Search for: biophysics
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    Machine learning and network analysis of molecular dynamics trajectories reveal two chains of red/Ox-specific residue interactions in human protein disulfide isomerase

    , Article Scientific Reports ; Volume 7, Issue 1 , 2017 ; 20452322 (ISSN) Karamzadeh, R ; Karimi Jafari, M. H ; Sharifi Zarchi, A ; Chitsaz, H ; Salekdeh, G. H ; Moosavi Movahedi, A. A ; Sharif University of Technology
    The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences... 

    Differentiation of inflammatory papulosquamous skin diseases based on skin biophysical and ultrasonographic properties: A decision tree model

    , Article Indian Journal of Dermatology, Venereology and Leprology ; Volume 86, Issue 6 , 2020 , Pages 752- Yazdanparast, T ; Yazdani, K ; Ahmad Nasrollahi, S ; Nazari, M ; Darooei, R ; Firooz, A ; Sharif University of Technology
    Wolters Kluwer Medknow Publications  2020
    The biophysical and ultrasonographic properties of the skin change in papulosquamous diseases. Aims: To identify biophysical and ultrasonographic properties for the differentiation of five main groups of papulosquamous skin diseases. Methods: Fifteen biophysical and ultrasonographic parameters were measured by multiprobe adapter system and high-frequency ultrasonography in active lesions and normal control skin in patients with chronic eczema, psoriasis, lichen planus, pityriasis rosea and parapsoriasis/mycosis fungoides. Using histological diagnosis as a gold standard, a decision tree analysis was performed based on the mean percentage changes of these parameters [(lesion-control/control)... 

    A new approach for touching cells segmentation

    , Article BioMedical Engineering and Informatics: New Development and the Future - 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008, Sanya, Hainan, 27 May 2008 through 30 May 2008 ; Volume 1 , 2008 , Pages 816-820 ; 9780769531182 (ISBN) Nasr Isfahani, S ; Mirsafian, A ; Masoudi Nejad, A ; Sharif University of Technology
    Automatic cell segmentation has various applications in different parts of science. The development of automated methods for cell segmentation, remains challenging in situations where there are touching cells. In this paper we propose a new method for separating touching cells. As the first step, we use a combination of graph segmentation algorithm and thresholding for segmenting foreground objects and producing a binary image. Next, boundary points of separation zone are selected by using a corner detection algorithm. Finally, the marker controller watershed transform is applied to separate touching cells at selected points. © 2008 IEEE  

    Complexity and variability of the center of pressure time series during quiet standing in patients with knee osteoarthritis

    , Article Clinical Biomechanics ; Volume 32 , 2016 , Pages 280-285 ; 02680033 (ISSN) Negahban, H ; Sanjari, M. A ; Karimi, M ; Parnian Pour, M ; Sharif University of Technology
    Elsevier Ltd 
    Background While several studies have investigated the traditional linear measures in patients with knee osteoarthritis, no study has yet reported the non-linear structure of postural sway in these patients. Methods We used two non-linear methods, recurrence quantification analysis (percent of determinism-%DET) and central tendency measure, to respectively investigate differences in the complexity and variability of sway dynamics between two groups of knee osteoarthritis patients (n = 27) and healthy controls (n = 27) under different conditions of postural and cognitive tasks. The experimental conditions included standing on (1) rigid surface with open eyes; (2) rigid surface with closed... 

    Bending Rigidity of Helical Microtubule structures

    , M.Sc. Thesis Sharif University of Technology Mortazavi, Hamed (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Microtubules are hollow cylindrical structures of 25 nanometer diameter inside cell membrane. Microtubule (MT) serves as a cell structure component and vesicular transport inside cell. It has been shown in recent researches that the persistence length in MTs is length dependent and increases about several times of counter length. Also helical structures of MTs have been found recently. In this research using Molecular Dynamic simulation of coarse-grained microtubular structures we compare persistence length of wild and helical microtubular structures. We show that the persistence length in helical structures is independent to the length.

