Search for: chemotaxis
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    Boundedness in the Higher-Dimensional Parabolic-Parabolic Chemotaxis System with Logistic Source

    , M.Sc. Thesis Sharif University of Technology Shakerian, Shaya (Author) ; Hesaaraki, Mahmoud (Supervisor)
    We Consider the Chemotaxi Systems in a smooth bounded domain as follow:{ █(ut = Δu-χ∇.(u∇v)+ f (u) x ϵ Ω ,t>0 @ @τ vt =Δv-v+u x ϵ Ω ,t>0)┤ Where χ∈ and f(u) =Au - Buα generalizes the logistic function with A≥0, B>0 and α>1. First for τ=0, global existence of such solutions for any nonnegative initial data is proved under the assumption that . Moreover, boundedness properties of the constructed solutions are studied. Next we assume that 2=α, τ>0 and we consider nonnegative solutions of the Neumann
    Boundary value problem for the chemotaxis system above in a smooth bounded convex domain . We will see that if B is sufficiently large then for all sufficiently smooth initial data the... 

    Simulation of Paramecium Swimming in an Environment with a Chemical Gradient

    , M.Sc. Thesis Sharif University of Technology Nematollahi Sarvestani, Ali (Author) ; Ahmadian, Mohammad Taghi (Supervisor) ; Shamloo, Amir (Supervisor)
    In the recent decade, researchers in the field of minimally invasive medicine have come up to the idea of utilizing micro organisms as smart micro robots. The advantage with this idea is the fact that problems such as energy supply and maneuvering are resolved for these sorts of micro swimmers. In this current work, a new numerical method for investigation of micro swimming is developed which is computationally efficient in characterizing locomotion of micro swimmers and using a finite element method software, locomotion of Paramecium has been investigated inside and outside a capillary tube. According to simulation results, it is possible to design a controlling system which is capable of... 

    Investigation of the Role of Biological Processes in Bacterial Transport through Porous Media

    , Ph.D. Dissertation Sharif University of Technology Biria, Davoud (Author) ; Roostaazad, Reza (Supervisor) ; Sahebghadam Lotfi, Abbas (Supervisor) ; Amoozegar, Mohammad Ali (Supervisor)
    To investigate the role of biological processes in bacterial transport through poroud media, six rod shaped and motile bacteria were isolated from a crude oil sample. A multi stage screening procedure was utilized to select the most appropriate isolate in microbial enhanced oil recovery applications (MEOR). It was identified and registered as Bacillus licheniformis MS3 in GenBank database. After that, the physical properties and chemical structure of its biosurfactant were determined and it was proved to be a new lipopeptide biosurfactant which was called licheniformin. Power law logistic model was utilized to investigate the kinetics growth of the MS3 strain on insoluble carbon sources ... 

    Blow-up For Chemotaxis Models

    , Ph.D. Dissertation Sharif University of Technology Sharifi Tabar, Mohsen (Author) ; Hesaaraki, Mahmoud (Supervisor)
    Moving of living organisms appears in many interesting problems, e.g. the growth of bacteria colonies, tumor growth, wound healing, color patterns of animals and etc. There are many ways to model such problems and PDE theory is widely used to investigate these problems. In this thesis, we study two well-known classic models. First, macroscopic “Keller–Segel” model and then kinetic “Othmer–Dunbar–Alt” System. Since these models have a nice behavior in two dimensions that they don’t have in other dimensions, we propose a way to alter them such that they behave in this way in all dimensions. Also none of the known models have the suitable dynamics in one dimension, so our model has the property... 

    Smart micro/nano-robotic systems for gene delivery

    , Article Current Gene Therapy ; Volume 17, Issue 2 , 2017 , Pages 73-79 ; 15665232 (ISSN) Pedram, A ; Nejat Pishkenari, H ; Sharif University of Technology
    Bentham Science Publishers B.V  2017
    Background: Small scale robotics have attracted growing attention for the prospect of targeting and accessing cell-sized sites, necessary for high precision biomedical applications and drug/gene delivery. The loss of controlled gene therapy, inducing systemic side effects and reduced therapeutic efficiency, can be settled utilizing these intelligent carriers. Methods: Newly proposed solutions for the main challenges of control, power supplying, gene release and final carrier extraction/degradation have shifted these smart miniature robots to the point of being employed for practical applications of transferring oligonucleotides (pDNA, siRNA, mRNA, etc.) in near future. Conclusion: In this... 

