Biological Systems Modeling
Hossein Banki-Koshki; Seyyed Ali Seyyedsalehi
Volume 17, Issue 2 , September 2023, , Pages 100-110
Abstract
Neuronal synchronization as a significant cognitive phenomenon of the human brain, has attracted the interest of neuroscience researchers in recent years. This phenomenon is generally investigated in discrete and continuous neuronal models or experimentally recorded signals of the brain. In this study, ...
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Neuronal synchronization as a significant cognitive phenomenon of the human brain, has attracted the interest of neuroscience researchers in recent years. This phenomenon is generally investigated in discrete and continuous neuronal models or experimentally recorded signals of the brain. In this study, for the first time, we investigate the weight synchronization instead of neuronal synchrony, in the training step of the artificial feedforward neural networks. The findings of the study show that the generalized weight synchronization occurs both during the training mode and in the non-training mode. Furthermore, as the training is completed, the synchronization increases between the weights. In this study, a new method is introduced in order to detect synchrony patterns using signal derivative and hierarchical clustering. We have also presented a criterion to quantify weight synchronization in different layers of the neural network. Accordingly, the results demonstrate that the lower layers of the network have a significantly higher level of weight synchrony than the upper layers.
Medical Robotics / Bio-Robotics
Elaheh Kafashi; Mohammad Ali Ahmadi Pajouh; Firooz Bakhtiari Nejad
Volume 14, Issue 4 , February 2021, , Pages 277-290
Abstract
Due to the high number of patients with cerebrovascular disease and stroke, which results in paralysis of organs on one side of the body, including the hand, as well as limitations in traditional rehabilitation methods, it is necessary to build devices to help these people. In this study, initially, ...
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Due to the high number of patients with cerebrovascular disease and stroke, which results in paralysis of organs on one side of the body, including the hand, as well as limitations in traditional rehabilitation methods, it is necessary to build devices to help these people. In this study, initially, given the challenges involved in designing an exoskeleton, the initial design was a mechanism for using it as a continuous passive motion to rehabilitate the fingers. This mechanism is tendon-based and covers both the flexion and extension of the fingers. For this purpose, two active and passive actuators have been used in the exoskeleton, respectively, to flex and extend the fingers. The distinctive feature of this design is its lightness, low volume, adjustability for different hands, compatibility, and comfort for the patient. Also, the kinematics and dynamics relationships modeled on the Lagrange method. The exoskeleton movement simulated in interaction with the finger with MATLAB sim-mechanics software. Finally, using simulation and modeling results, the final design was performed by considering the force of 40 N along the tendon, the exoskeleton made for the index finger. Also, the results of analytical modeling and simulation compared; the error rate of modeling obtained. In the worst case, this value was 15% for the first and second finger joints and 20% for the third joint.
Biological Systems Modeling
Seyede Fatemeh Ghoreishian Amiri; Mohammad Pooyan
Volume 14, Issue 4 , February 2021, , Pages 321-331
Abstract
Parkinson's disease (PD) is a neurological disorder that mainly affects dopamine-producing neurons and motor system. The most obvious symptoms of PD are tremor, slow movement, stiffness and difficulty with walking. Walking in PD is slower than normal walking. In this paper, the gait in patients ...
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Parkinson's disease (PD) is a neurological disorder that mainly affects dopamine-producing neurons and motor system. The most obvious symptoms of PD are tremor, slow movement, stiffness and difficulty with walking. Walking in PD is slower than normal walking. In this paper, the gait in patients with PD is modeled by a mathematical and computational method. This model includes structures which are involved in PD, such as basal ganglia, thalamus, cortex, supplementary motor area (SMA), muscle and joint-load dynamics. The output of the model is walking speed in PD. The output value is 0.83 m/s, which is in the range reported by clinical results (0.18-1.21 m/s). Some methods which increase the gait speed in PD are investigated too. These methods include deep brain stimulation, drug prescription and strengthening the muscles. The results show that each of these methods will improve the gait speed, in fact, by using these methods, the value of output increases and approaches the walking speed range in healthy individuals (1.36-1.30 m/s). Moreover, the effect of rigidity on gait speed is studied; it has been observed that the stiffness and speed of the gait are inversely related. Finally a control method is offered which improve the gait speed by increasing the magnitude response of the closed-loop system.
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%.
