathematical and computational models are great help to better understand cancer related phenomena. It may even improve common therapies or introduce new therapies. In this paper, a new multiscale cellular automata model of tumor growth based on the tumor micro-environment is introduced. Two separate square lattices are presumed for metabolic and cellular spaces. One of the following four states can be devoted to each cell in the cellular lattice: proliferating cancer, non- proliferating cancer, necrotic, and normal cells. Changing the cell's state and tumor growth is discussed in this lattice. However, production/consumption, and the diffusion of nutrients (oxygen and glucose) and also waste products including lactic acid are studied in the metabolic lattice. In this study, we determined the stochastic rules of altering the states of each cell based on the concentration rates of nutrients and lactic acid. The growth fraction and necrotic fraction were used as output parameters beside a 2-D graphical display of growth. The changes in the level of nutrients in the metabolic lattice and the effect of acidity on the growth of tumor have been reported in this paper. Our simulations faithfully reproduce the in vivo experimental observations reported for cholangiocarcinoma.
Biological Computer Modeling / Biological Computer Simulation
Mahdie Roghani Yazdi; Nadia Naghavi; Faride Sadat Hosseini
Volume 9, Issue 2 , July 2015, , Pages 143-161
Abstract
A tumor cannot grow more than a few millimeters without a blood supply (avascular tumor), and for further growth it must initiate angiogenesis process. A vascularized tumor, which is permeated with blood vessels, rapidly increases in mass because of the new source of oxygen. In this study, a discrete ...
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A tumor cannot grow more than a few millimeters without a blood supply (avascular tumor), and for further growth it must initiate angiogenesis process. A vascularized tumor, which is permeated with blood vessels, rapidly increases in mass because of the new source of oxygen. In this study, a discrete mathematical model of angiogenesis process with considering the penetration of blood flow through the vessels in the two-dimensional network is presented. This structure is coupled with an adaptive model of sprouts spacing along the parent blood vessel at the beginning of the angiogenesis process. Then, progression of these sprouts in the extracellular matrix and their penetration into the tumor as well as penetration of blood flow through the capillary structure is presented. This model incorporates three steps of adaptive sprout spacing along the parent blood vessel, sprout progression, and blood flow and network remodeling. Then, based on the simulated vasculature network, oxygentransmission and other vital chemicals needed for continuous tumor growth are simulated. In this model we assumed that the growth of the tumor is driven by cell division. The tumor growth and angiogenesis are coupled by the changes of micro environment including oxygen, tumor growth factor, and the extracellular matrix concentration. Also, we have tried to create space and time adaptations in parameters of the model.
Biological Computer Modeling / Biological Computer Simulation
Seyed Hojat Sabzpoushan; Niloofar Shahidi; Azadeh Ghajarjazy
Volume 9, Issue 4 , February 2015, , Pages 351-360
Abstract
Abnormal oscillations of ventricular cell action potential can lead to cardiac arrhythmias. Early afterdepolarizations (EADs) is one kind of these oscillations that have been widely studied in the field of cardiac arrhythmias diagnosis and therapies. Nowadays although ventricular cell models have been ...
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Abnormal oscillations of ventricular cell action potential can lead to cardiac arrhythmias. Early afterdepolarizations (EADs) is one kind of these oscillations that have been widely studied in the field of cardiac arrhythmias diagnosis and therapies. Nowadays although ventricular cell models have been developed, yet dynamical mechanisms of EADs remain unknown that need more researches. In this paper, using phase plane analysis of a minimal model of ventricular cell, we show that EADs are occurred as a result of Hopf and homoclinic bifurcations in ventricular cell. We also show that during period pacing, chaos happens at the transition from no EAD to EADs. This result provides a distinct explanation for the EAD behavior of the cardiac cells and also explains EADs dynamics in accordance with experiment results. While this research was performed for ventricular cells, but the achieved results can be extend to other excitable systems and used in the prediction of oscillation due to the changes of system parameters.