    Simulation of Paramecium Chemotaxis Exposed to Calcium Gradients

    , Article Cell Biochemistry and Biophysics ; Volume 74, Issue 2 , 2016 , Pages 241-252 ; 10859195 (ISSN) Nematollahi Sarvestani, A ; Shamloo, A ; Ahmadian, M. T ; Sharif University of Technology
    Humana Press Inc  2016
    Paramecium or other ciliates have the potential to be utilized for minimally invasive surgery systems, making internal body organs accessible. Paramecium shows interesting responses to changes in the concentration of specific ions such as K+, Mg2+, and Ca2+ in the ambient fluid. Some specific responses are observed as, changes in beat pattern of cilia and swimming toward or apart from the ion source. Therefore developing a model for chemotactic motility of small organisms is necessary in order to control the directional movements of these microorganisms before testing them. In this article, we have developed a numerical model, investigating the effects of Ca2+ on swimming trajectory of... 

    One-dimensional chemotaxis kinetic model

    , Article Nonlinear Differential Equations and Applications ; Volume 18, Issue 2 , 2011 , Pages 139-172 ; 10219722 (ISSN) Sharifi tabar, M ; Sharif University of Technology
    In this paper, we study a variation of the equations of a chemotaxis kinetic model and investigate it in one dimension. In fact, we use fractional diffusion for the chemoattractant in the Othmar-Dunbar-Alt system (Othmer in J Math Biol 26(3):263-298, 1988). This version was exhibited in Calvez in Amer Math Soc, pp 45-62, 2007 for the macroscopic well-known Keller-Segel model in all space dimensions. These two macroscopic and kinetic models are related as mentioned in Bournaveas, Ann Inst H Poincaré Anal Non Linéaire, 26(5):1871-1895, 2009, Chalub, Math Models Methods Appl Sci, 16(7 suppl):1173-1197, 2006, Chalub, Monatsh Math, 142(1-2):123-141, 2004, Chalub, Port Math (NS), 63(2):227-250,... 

    Modeling of microfluidic microbial fuel cells using quantitative bacterial transport parameters

    , Article Journal of Power Sources ; Volume 342 , 2017 , Pages 1017-1031 ; 03787753 (ISSN) Mardanpour, M. M ; Yaghmaei, S ; Kalantar, M ; Sharif University of Technology
    Elsevier B.V  2017
    The objective of present study is to analyze the dynamic modeling of bioelectrochemical processes and improvement of the performance of previous models using quantitative data of bacterial transport parameters. The main deficiency of previous MFC models concerning spatial distribution of biocatalysts is an assumption of initial distribution of attached/suspended bacteria on electrode or in anolyte bulk which is the foundation for biofilm formation. In order to modify this imperfection, the quantification of chemotactic motility to understand the mechanisms of the suspended microorganisms’ distribution in anolyte and/or their attachment to anode surface to extend the biofilm is implemented... 

    Microfluidic devices as invitro microenvironments for -stem cell culture

    , Article Proceedings of the IASTED International Conference on Biomedical Engineering, BioMed 2014 ; 2014 , pp. 83-88 Shamloo, A ; Abeddoust, M ; Mehboudi, N ; Sharif University of Technology
    Many potential therapies are currently being studied that may promote neural regeneration and guide regenerating axons to form correct connections following injury. It has been shown that adult neurons have some limited regenerative capabilities, and the lack of connection formation between neurons is not an intrinsic inability of these cells to form axons after being damaged, but rather the inhibitory microenvironment of the injured tissue prevents regeneration. In this study, the polarization and chemotaxis of neuronal stem cells (NSC) in response to quantified gradients of nerve growth factor (NGF) was examined. To accomplish this, a microfluidic device was designed and fabricated to... 