Neuro-Muscular Engineering
Ali Falaki; Farzad Towhidkhah
Volume 5, Issue 2 , June 2011, , Pages 127-141
Abstract
Based on previous studies, human motor control system may apply two control strategies, impedance control and model based control, for learning motor skills and counteracting environmental instabilities. Since interaction among these controllers is not fully studied, the investigation of impedance and ...
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Based on previous studies, human motor control system may apply two control strategies, impedance control and model based control, for learning motor skills and counteracting environmental instabilities. Since interaction among these controllers is not fully studied, the investigation of impedance and model based controllers function during learning period seems desirable. In this study a supervisory controller was used to coordinate the model based and impedance controllers. Coordinating model based controller and impedance controller by using supervisory unit will result in simultaneously adjustment of forward motor command and joint stiffness. In order to evaluate performance of the suggested model, it was applied to arm reaching movements in the presence of external force fields. Results showed that both suitable impedance values and a proper internal model are required to fulfill movements similar to those of humans under different circumstances. Research has shown that central nervous system is able to purposefully modulate arm impedance to counteract environmental disturbances. This study showed that beside this modulation, the maximum motor learning may occur in direction with the least impedance and the most kinematic error. It also concluded that confronting abrupt changes in disturbance, the system managed to decrease error without learning the new dynamic using previous knowledge by supervisory system. A part of this compensation is due to stiffness variations and another part is due to decreasing the influence of model based controller.
Neuro-Muscular Engineering
Amir Hosein Eskandari; Ehsan Sedaghat Nejad; Seyed Javad Mousavi; Mohsen Asghari; Mohammad Parnianpour
Volume 5, Issue 3 , June 2011, , Pages 257-273
Abstract
Selection of muscle activation pattern to reach a specific goal by considering the complexities of neuromuscular system and the way it overcomes these complications, is of researchersinterest in motor control. One proposed solutionfor resolving thesecomplexities is the concept of simple module (synergies) ...
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Selection of muscle activation pattern to reach a specific goal by considering the complexities of neuromuscular system and the way it overcomes these complications, is of researchersinterest in motor control. One proposed solutionfor resolving thesecomplexities is the concept of simple module (synergies) that the combination of them leads to more complex activities. In the present work, the existence and arrangement of synergies in the lumbar spine are proved. For this purpose, a model with 18-muscles in level L4-L5 is utilized in the static condition. In order to obtaina muscular and stability synergies, muscle activation, which are obtained by exerting moments in 2D and 3D spaces and angular stiffness to the model,are used. The results show that six muscular synergies suffice to be able to reach any point in the moment space. Also, three stability synergies can reconstruct a part of joint angular stiffness space. In addition, the obtained muscular synergies are robust against changes in the amplitude of exerted moment. In this study, it is shown that one can generates any task involves producing determined moment and angular stiffness in the joint, by combining muscular and stability synergies together.
Biomechanical Motor Control / Motor Control of Human Movement
Hamed Ghomashchi; Ali Esteki; Ali Motie Nasrabadi; Fereydoun Nowshiravan Rahatabad
Volume 4, Issue 3 , June 2010, , Pages 177-185
Abstract
In this study a simple inverted pendulum model with PID controller and delayed feedback is used to model standing-still postural control system for the purpose of achieving useful information about its underlying control structure. Using the Genetic algorithm and an experimental study results, the model ...
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In this study a simple inverted pendulum model with PID controller and delayed feedback is used to model standing-still postural control system for the purpose of achieving useful information about its underlying control structure. Using the Genetic algorithm and an experimental study results, the model and the controller parameters were estimated in a way that the model mimics real experimental sway patterns. The controller parameters found meaningful interpretations and it is shown that degeneration of postural control system affects the values of the parameters. Our findings indicate that although the simple models are not able to describe complexities of postural control system and interactions between its components, they can help us to improve our understanding of postural control system, its performance, its features and the way that the features change.
Targeted Drug Delivery / Smart Drug Delivery / Drug Targeting
Nadia Naghavi; Amene Sazgarnia; Mohammad Hossein Miranbaygi
Volume 4, Issue 3 , June 2010, , Pages 209-218
Abstract
Today, the idea of photodynamic therapy (PDT) is considered as one of the fundamental basis of the new cancer treatment methods. One of the important issues in the application of this therapy is choosing the optimal dosimetry method. At best, PDT dosimetry should be done based on estimation of the accumulated ...