    Analysis and Simulation of Cell Migration with VCM Software

    , M.Sc. Thesis Sharif University of Technology Sadeghizadeh, Sajjad (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Cells in their surrounding environment subjected to biochemical and biomechanical stimuli and respond to this signals. The mechanism by which cells transduce external mechanical signals into responses is called Mechanotransduction and cell use this mechanism to sense and respond to extracellular signals. Cells control processes like migration and division by mechanosensing. Cell migration is one of the most important responses to Cell-ECM interaction. This migration underlies many biological processes including embryogenesis, wound healing, tumorogenesis, morphogenesis and immune defense, so the study of cell migration is of particular importance. If there are external signals in cells... 

    OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

    , Article Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN) Haji Abdolvahab, R ; Mobasheri, H ; Nikouee, A ; Ejtehadi, M. R ; Sharif University of Technology
    Elsevier B.V  2016
    The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage... 

    The role of mscl amphipathic n terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels

    , Article Nature Communications ; Volume 7 , 2016 ; 20411723 (ISSN) Bavi, N ; Cortes, D. M ; Cox, C. D ; Rohde, P. R ; Liu, W ; Deitmer, J. W ; Bavi, O ; Strop, P ; Hill, A. P ; Rees, D ; Corry, B ; Perozo, E ; Martinac, B ; Sharif University of Technology
    Nature Publishing Group  2016
    The bacterial mechanosensitive channel MscL gates in response to membrane tension as a result of mechanical force transmitted directly to the channel from the lipid bilayer. MscL represents an excellent model system to study the basic biophysical principles of mechanosensory transduction. However, understanding of the essential structural components that transduce bilayer tension into channel gating remains incomplete. Here using multiple experimental and computational approaches, we demonstrate that the amphipathic N-terminal helix of MscL acts as a crucial structural element during tension-induced gating, both stabilizing the closed state and coupling the channel to the membrane. We... 

    A low cost, efficient method for chip fabrication in cell analysis

    , Article 2016 23rd Iranian Conference on Biomedical Engineering and 2016 1st International Iranian Conference on Biomedical Engineering, ICBME 2016, 23 November 2016 through 25 November 2016 ; 2017 , Pages 93-96 ; 9781509034529 (ISBN) Rahmani, A ; Mohammadi, A ; Kalhor, H ; Sharif University of Technology
    in recent decades, DEP due to its high efficiency has been exploited widely in separation and manipulation of bioparticles. In the present work a simple, low-cost, and efficient procedure for fabrication of microfluidic chips applied in medicine and biochemistry has been presented. In this method, electrodes are not in direct contact with biological samples which results in elimination of conventional systems' cons. Efficacy of the designed system has been evaluated by injecting samples containing yeast and Ecoli cells into the system and analyzing their trajectory. Experimental results demonstrate that precise adjustment of voltage and frequency can lead to the desired separation in this... 

    A novel stable robust adaptive impedance control scheme for ankle prostheses

    , Article 5th RSI International Conference on Robotics and Mechatronics, IcRoM 2017, 25 October 2017 through 27 October 2017 ; 2018 , Pages 63-68 ; 9781538657034 (ISBN) Heidarzadeh, S ; Sharifi, M ; Salarieh, H ; Alasty, A ; Sharif University of Technology
    A stable robust adaptive impedance control strategy is introduced here as a model-based low-level control scheme for active ankle prostheses. The effects of amputee-prosthesis and prosthesis-environment interactions are included in the controller design. An interesting feature of the proposed controller is that only shank and ankle angles and angular velocities, and ground reaction forces are required to implement the control law. In other words, no feedback from amputee-prosthesis interaction forces and moment, global or local positions, and accelerations of amputated place is required. Using a Lyapunov analysis, exponential convergence characteristics of the proposed controller are proven.... 

