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ejtehadi--mohammad-reza
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Comparing EC and GO Model in Protein Folding Simulation
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Proteins are one of the most important bio-molecules. they play an important role in every aspect of living organisms. The information for synthesizing these important molecules is coded in the DNA of that organism. After the coded data is read and transcribed by some other bio-molecules that are proteins themselves, the protein is made and starts it's biological function in different organs. For this reason, investigating properties of proteins helps us to better understand how life works. Understanding the dynamics of proteins, which are some polymers with special energy landscape properties, has attracted the attention of physicists in the 20th century. Proteins are chains of amino...
Phase Separation in Binary Liquid Crystal Mixtures
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Phase separation of a 50:50 binary system composed of two prolate ellipsoids with different axis ratios is investigated through molecular dynamics simulation. The system can be considered as a coarse-grained model of a binary liquid crystal mixture. Phase separation has been detected in the system by changing the density as the control parameter. The system goes through two different phase changes, one being the phase change due to phase separation and the other one due to orientational phase transition. In the latter case coexistence of the two particles results in simultaneous phase transition
Topologic Properties Of The Energy Landscape Network In Frustrated Systems
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
The study of Energy Landscape of physical systems has a key role in complex problems. In this project we have enumerated the energy landscape of a finite squared lattice spin glass with nearest neighbored interactions to study its behavior. We choose the coupling constants of this spin glass system with Heb rule. According to this rule the coupling constants are chosen in a way to make specific patterns of spin configuration as a local minimum. We have studied these spin glasses with different number of patterns. In our computation we saw a significant difference between spin glasses with odd and even number of patterns. We addressed this behavior to properties of coupling constant...
Study of Net Current of Particles in 2D Pulsated Potential Landscape
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
In systems possessing spatial or dynamical symmetry breaking, Brownian motion combined with unbiased external input signals, deterministic and random alike, can assist directed motion of particles at nanoscale. “Brownian motors” are devices by whi thermally or extrinsically activated processes are controlled and used to generate directed motion in space. Rectification devices involving asymmetric substrates are termed ratets and if the potential priodically turns on and off in time, it is called “Pulsated Ratet.“ In this resear net current of particles in 2D pulsated asymmetric potential landscapes is surveyed theoretically and by
Monte Carlo method simulation
Monte Carlo method simulation
Protein-Nanoparticle Interactions
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
In this thesis, proteinnanoparticle interactions have been studied using Molecular Dynamics simulation. sT fN, is the studied protein in this work. It is one of the most important proteins in the blood fluid. In this work, nanoparticle has been modeled as a surface; because the radius of gyration of sT fN is less than 3nm, so when it is near an enough big nanoparticle (100200 nm), nanoparticle seems as a surface from the view of protein. The surface of nanoparticle consists of sodium ions. Surface of nanoparticle, has been modeled using two types of surface:flat surface and nonflat surface. Protein interaction with surface, has been studied in two different initial orientations with respect...
DNA Chains Entanglement in Confined Geometries
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Our bodies are made from billions of individual cells and DNA is the control central of each cell. In addition to linear DNAs, there are circular DNAs in nature. Circular DNAs cause new topological structures such as knots and catenanes. These topological structures form during biological proccesses such as replication. For example during replication, two daughter circular DNAs may link together and form catenanes. Anzymes named topoisomerases can simplify the topology of circular DNAs. Type 2 topoisomerases is used for simplification of catenanes. These anzymes do it with breaking a double-strand DNA and passing through another one. In comparison with DNAs, topoisomerases are very small and...
Inference for Network Parameters in Stochastic Epidemic Models
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Different models describing the procedure of epidemics are complicated and involving numerous factors. Some of these models that used a stochastic network for modelling epidemics had been successful in statistical prediction of spreading epidemics. However, in many cases there is no direct way to determine parameters of these models. In this thesis it has been desired to estimate those parameters based on historical data of epidemics To estimate structural parameters, concerning epidemic network, two independent inference have been studied. In the first inference, the probability of disease transmission from one person to another is estimated.