Biological Computer Modeling / Biological Computer Simulation
Mohammad Jazlaeiyan; Hadi Shahriar Shahhoseini
Volume 8, Issue 4 , February 2015, , Pages 371-383
Abstract
Human visual system operates superior than best machine vision systems in object recognition. So, researchers in machine vision and neuroscience try to model human visual system in order to employ it in machine. HMAX is one of the best operating models in this area. It is based on the function of brain ...
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Human visual system operates superior than best machine vision systems in object recognition. So, researchers in machine vision and neuroscience try to model human visual system in order to employ it in machine. HMAX is one of the best operating models in this area. It is based on the function of brain cells in the ventral stream of visual cortex and contains four computational layers. In the learning stage, many image partitions called image patches are extracted randomly with different sizes from training images. This random selection of image patches is one of the drawbacks of HMAX which decreases the performance and increases the computational complexity of the algorithm. In this paper, a novel patch selection from the set of random patches is proposed. In this method, using a recursive approach, optimal patches are selected from optimal features of training images by mutual information maximization feature selection. The performance of proposed algorithm in binary classification (existence or non-existence of objects in the images) is compared with HMAX and the superiority is proved.
Biomechanics of Bone / Bone Biomechanics
Mohammad Nikkhoo; Ali Tahassori; Mohammad Haghpanahi
Volume 8, Issue 3 , September 2014, , Pages 203-212
Abstract
To develop the advanced technologies in medical device industry, design and manufacturing of cervical cage was performed in Iran for the first time. This research-based industrial project should be accomplished based on precise biomechanical studies and mechanical tests. Hence, this study presents the ...
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To develop the advanced technologies in medical device industry, design and manufacturing of cervical cage was performed in Iran for the first time. This research-based industrial project should be accomplished based on precise biomechanical studies and mechanical tests. Hence, this study presents the optimization and biomechanical functional investigations of the first Iranian cervical cage (Manufactured by Attila Ortopaed Co.). For this purpose the intact cervical spine (C2-C7) was developed and was validated with in-vitro experiments. Three inputs (i.e. geometrical parameters of the cage) and two outputs (i.e. deformation of the teeth in static and dynamic tests) parameters were selected for optimization procedure. Furthermore, the surgery in C5-C6 level was simulated by implanting the cervical cage. Finally, the biomechanical responses were investigated. The result confirmed that the biomechanical response of cervical cage is within the standard range and can be used well in clinics for surgical procedures.
Cardiovascular Biomechanics
Farzad Forouzandeh; Mahdie Haji-Bozorgi; Behrooz Meshkat; Nasser Fatouraee
Volume 8, Issue 3 , September 2014, , Pages 241-248
Abstract
Coronary Artery Diseases are one of the main reasonsof mortality. When these arteries occlude, usually a CoronaryArtery Bypass Graft (CABG) surgery is performed. Sine humanSaphenous Veins (SV) is used for CABG, they are of interest forresearchers. In this study human SV samples undergo inflationtest, ...
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Coronary Artery Diseases are one of the main reasonsof mortality. When these arteries occlude, usually a CoronaryArtery Bypass Graft (CABG) surgery is performed. Sine humanSaphenous Veins (SV) is used for CABG, they are of interest forresearchers. In this study human SV samples undergo inflationtest, using an inflation test device. Displacements of the samplesfor different pressures are analyzed, and average values are usedas input of a computational method. In the numerical simulationthe tissue is assumed as an elastic, isotropic, and homogenoussolid material, and its output is Young’s Modulus (E) ofthetissue. Results show that E of the SV increases linearly with thedistension pressure. Although simplifications were applied in thisstudy, it can be helpful for giving a basic insight aboutmechanical properties of human Saphenous Vein, which can befollowed by more realistic studies in the future.