    Interpretation of the electrochemical response of a multi-population biofilm in a microfluidic microbial fuel cell using a comprehensive model

    , Article Bioelectrochemistry ; Volume 128 , 2019 , Pages 39-48 ; 15675394 (ISSN) Mardanpour, M. M ; Saadatmand, M ; Yaghmaei, S ; Sharif University of Technology
    Elsevier B.V  2019
    The present study investigates the diversification and dynamic behavior of a multi-population microfluidic microbial fuel cell (MFC) as a biosensor. The cost effective microfluidic MFC coupled to a comprehensive model, presents a novel platform for monitoring chemical and biological phenomena. The importance of competition among different microbial groups, hierarchical biochemical processes, bacterial chemotaxis and different mechanisms of electron transfer were significant considerations in the present model. The validation of the model using experimental data from a microfluidic MFC shows an appropriate match with the hierarchal biodegradation processes of a complex substrate as well as... 

    Cell-cell interactions mediate cytoskeleton organization and collective endothelial cell chemotaxis

    , Article Cytoskeleton ; Vol. 71, issue. 9 , 2014 , p. 501-512 Shamloo, A ; Sharif University of Technology
    This study investigates the role of cell-cell and cell-ligand interactions in cytoskeleton organization of endothelial cells (ECs) and their directional migration within a microfluidic device. The migration of ECs in response to a biochemical factor was studied. Mathematical analysis of the cell migration pathways and cellular cytoskeleton revealed that directional migration, migration persistence length, migration speed, and cytoskeletal stress fiber alignment can be mediated by the level of cell contacts as well as the presence or absence of a biochemical polarizing factor. It was shown that in the presence of a biochemical polarizing factor, higher cell density and more frequent cell... 

    A novel model for predicting bioelectrochemical performance of microsized-MFCs by incorporating bacterial chemotaxis parameters and simulation of biofilm formation

    , Article Bioelectrochemistry ; Volume 122 , 2018 , Pages 51-60 ; 15675394 (ISSN) Kalantar, M ; Mardanpour, M. M ; Yaghmaei, S ; Sharif University of Technology
    Elsevier B.V  2018
    Bacterial transport parameters play a fundamental role in microbial population dynamics, biofilm formation and bacteria dispersion. In this study, the novel model was extended based on the capability of microsized microbial fuel cells (MFCs) as amperometric biosensors to predict the cells' chemotactic and bioelectrochemical properties. The model prediction results coincide with the experimental data of Shewanella oneidensis and chemotaxis mutant of P. aeruginosa bdlA and pilT strains, indicating the complementary role of numerical predictions for bioscreening applications of microsized MFCs. Considering the general mechanisms for electron transfer, substrate biodegradation, microbial growth... 

    A model for cell density effect on stress fiber alignment and collective directional migration

    , Article Physical Biology ; Volume 12, Issue 6 , 2015 ; 14783967 (ISSN) Abeddoust, M ; Shamloo, A ; Sharif University of Technology
    In this study, numerical simulation of collective cell migration is presented in order to mimic the group migration of endothelial cells subjected to the concentration gradients of a biochemical factor. The developed 2D model incorporates basic elements of the cell, including both the cell membrane and the cell cytoskeleton, based on a viscoelastic cell mechanic model. Various cell processes - including cell random walk, cell-cell interactions, cell chemotaxis, and cellular cytoskeleton rearrangements - are considered and analyzed in our developed model. After validating the model by using available experimental data, the model is used to investigate various important parameters during... 

    A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    , Article Journal of Micromechanics and Microengineering ; Volume 26, Issue 1 , November , 2015 ; 09601317 (ISSN) Shamloo, A ; Amirifar, L ; Sharif University of Technology
    Institute of Physics Publishing  2015
    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be... 

    A computational model for estimation of mechanical parameters in chemotactic endothelial cells

    , Article Scientia Iranica ; Volume 23, Issue 1 , 2016 , Pages 260-267 ; 10263098 (ISSN) Kiyoumarsioskouei, A ; Shamloo, A ; Azimi, S ; Abeddoust, M ; Saidi, M.S ; Sharif University of Technology
    Sharif University of Technology 
    A cell migration numerical simulation is presented to mimic the motility of endothelial cells subjected to the concentration gradients of a Forebrain embryoniccortical neuron Conditioned Medium (CM). This factor was previously shflown to induce the directional chemotaxis of endothelial cells with an over-expressed G protein coupled receptor 124 (GPR 124). A cell simulator program incorporates basic elements of the cell cytoskeleton, including membrane, nucleus and cytoskeleton. The developed 2D cell model is capable of responding to concentration gradients of biochemical factors by changing the cytoskeleton arrangement. Random walk force, cell drag force and cell inertial effects are also...