In the second, using Bayesian inference,...
In the second, using Bayesian inference,...
Monte Carlo Simulation of Asymmetric Elastic Rod Model and Calculation of
Probability of Loop Formation
,
M.Sc. Thesis
Sharif University of Technology
;
Ejtehadi, Mohammad Reza
(Supervisor)
Abstract
Sharply bent DNA plays an important role in many biological processes such as gene regulation, DNA replication and recombination. DNA cyclization experiments are well suited to study of sharply bent DNA, because they are sensitive to strongly bent conformations. Results of these experiments show that short length DNA molecules are more flexible than predicted by elastic rod model. Therefore, based on these experiments, the elastic rod model is not a suitable model for explaining elastic behavior of DNA at small lengths, although it can explain DNA elasticity at large length scales. Recently, it has been shown that a new model called asymmetric elastic rod model can explain high flexibility...
Effect of Myr-MA Protein on the Local Curvature of HIV Virus Membrane
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
HIV virus in its life cycle in order to leave the host cell uses Gag polyprotein assembling on the inner leaflet of the membrane. Gag polyprotein could interact with the cellular membrane via Myr-MA protein inserted in its amino terminal. Based on the exprimental data, HIV matrix proteins (MA) assemble as hexamers of trimers on the membrane to form a hexagonal lattice. In this study, membrane anchoring of MA proteins and the effect of a hexamer of MA trimers on the local curvature of membrane have been simulated using a coarse-grained model. The results suggest that MA binding to the membrane is mainly due to electrostatically interactions between the HBR motif of MA with PIP2 lipids. In...
Bending Rigidity of Helical Microtubule structures
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
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.
Solving Delayed SIRS Meanfield Model on Homogeneous Networks
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
In this work we simulate SIRS1 model on homogeneous networks by means of simulation, then we drove meanfield equations for this model and compared the solution of these equations to the simulations results on the network. To obtain a new model closer to the reality, we modified the SIRS model and introduce history to the convenient model. After simulation of this model we redrove the equations with history and found that this model can show bifurcation so we found the phase diagram for this model. And in the last part we introduced history to a meanfield model with pair approximation and drove the equations and try to solve
them numerically.
them numerically.
Mechanical Model in Cell and Nucleus Deformation
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Now a days, the ability of measuring the mechanical properties of the living cells in in experiments has been increased. Experiments shows that the stem cells could alter their faith in different mechanical situations, but an integrated model about this phenomenon in literature has not been introduced yet. In this research thesis s minimal cell model (MMC) is developed to capture the behavior of the cells on substrates with varying mechanical properties and morphologies, MMC consists of large scale models for outer membrane of the cell and nuclear envelope, cytoplasmic area, chromatin fibers and Extra cellular matrix. Each component of the MMC will be placed in an integrated software to...
Topological Defects in Active Nematics
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Topological defects are specific signatures of liquid crystals. Their presence in liquid crystals are so often that they are ”vestiges” of such flows. With their presence inside a flow, they cause global change to the director field by dictating specific orintational restrictions. So their global effects on the flow are substantial. In active nematics, not only they dictate the global structure of the director, but also they act as local sources of motion and behave like self-propelled particles. In this thesis, a detailed dynamics of active liquid crystals and their topological defects is presented. Then, Solving equations of motion for such systems using computer numerical analysis, the...
Structure of DNA Confined in Nano-Environment
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Ejtehadi, M. R. (Mohammad Reza)All cells store their hereditary information in the same linear chemical code, DNA molecule. These information organize all activities of the cell. Therefore, studying various properties of DNA is a big step toward understanding life. Physicists are interested in elastic properties of DNA molecule. DNA is somehow a chain of successive atoms that have been arranged in a helical ladder shape. DNA is a stiff polymer so one has to use a large amount of energy to bend it. Interestingly, in most of the natural cases, DNA is highly packed into spaces that are much smaller that its total length. Cell’s nucleus and viral capsids are some examples. Virus maybe the...