Biological Computer Modeling / Biological Computer Simulation
Gelare Valizadeh; Fateme Fatemi; Mahmoud Shahabadi; Mohammad Ali Oghabian; Majid Pouladian
Volume 8, Issue 2 , June 2014, , Pages 125-133
Abstract
MTDDS is an innovative treatment modality to completely tumor remission with no negative side effect. In this method functionalize magnetic nanoparticles are designed as the drug carrier to get the specific target in the body. Anticancer agents are bounded to magnetite nanoparticles with biocompatible ...
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MTDDS is an innovative treatment modality to completely tumor remission with no negative side effect. In this method functionalize magnetic nanoparticles are designed as the drug carrier to get the specific target in the body. Anticancer agents are bounded to magnetite nanoparticles with biocompatible starch coating suspended in the fluid. Now if they are injected intra-arterially near the target volume, they would be trapped at the target region via a local applied magnetic field with the high gradient near the target site. In this paper we have evaluated some nanoparticle trajectories with different size in order to evaluate the effect of the size on the efficiency of the magnetic drug targeting system.
Tissue Engineering
Zakieh Alihemmati; Bahman Vahidi; Nooshin Haghighipour
Volume 8, Issue 2 , June 2014, , Pages 135-149
Abstract
Body cells, including mesenchymal stem cells are subject to a lot of mechanical forces. The type and magnitude of these forces are different in different physiological and pathological conditions. They cause a wide variety of cell responses and are able to change metabolisms and functions of the cell. ...
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Body cells, including mesenchymal stem cells are subject to a lot of mechanical forces. The type and magnitude of these forces are different in different physiological and pathological conditions. They cause a wide variety of cell responses and are able to change metabolisms and functions of the cell. Analysis of stem cell response to mechanical stimulation is very important in recognizing healthy and diseased condition of tissues and cells. Differentiation potential of mesenchymal stem cells to specialized cells makes them important cell sources in tissue engineering. In this study, atomic force microscopy and finite element method and used mechanical effects on a stem cellaresimulated which includes cell behavior due to strain andstress distributions in internal components of the cell. In this study, the ADINA software used to simulate mechanical behavior of the cell components (cell membrane, cytoplasm and nucleus) under a compressiveload. Results indicate mechanical response of stem cells in the body through which they can differentiate into bone cells and cartilage under compressive loads in the physiological range. This study has some considerable innovations as compared with the similar studies in the literature which is because of the kind of cells has been used (adipose-derived stem cells) as well as and also using precise material models for cell components based on the data extracted from laboratory tests for mechanical properties of the cell. Furthermore, this study can be considered as an important initial step for future studies on different patho-cells and analyzing their responses to mechanical loading using a similar method of this study to find new diagnostic methods. Also, it can be used to deepen pathological studies of the cells and the tissues.
Bioelectromagnetics
Mohammad Reza Yousefi; Reza Jafari; Hamid Abrishami Moghaddam
Volume 8, Issue 1 , March 2014, , Pages 69-86
Abstract
In this paper, a combined wavelet based mesh free method has been presented to solve the forward problem in magnetic induction tomography (MIT). Being a non-contact safe imaging technique, MIT has been an appropriate method for noninvasive industrial and medical imaging. In this imaging method, a primary ...
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In this paper, a combined wavelet based mesh free method has been presented to solve the forward problem in magnetic induction tomography (MIT). Being a non-contact safe imaging technique, MIT has been an appropriate method for noninvasive industrial and medical imaging. In this imaging method, a primary magnetic field is applied by one or more excitation coils to induce eddy currents in the material to be studied, and then the secondary magnetic field from these eddy currents is detected in sensing coils. Image reconstruction is obtained from estimated electric conductivity coefficients by using measurement data and solutions of forward and inverse problems. In general, the forward problem is solved using finite element method (FEM) with acceptable accuracy but in problems involving moving objects or objects with changing geometrical appearance, mesh distortion is inevitable and susceptible to producing error in numerical results. Since the solution of the FEM depends on the mesh shape and boundary condition constraints are difficult to be applied to the mesh free method, in this paper, the combined wavelet based mesh free approach is suggested to resolve the disadvantages of both methods in the MIT forward problem. In order to apply interface conditions between the two finite element and mesh free sub-domains, slope jump functions are entered to the set of basis functions. The simulation results obtained by the proposed method are compared with the FEM in terms of accuracy and computational cost.
