Sharif Digital Repository

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  

Confining nematic liquid crystal between two curved boundary conditions while the nematic molecules have a degenerate planar anchoring leads to complex and beautiful textures of molecular disparagement(defect) in the bulk and on the surfaces. Such the liquid crystal shells are made with double-emulsion techniques in microfluidic devices have provided applications for micro-scale colloidal linkers.In this work, we have numerically minimized the elastic energy in one-constant approximation in present of Fournier’s degenerate surface potential with finite element method. The nematic shell is confined between two spherical surfaces that we have studied the final energies and their related... 

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... 

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.
 

Structure of colloidal particles in anisotropic solvent with long-range orientational ordering, such as nematic liquid crystals, has attracted great attention in science and technology. The nematic director is distorted from its uniform orientation in the bulk due to anchoring on the surface of the colloidal particles. These elastic distortions create topological defects around the particles and induce long and short range anisotropic interactions between the particles. Depending on the anchoring type and the colloidal geometry, the particle-defect can induce a long-range dipolar-dipolar, quadrupolar-quadrupolar and/or dipolar-quadrupolar potential.Experimentally, the colloidal interactions... 

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... 

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... 

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.
 

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 ratets and if the potential priodically turns on and off in time, it is called “Pulsated Ratet.“ In this resear net current of particles in 2D pulsated asymmetric potential landscapes is surveyed theoretically and by
Monte Carlo method simulation  

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... 

Proteins are of fundamental importance for life on Earth and participate in virtually every process within cells. The function of a protein depends on its three dimensional structure. If this is disrupted, the protein loses its biological activity. In addition to temperature, pressure and ionic strength, pH is also an important factor that affects the configuration of proteins. Proteins contain acidic and basic residues. Variations in pH lead to changes in distribution of atomic charge, which in turn affect the stability and function of proteins. Protein folding occurs in a specific pH range, a deviation from which may facilitate misfolding or Amyloid aggregation. It is therefore necessary... 

Molecule of DNA is one of the most important biomolecule in cell which contains genetic information to supply the required proteins for body. Evidence shows prefered binding sequence for proteins exist to interact with proteins which this preference is determined not only by specefic chemical interactions between DNA and protein, but also specific suitable geometrical arrangements of DNA have important role to inding DNA oligomer and protein, such as winding DNA around histon to creating nucleosome is related to curvature and deformability of DNA. Thus knowing elastic behaviour and properties of DNA helps us to approach the answer of such questions. Despite the recent dvancement in labratory... 

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.... 

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,... 

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... 

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... 

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... 

Polymer translocation through the nanopores is one of the fundamental macromolecular processes in life. Some examples are , mRNA translocation through nuclear pores, injection of DNA from a virus head into a host cell, protein translocation across biological membranes through membrane channels. Also some applications are suggested for the process, e.g. DNA sequencing by probing the signals during the translocation, drug delivery and/or gene therapy. During the translocation the polymer should pass entropic barrier of the pore and it can be facilitated by changing the chemical potential, application of eclectic field, flow field, or chemical concentrations. In electrically driven... 

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.... 

Topological defects are interesting phenomena which can be observed in ordered phases such as oriented active fluids or nematic liquid crys¬ tals. Topological defects are determined by the overall structure of the director field in an active fluid in nematic phase and by exerting force to the units of the active particles they can interact or cause motion in the environment. Studying them as particles with dynamical equations, instead of studying the director field of the nematic environment, would provide us the power to study the characteristics of their motion. The equations of motion for multi¬defect systems have been previously stud¬ ied and in this work we focus on the chaotic...