Study on Dynamics of Charged Study on Dynamics of Charged Polyelectrolytes in Inhomogeneous Electric Fields and Its Application in Translocation Phenomenon
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Polymers not just because of their increasing applications in industry but according to their fundamental role in biological mechanisms, has been a topic of interest among different scientific groups. Chemical structure, acroscopic properties and dynamical behavior of these macromolecules are studied in different ways. An important sub-group of polymers are those which according to their chemical properties, after dissolving, release some ions in water and become charged and called polyelectrolytes. A polyelectrolyte with vital importance in our life is DNA which encodes the genetic instructions used in the development and functioning of all known living organisms. One of the main goals in...
DNA Molecule in Confined Geometries
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
DNA molecule is one of the most important macromolecules in cell, which carries genetic information for life. DNA is often in confined geometries, such as, packaging in cell and DNA-protein interactions. While DNA is nearly a stiff polymer, its elastic behaviour plays a crucial role on its functionalities.Therefore, investigating the elastic and mechanical properties of DNA is really important.The elastic behaviour of a long and free DNA can be predicted very accurately by ”worm-like chain“ (WLC) model. In WLC model, DNA is assumed as a elastic rod with harmonic potential of local bending and twist.Many structural properties of DNA have been ignored in this model. But in recent years, by...
”A Study on the Process of Passive Uptake of Nanoparticles by Coarse-Grained MD Simulation”
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
The aim of this thesis is to investigate the passive wrapping of nanoparticles by a lipid membrane in the uptake process using molecular dynamics computer simulations. The simulations are carried out by the Virtual Cell Model (VCM) software package, a computational framework that creates a large scale coarse-grained multi-component cell model developed by Prof Mohammad Reza Ejtehadi’s Soft Matter Group at Sharif University of Technology. VCM can model the dynamics of different parts of the cell and investigate their mechanical properties.A chapter of this thesis contributes to further development of the membrane model used in the VCM to simulate nanoparticles interactions with a membrane....
Conformational Substates of Wild Type and Mutant (V68N) Myoglobin-CO
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Folded protein experience several conformational substates. Each substate reperesents a minimum in the free energy surface of the system. Since Myoglobin is the smallest protein that can reversibly bind to gas molecules and, it can be used as prototype for more complex systems.IR pecrtum of CO inside of myolgobin shows that distinct conformational substates can occur. It was shown that Histidine residue inside heme pocket plays an essential rolle in structural properties of substates. In this study, we used molecular dynamice simulation together with umbrella sampling method to obtain free energy profile of MbCO system. The configuration of distal Histidine (His64), CO and Heme is studied...
Equilibrium States of Nano scaled DNA-loops in Different Elastic Models
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
DNA cyclization mechanism, has an important role in many biological processes such as gene regulation, DNA replication and recombination. In addition there are DNA-loops in Bacteria an around the Histones in Chromosomes in scale of 5-100 nm. We need to a appropriate model to study about bending and loop formationin in this important molecule which is able to describe elasticity properties of DNA.One of the most successful models, to describe the physical behaviour of a long DNA molecule, is the elastic rod model. In this model, DNA is considered as a ixable rod that its bending energy is isotropic. Asymmetric elastic rod model is another model to describe elasticity properties of DNA....
Elasticity of DNA Molecule The Role of Anisotropy, Asymmetry and Nonlocal Interactions
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
The DNA Molecule carries genetic information in almost all living organisms. The information coded on DNA is an instruction which organizes and conducts all living activities of the living organism. The role of DNA in biological processes is so fundamental that life, as we know, is not possible without DNA. Therefore, studying the biological properties of DNA is crucial for understanding the nature of life. In biological conditions, DNA molecule can be found in highly packed configurations. Since the DNA is a rather stiff molecule, the formation of these configurations cost a considerable amount of energy. The elasticity of DNA plays an important role here. The important question is: how...