Biomimetics
Mohammad Reza Nikmaneshi; Bahar Firoozabadi; Mohammad Saeid Saeidi
Volume 7, Issue 2 , June 2013, , Pages 97-105
Abstract
The front part of a cell is divided to two regions called lamellum and lamellipodium (lamellipodial). Internal flows in this part plays an essential role for cell migration. Indeed, there are many protein filaments called actin in lamellum and lamellipodium, which induce the cell motion with polymerization ...
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The front part of a cell is divided to two regions called lamellum and lamellipodium (lamellipodial). Internal flows in this part plays an essential role for cell migration. Indeed, there are many protein filaments called actin in lamellum and lamellipodium, which induce the cell motion with polymerization in the leading edge of the cell. The actin filaments adhere to the extracellular matrix (ECM) by means of focal adhesions and they have contact by myosin motor proteins. The myosin motor proteins cause actin retrograde and anterograde flow exerted contractile stress on them. The focal adhesions exert frictional stress on the actin filaments. In this work, we developed a two-dimensional continuum model of the fanshaped lamellipodial to obtain the actin retrograde flow. In addition, the actin filaments are assumed as a highly viscous Newtonian fluid. We also investigated the effects of the myosin distribution and cell speed on the actin flow. Our results include actin flow and myosin distribution in the moving cell, and we also illustrate their relation together. These results accord to reported experimentally and numerically data, and are verified with them.
Robotic Surgery / Robot-Assisted Surgery
Marzie Saeidirad; Heidar Ali Talebi; Mohammad Zareinejad; Mohammad Reza Dehghan
Volume 7, Issue 4 , June 2013, , Pages 287-296
Abstract
Computationally fast biomechanical models are required to present the actual behavior of soft tissue in real-time simulation. These models are applied in medical diagnosis, surgical planning and training. One of the challenges in the surgical simulation is soft tissue cutting that requires topology changes ...
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Computationally fast biomechanical models are required to present the actual behavior of soft tissue in real-time simulation. These models are applied in medical diagnosis, surgical planning and training. One of the challenges in the surgical simulation is soft tissue cutting that requires topology changes and elements remeshing in real-time.This paper present a new algorithm for soft tissue cutting using its geometric analysis. This method creates a less number of degrees of freedom and shows a stable simulation that leads in less tissue damage as compared to other methods. According to the simulation results, the proposed algorithm has a relatively high speed. In addition, a mapping method has been proposed that relates physical and visual model and consequently shows a more realistic surgery. In order to achieve a physics based, accurate and reliable force model, Finite Element Method is used. Finally, the proposed algorithm is simulated for three-dimensional soft tissue tumor and evaluated using the SOFA-Framework.
Biological Computer Modeling / Biological Computer Simulation
Seyed Hojat Sabzpoushan; Fateme Pourhasan Zadeh; Zohre Agin
Volume 7, Issue 1 , June 2013, , Pages 65-73
Abstract
A great number of people are diagnosed with a brain tumor, annually. Glioblastoma multiform (GBM) is the most common and deadliest malignant primary brain tumor. Therefore, the study of the growth of GBM is one of the issues considered by researchers. Many mathematical models to simulate the growth of ...
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A great number of people are diagnosed with a brain tumor, annually. Glioblastoma multiform (GBM) is the most common and deadliest malignant primary brain tumor. Therefore, the study of the growth of GBM is one of the issues considered by researchers. Many mathematical models to simulate the growth of GBM brain tumor have been proposed. These models help scientists to understand the process of tumor growth in order to achieve effective treatment. To simulate the tumor growth, a four dimensional (4D) model using cellular automata (CA) method is presented in this paper. A three dimensional (3D) lattice constituted by Voronoi tessellation is used. Spatial distribution of grid points in 3D has been generated by using Random Sequential Addition (RSA). In the utilized lattice, each cell is a polyhedron with various number of edges and neighboring. Delaunay triangulation is applied to find neighboring cells. Each cell in this lattice can be necrotic, non-proliferative, proliferative, non-tumorous or normal. The simulation is capable to exhibit a tumor growth of 0.1 mm to 25 mm in radius. The proposed model has been compared with experimental data in four temporal stages: spheroid, detectable lesion, diagnosis and death. Studies show that the accuracy of the presented model is generally about 85%.