    Simulation of mechanical force in skeletal muscle according to the intracellular Ca2+ concentration level

    , Article 2017 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Karami, M ; Grasa, J ; Calvo, B ; Zohoor, H ; Firoozbakhsh, K ; Sharif University of Technology
    Active behavior in skeletal muscle soft tissue is affected by electrical, chemical and mechanical parameters. More realistic model of skeletal muscle demands detailed formulation which is able to involve other parameters in addition to mechanical ones. In this paper a new formulation for considering Ca2+ level (as the most important chemical factor) along with mechanical parameters in force producing process of skeletal muscle is introduced and validated comparing simulated results with some experimental data. Prepared skeletal muscle behavior is able to predict the maximum generated force in muscle according to the concentration of intracellular Ca2+ level and muscle contraction velocity... 

    Robot control using an inexpensive P300 based BCI

    , Article 26th National and 4th International Iranian Conference on Biomedical Engineering, ICBME 2019, 27 November 2019 through 28 November 2019 ; 2019 , Pages 204-207 ; 9781728156637 (ISBN) Bahman, S ; Shamsollahi, M. B ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Brain Computer Interfaces (BCI) are an important concept of biomedical engineering because of their ability to improve life conditions for people with different disabilities. Lots of studies have worked on important characteristics of BCI systems, such as speed and accuracy, whereas price is an important aspect too. Thus, a low cost BCI system with high accuracy clearly can help more people. Our purpose in this study is to design a P300 based BCI system using a low-priced EEG headset which has an acceptable accuracy. Our final design got a mean real-time accuracy of 93.3% which is comparable to systems with much more expensive hardware. © 2019 IEEE  

    Speckle noise reduction of ultrasound images using M-band wavelet transform and wiener filter in a homomorphic framework

    , Article 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008, Sanya, Hainan, 27 May 2008 through 30 May 2008 ; Volume 2 , 2008 , Pages 510-515 ; 9780769531182 (ISBN) Vosoughi, A ; Shamsollahi, M. B ; Sharif University of Technology
    In this paper we make use of M-band discrete wavelet transform (MDWT) and Wiener filter for speckle noise suppression of ultrasound images. Assuming multiplicative model for speckle noise, by applying logarithmic transform to noisy observation we convert multiplicative noise to additive one. Then, speckle noise can be reduced by taking the M-band wavelet transform of log-transformed observation and employing an adaptive thresholding technique. In order to improve the performance of this denosing approach, we propose a preprocessing stage which exploits Wiener filtering. Through this stage logtransformed observation is separated into two images and then each of these two images is denoised... 

    Analysis of Motility Phases of Binary Active Matter

    , M.Sc. Thesis Sharif University of Technology Tahaei, Ali (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    The study of active matter has gathered a great deal of attention in the past decades. The collective behavior of living matter such as the murmuration of the flocks of birds is an example of these systems. In order to study different aspects of these systems, variant models have been studied and change of behavior, phase shift and the existence of multiple phases has been observed.Vicsek model was one of the first models studying these systems, where an aligning pairwise interaction causes the agents to move in the same direction.We investigated Vicsek model by considering an overdamped Langevin dynamics for fewparticle systems. We showed Vicsek model in fewparticle systems induces... 

    Quantitative evaluation of parameters affecting the accuracy of Microsoft Kinect in GAIT analysis

    , Article 2016 23rd Iranian Conference on Biomedical Engineering and 2016 1st International Iranian Conference on Biomedical Engineering, ICBME 2016, 23 November 2016 through 25 November 2016 ; 2017 , Pages 306-311 ; 9781509034529 (ISBN) Jamali, Z ; Behzadipour, S ; Sharif University of Technology
    To date various commercial systems have been used in the GAIT analysis. These systems have some difficulties for clinical use, such as interfering with normal movement and high prices. The possibility of utilization of Kinect as a sensor for GAIT analysis has been studied in this research. The accuracy of Kinect in calculation of GAIT parameters such as lower limb joint angles, stride time, and stride length were computed during normal walking. The effects of the sensor's position and direction relative to the walkway were also investigated. The Kinect sensor was installed at different positions toward the motion path. In each position the data was recorded by both Kinect and a commercial... 