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Today, the idea of photodynamic therapy (PDT) is considered as one of the fundamental basis of the new cancer treatment methods. One of the important issues in the application of this therapy is choosing the optimal dosimetry method. At best, PDT dosimetry should be done based on estimation of the accumulated singlet oxygen dose within the target tissue and comparison with the threshold value to ensure the efficacy of the treatment. In order to estimate the accumulated singlet oxygen level within the tissue, the most appropriate method is modeling the process of treatment. In this context, it is necessary to obtain enough information about the drug concentration within the target tissue, the amount of light absorbed by the drug, the amount of oxygen into the tissue, and the interactions between them that produce singlet oxygen. In this study modeling and simulation of the photobleaching has been investigated, considering the importance of the level of drug concentration in the target tissue which would be decreased by photobleaching. Simulation was done with Matlab software. A Comparison of simulation results with those of experimental methods showed that in the state of non-uniform drug distribution, simulation follows experimental results at the initial phase of rapid decline of drug concentration.
Tissue Engineering
Fateme Shamsi; Mohsen Janmaleki; Nasser Fatouraee
Volume 3, Issue 4 , June 2009, , Pages 265-274
Abstract
In this study a mechanism was modeled to control the jet path of nanofibers produced by electrospinning through inducing a magnetic field over the jet path. Firstly, a model was developed for the jet path in which the fibers composed of a series of viscoelastic segments. Considering the mass and momentum ...
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In this study a mechanism was modeled to control the jet path of nanofibers produced by electrospinning through inducing a magnetic field over the jet path. Firstly, a model was developed for the jet path in which the fibers composed of a series of viscoelastic segments. Considering the mass and momentum conservation and maxwellian model of stretching viscoelastic segments using three equations governing the jet dynamics of the jet model in electrospinning, a program was developed in MATLAB with Runge–Kutta method. After ensuring the accuracy of the model, its behavior was evaluated in the presence of a magnetic field. The field induced a uniform force distribution over the jet. As the intensity of the magnetic field increased; the instability and bending radius of the jet reduced. The results of the research showed that utilizing a suitable mechanism for applying magnetic field can provide help in controlling the jet path and alignment of the nanofibers.
Gait Analysis
Mohsen Sadeghi Mehr; Davoud Naderi; Nader Farahpour; Saeed Davoud Abadi Farahani
Volume 3, Issue 3 , June 2009, , Pages 179-187
Abstract
The present study was devoted to determine the standing human body reactions to perturbation of a base plate in the frontal plane, in order to preserve its stability. A base plate with sinusoidal fluctuation was designed and built and then markers were mounted on the specified locations on it and the ...
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The present study was devoted to determine the standing human body reactions to perturbation of a base plate in the frontal plane, in order to preserve its stability. A base plate with sinusoidal fluctuation was designed and built and then markers were mounted on the specified locations on it and the skin of subjects before testing. During testing the subjects (N=10) tried to preserve their stability against perturbations. By using Motion Analysis System, the body responses of subjects were analyzed. Using inverse dynamic methods and experimental kinematic results, forces and moments applied to the joints and between feet soles and the base plate were determined. In theoretical study, the kinematic and dynamic equations of motion of a robotic model of human body in frontal plane by using repetitive Newton-Euler method were obtained. Based on the stability of the model and supporting vertical forces criterion an object function was defined, in order to assure the stability of the model. By optimization of the object function, angle of the model joints under perturbation and its first and second derivatives were determined. The good agreement of the theoretical and experimental results states that in similar conditions a robotic model can be used instead of expensive and time-consuming experiments.
Biological Computer Modeling / Biological Computer Simulation
Pejman Ghassemi; Mohammad Hossein Miranbaygi
Volume 2, Issue 4 , June 2008, , Pages 305-315
Abstract
In this research we present a new method to evaluate changes in size and refractive index of Titanium dioxide (TiO2) nanoparticles which are the main component of anti-UV creams. The main objective of this research is assessing the impact of changing in size and refractive index of TiO2 on the polarization ...