Biological Computer Modeling / Biological Computer Simulation
Hosein Ghasemi; Mohammad Saeid Saeidi; Bahar Firoozabadi
Volume 7, Issue 3 , June 2013, , Pages 255-264
Abstract
Knowledge regarding particle deposition processes in the pulmonary system is important in aerosol therapy and inhalation toxicology applications. The present work describes a computational model of human lung airway consisting of the three-generation pathway from the trachea down to segmental bronchi. ...
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Knowledge regarding particle deposition processes in the pulmonary system is important in aerosol therapy and inhalation toxicology applications. The present work describes a computational model of human lung airway consisting of the three-generation pathway from the trachea down to segmental bronchi. In order to more appropriately model human air passage, an asymmetric geometry (i.e. three generation airway) is extracted from the 1th to 3th branches of the Hoursfield model and on dealing with the complexities of simulations (e.g. computation time) structured mesh is developed which also leads to more accurate computations. The fully three-dimensional incompressible laminar Navier– Stokes equations and continuity equation have been solved using CFD home code on generated mesh. Computations are carried out in the Reynolds number range of 800–1800, corresponding to mouthair breathing rates ranging from 0.18 to 0.41 l/s, representative. The study leads to establishing relations for overall particle deposition efficiency in the second generation of bronchial tree as a function of two dimensionless groups of Reynolds and Stocks numbers. Furthermore, interpretation of correlations are enlightened the fact of that in the initial generations of bronchial trees, consideration of asymmetric geometry has a significant influence on the particle deposition pattern. The results of the paper are valuable in aerosol therapy and inhalation toxicology.
Orthotics & Prosthesis
Mostafa Lashgari; Farzan Ghalichi; Behnam Mirzakouchaki
Volume 7, Issue 4 , June 2013, , Pages 341-349
Abstract
Orthodontic specialists interest in study of tooth movement mechanic, such as the relationship between applied force and the rate of tooth movement in orthodontic treatment. It is because of the complexity and variety of factors that can affect orthodontic treatment. The friction force at the contact ...
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Orthodontic specialists interest in study of tooth movement mechanic, such as the relationship between applied force and the rate of tooth movement in orthodontic treatment. It is because of the complexity and variety of factors that can affect orthodontic treatment. The friction force at the contact surfaces with an undetermined magnitude, makes the orthodontic treatment unpredictable. In this study, friction coefficient and forces were investigated in new designed bracket that had beveled edge which has been modeled based on standard bracket. Torque, tip and angulations angles of the brackets slot are designed. Arch wires were modeled by two rectangular and circular cross-sections and the effect of geometry on the stress distribution and the friction force was investigated using Finite Element Method (FEM). The results have showed that the stress concentration generated in the bracket which has been the most curvature, decreased compared to the standard bracket at the contact wire and bracket braces. In addition, results have showed that friction in the beveled edge bracket was significantly decline compared to the standard bracket and also are less than the type with minor curvature. Results of investigation of friction between the two types of round and square wire, have revealed that the round wire has lower friction and confirmed previous studies. Finally, due to the reduced friction in the brackets which have been the most curvature, this type of design is appropriate to decrease friction force.
Biomedical Signal Processing / Medical Signal Processing / Biosignal Processing
Mina Amiri; Edmond Zahedi; Fereydoun Behnia
Volume 7, Issue 1 , June 2013, , Pages 85-95
Abstract
It is proved that the endothelial (artery inner lumen cells) function is associated with cardiovascular risk factors. Among all the common non-invasive methods employed in the research setting for assessing endothelial function, flow-mediated dilation is the most widely used one. This technique measures ...