    Functional brain networks in parkinson's disease

    , Article 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Akbari, S ; Fatemizadeh, E ; Reza Deevband, M ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2018
    Parkinson's disease (PD) is the second most common and progressive neurological disorder. Parkinson's signs are caused by dysfunction in PD patient's brain network. Newly, resting state functional magnetic resonance imaging has been utilized to assess the altered functional connectivity in PD patients. In this study, we investigated the properties of the brain network topology in 19 PD patients compared to 17 normal healthy group by means of graph theory. In addition, we used four different graph formation methods to explore linear and nonlinear relationships between fMRI signals. Each correlation measure created a weighted graph for each subject. Different graph characteristics have been... 

    A centrifugal microfluidic platform to measure hemoglobin of whole blood

    , Article 2017 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Mahmodi Arjmand, E ; Saadatmand, M ; Bakhtiari, M. R ; Eghbal, M ; Balaei, A ; Sharif University of Technology
    Microfluidics has been becoming more and more popular over last two decades. The reason for this, is inherent features of microfluidics including low consumption of samples and reagents, high sensitivity, short analysis time, and low cost. As well as, centrifugal microfluidics as a subset of microfluidics has been able to prove itself as a helpful tool in analytic assays. The main application of centrifugal microfluidic devices is being used in point-of-care testing systems. Herein, we presented a microfluidic disc for measuring hemoglobin(Hb) concentration in the EDTA-anticoagulated venous blood using cyanmethemoglobin method. In this experiment, at first a hand-made standard solution was... 

    Detection of human attention using EEG signals

    , Article 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Alirezaei, M ; Hajipour Sardouie, S ; Sharif University of Technology
    Attention as a cognitive aspect of brain activity is one of the most popular areas of brain studies. It has significant impact on the quality of other activities such as learning process and critical activities (e.g. driving vehicles). Because of its crucial influence on the learning process, it is one of the main aspects of research in education. In this study, we propose a brand new protocol of brain signal recording in order to classify human attention in educational environments. Unlike other protocols used to record EEG signals, our protocol does not require strong memory and strong language knowledge to carry out. To this end, we have recorded EEG signals of 12 subjects using the... 

    A Physiological model-based study of flow-mediated dilation in peripheral arteries using finger photoplethysmogram signal

    , Article 2017 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Habib Parsafar, M ; Zahedi, E ; Vosoughi Vahdat, B ; Sharif University of Technology
    Flow-mediated dilation measurement in the brachial artery using ultrasound imaging (FMD-US) is a common noninvasive procedure for endothelial function evaluation in the peripheral arteries. As FMD-US is operator-dependent and involves onerous equipment, its use has been mostly confined to research settings. In this paper, we propose to use the more accessible finger photoplethysmogram signal in conjunction with the FMD test (FMD-PPG) as a surrogate method. To this end, a tube-load physiological model of the upper arterial path in the arm is developed. Signals acquired from young and elderly subjects (N=20) are then investigated using model parameter estimation by the genetic algorithm. Our... 

    Robust ground reaction force estimation and control of lower-limb prostheses: theory and simulation

    , Article IEEE Transactions on Systems, Man, and Cybernetics: Systems ; 2018 ; 21682216 (ISSN) Azimi, V ; Nguyen, T. T ; Sharifi, M ; Fakoorian, A ; Simon, D ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2018
    Ground reaction force (GRF) characteristics of amputee walking are important for the analysis of clinical gait data, and also to update model reference adaptive impedance (MRAI) controllers. GRF estimation is a better alternative than direct GRF measurement because of the disadvantages of load cells, such as high cost, integration difficulties due to weight and physical dimensions, the possibility of overload, and measurement noise. This paper presents four robust MRAI observer/controller combinations for GRF estimation-based control of a prosthesis and a legged robot model in the presence of parametric uncertainties and unmodeled dynamics, in which the robot model is employed to mimic...