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In this research we present a new method to evaluate changes in size and refractive index of Titanium dioxide (TiO2) nanoparticles which are the main component of anti-UV creams. The main objective of this research is assessing the impact of changing in size and refractive index of TiO2 on the polarization state of backscattered light. The proposed technique is based on modeling the propagated polarized laser beam inside a phantom and evaluating the change in the polarization of backscattered light. The phantom is simulated by software to have the polarization properties of anti-UV creams. As scattering particles (TiO2) in these creams configure polarization properties, then through modeling we have simulated the phantom with matrix of resin epoxy that has unit refractive index including Titanium dioxide nanoparticles. It will be shown that size parameter and relative refractive index of these particles influence cream's properties like purity, quality, coating power and degree of filtration and directly affect its polarization properties. The measurement technique which is presented here is based on scattering polarimetry. To assess the scattering phenomenon, the polarization state of incident and backscattered light is analyzed by simulating a laboratory polarimeter. Then polarization information of the simulated phantom is extracted as Mueller matrix and degree of polarization index. All modeling and simulations are performed in MATLAB 2006 and the results are presented towards the end part of the paper. The main outcome of this research is the ability of extracting and the recognition of those elements of the Mueller matrix which are very sensitive to changes in size parameter and relative refractive index of TiO2. That will define the main markers for quality assessment of anti-UV creams.
Speech processing
Ayoub Daliri; Farzad Towhidkhah; Shahriar Gharibzadeh; Yaser Shekofteh
Volume 2, Issue 2 , June 2008, , Pages 123-129
Abstract
Speech production is one of the most complicated physiological systems including different subsystems. These subsystems must work together in a synchronous manner. One of the important sub-systems is the jaw. Although different models have suggested for jaw, no suitable model has been proposed yet to ...
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Speech production is one of the most complicated physiological systems including different subsystems. These subsystems must work together in a synchronous manner. One of the important sub-systems is the jaw. Although different models have suggested for jaw, no suitable model has been proposed yet to consider the interactions between muscles, bones and nervous system. In this paper, using Spring-Damper-Mass and a nonlinear concept, we introduced a novel model for jaw movement during speech production. Experimental data were used to estimate the model parameters. Computer simulation results showed that the model could generate the jaw movement patterns similar to those observed in physiological behavior. Generality and simplicity of the model are two model features useful for more investigation of the jaw movement in different tasks.
Biological Computer Modeling / Biological Computer Simulation
Azade Ahouraei; Farzad Towhidkhah; Fateme Haji Ebrahim Tehrani; Rasoul Khayati
Volume 1, Issue 1 , June 2007, , Pages 63-69
Abstract
Jaundice (hyperbilirubinemia) is a common disease in newborn babies. Under certain circumstances, elevated bilirubin levels may have detrimental neurological effects. In some cases, phototherapy is needed to lower the level of total serum bilirubin, which indicates the presence and severity of jaundice. ...
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Jaundice (hyperbilirubinemia) is a common disease in newborn babies. Under certain circumstances, elevated bilirubin levels may have detrimental neurological effects. In some cases, phototherapy is needed to lower the level of total serum bilirubin, which indicates the presence and severity of jaundice. Recently, diagnosis and treatment modeling of disease have been considered by many researchers. In this paper, we present two models for classification and prediction of neonatal jaundice. The models are based on recorded data of Iranian Neonates. This study is oriented on the basis of following procedures: a short review on physiology of Jaundice, and then description of the models. Two three-layer feed forward neural networks were used in the modeling. The neural network model for classification is able to specify the type of jaundice, and the model for prediction can evaluate the risk of jaundice for newborns. These models can be used to decrease the risk in the critical cases as well as the cost of treatment.
Neuro-Muscular Engineering
Mehrak Mahmoudi; Mohammad Jafar Abd Khodaei; Saeide Khatibirad
Volume -2, Issue 1 , July 2005, , Pages 9-16
Abstract
A mathematical model is presented for simulation of neurotransmitter release in the synaptic cleft of a neuromuscular junction. Chaudhuri's model is improved by adding calcium diffusion effect on the neurotransmitter release. When an action potential occurs, the calcium channels on presynaptic membrane ...
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A mathematical model is presented for simulation of neurotransmitter release in the synaptic cleft of a neuromuscular junction. Chaudhuri's model is improved by adding calcium diffusion effect on the neurotransmitter release. When an action potential occurs, the calcium channels on presynaptic membrane will open and allow calcium ions to enter in presynaptic terminal. Then, these ions diffuse between calcium channels and release sites, where clearance mechanisms remove some of them. The model is defined by some partial differential equations which are solved by numerical methods. Solving these equations, the temporal changes of calcium concentration in the release sites and the amount of neurotransmitter release at each time are obtained. Finally, the effect of two consecutive action potential pulses on the above mechanisms is studied.