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It is proved that the endothelial (artery inner lumen cells) function is associated with cardiovascular risk factors. Among all the common non-invasive methods employed in the research setting for assessing endothelial function, flow-mediated dilation is the most widely used one. This technique measures endothelial function by inducing reactive hyperemia using temporary arterial occlusion and measuring the resultant relative increase in blood vessel diameter via ultrasound. In this paper, the limitations associated with the ultrasound technique are overcome by using the photoplethysmogram (PPG) signal recorded during FMD. The correctness of this approach is investigated by modeling the AC changes of PPG after FMD by a 2nd order autoregressive model. A sensitivity of 78.6%, specificity of 81.6% and total accuracy of 80% were achieved in classification of 16 healthy and 14 diabetic subjects.
Biomimetics
Behzad Seyfi; Hosein Mansourinejad; Bahman Vahidi; Nasser Fatouraee
Volume 6, Issue 3 , June 2012, , Pages 169-175
Abstract
Peristaltic flow is one of the important mechanisms of fluid transmission. In addition to the divers engineering applications, this mechanism plays an important role in biological organs such as digestion system and urine excretion. In this paper, urine bolus transportation in ureter has been investigated ...
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Peristaltic flow is one of the important mechanisms of fluid transmission. In addition to the divers engineering applications, this mechanism plays an important role in biological organs such as digestion system and urine excretion. In this paper, urine bolus transportation in ureter has been investigated experimentally using a peristaltic flow simulator apparatus. Some of the features of this apparatus worth mentioning are its ability to use it to investigate the influence of some important parameters in peristaltic flow, such as the effect of pressure difference between the kidney and the bladder on the quantity of discharge and reflux rates, effect of the mean velocity of bolus transport on discharge rate, existence of fluid film and its effect on bolus discharge rate, and effect of fluid bolus length on reflux rate. Then we compare the obtained results with the similar theoretical studies. It was observed that an increase in the pressure difference between inlet and outlet decreases the ratio of reflux to initial volume of the bolus, and it increases the discharge rate. Moreover, the quantities of reflux and discharge rate decrease by decreasing the bolus transport velocity. It was also observed that the thickness of the fluid film has an inverse relation with respect to the discharge rate and with increasing the bolus length reflux is increasing.
Fluid-Structure Interaction in Biological Media / FSI
Alireza Hashemi Fard; Nasser Fatouraee
Volume 5, Issue 1 , June 2011, , Pages 1-12
Abstract
The heart muscle is supplied via the coronary arteries. The coronary arteries are deformed in each cardiac cycle by the contraction of the myocardium. The aim of this work was to investigate the effects of physiologically idealized cardiac-induced motion on flow rate in human left coronary arteries. ...
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The heart muscle is supplied via the coronary arteries. The coronary arteries are deformed in each cardiac cycle by the contraction of the myocardium. The aim of this work was to investigate the effects of physiologically idealized cardiac-induced motion on flow rate in human left coronary arteries. The blood flow rate were numerically simulated in an elastic modeled left anterior descending coronary artery (LAD) having a uniform circular cross section. Blood was considered to be a non-Newtonian fluid and Arterial motion was specified based on monoplane physiologically idealized bending. Simulations were carried out with dynamic pressure difference conditions between inlet and outlet in both fixed and moving LAD models, to evaluate the relative importance of LAD motion, flow rate, and the interaction between motion and time-averaged flow rate. LAD motion was caused variations in time-averaged flow rate in the moving LAD models as compare as the fixed models. There was significant variability in the magnitude of this motion-induced flow variation. However, the magnification of time-averaged flow rate is depending to specification of the cardiac motion. Furthermore, the effects of pressure pulsatility dominated LAD motion induced effects; specifically, there were local flow variation and secondary flow in the simulations conducted in moving LAD models.
