Sharif Digital Repository

Phospholipid membranes and vesicles play important roles in the cellular functioning, otein signaling and material transport inside cells. Protein-embedded vesiclesare also used for targeted drug delivery. In this thesis, we use molecular dynamicsmethods and study (i) the formation of vesicles from flat lipid bilayers (ii) the mechanicalproperties of vesicles under compressive forces (iii) the shape variations ofvesicles with and without transmembrane proteins (iv) protein clustering.We grow our vesicles from lipid bilayers, which may contain proteins with differentconcentrations. We start with a random initial distribution of proteins that allowsus to monitor the clustering and... 

Phospholipid vesicles are able to carry drugs or DNA to infected or cancerous cells. The blood flow can carry them to their target positions but their performance will be enhanced if they complete their attack by swimming in final stages of their journey. Vesicles built only by lipid molecules have rotational symmetry and undergo a random motion in their solvents without having a preferred direction. In this project, we break the symmetrical shape of phospholipid vesicles by a cluster of transmembrane proteins. We use a triangulated model of the membrane, apply the method of multi-particle collision dynamics to the motion of solvent particles, and simulate the motility of vesicles for... 

Hard disk drives are the main component of computers for permanent data storage. The security of the stored data is related closely to the air gap between the read-write head and the surface of disk. This gap which is created by the aerodynamic force between head and the disk is altered continually by lateral oscillations of disk. In the extreme condition of zero gap and contact between the protective coating layer and subsequently the magnetic material of the disk with the head, the disk will be scratched and damaged. Therefore, the active or passive control of these vibrations has a particular importance in the technology of manufacturing of hard disks. The first step in active control... 

Light has planar wavefront as it propagates in vacuum but in the atmosphere, because it passes through layers with different refractive indices, this planar wavefront is lost. Consequently light is distorted when it enters optical instruments. This issue results in images with low resolution. Adaptive optics is a method used for compensation of these distortions in order to obtain higher resolution. So far adaptive optics systems are successfully used in ground based telescopes and an increasing effort on developing and improving these systems is made. Most of these studies are performed from the optics point of view, but techniques from control theory can be applied to adaptive optics... 

Turbulence can distort and corrupt the image in quite a few ways when light from a distance star or another astronomical object enters the Earth's atmosphere. It is inevitable that all images produced by any telescope on ther Earth are blurred by these distortions. Adaptive Optics is a technology used to improve the performance of optical systems by reducing the effect of wavefront distortions: it aims at correcting the deformations of an incoming wavefront by deforming a mirror in order to compensate for the distortion. The research work reported in this thesis presents a solution to the surface shape control problems in a Deformable Mirror system. Our first goal is to derive equations that... 

The design and control of collective robots for different purposes has been one of the most interesting subjects in recent years. Interacting particles (both in engineering and nature) can not only be self-organized, but also show a myriad of amazing features. A lot of different types of collective motion can be seen in nature (like fishes, birds, bacteria, insects, to name but a few) which interacting with each other to form complicated patterns with ingenious purpose like foraging, predator escaping and so forth. Understanding these natural phenomena (like vortex formation) can be helpful in designing artificial systems, the usage of which are underwater or space vehicles performing a... 

Attitude control of rigid bodies is a complicated but attractive problem in dynamics. One of its main practical applications is in satellite attitude control and specifically in space telescope orientation control. Using fuel thrusters is not only expensive in most cases, but also it cannot be considered as an appropriate solution from reliability and economic aspects in long-term applications such as space telescopes and telecommunication satellites. On the other hand, magnetic torquers and momentum wheels cannot be utilized for rapid and large maneuvers due to their inability in generating large torques, which are needed in such maneuvers. As a result, another type of attitude control... 

The turbulence in the atmosphere will limit the performance of astronomical telescopes on the ground thus a technique for solving this problem is needed that is Adaptive optics technique. We know Adaptive optics in its simplest definition as a process to improve the quality of image by means of deformation of the wave fronts to compensate the beam path anomalies. The main components of this system are the wave front sensor and deformable mirror. Deformable mirror is used in the system of this technique also plays an important role in the correction of anomalies of eye. Type of actuators that can be used for deformable mirror, pattern of them, and also the way of connecting the actuators to... 

Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical... 

The planet earth has a variety of periodic motions in space, with periods varying from a day to thousands of years. The essence of studying the rotational motion of our planet is closely related to various phenomena such as, the long term variation of the earth’s climate, volcanic activities, ice ages, earth’s past dynamics, etc. furthermore, understanding the precise motion of the earth is an essential part of our astronomical observations. One of the many kinds of rotational motions, which has attracted many attentions is called Chandler wobble. Any irregularly shaped solid body rotating about some axis that is not aligned with its figure axis will wobble as it rotates. Although it has... 

Each of us at some point in our life has been astonished by the observation of the collective motion of certain animals such as birds, fishes or insects. These coherent and synchronized structures are apparently produced without the active role of a leader in the grouping and it has been reported even for some microorganisms such as bacteria or red blood cells. In all the mentioned examples agents are surrounding with the moving fluid which can affect the collective behavior of the system. The collaborative flock of birds in windy conditions and the swimming of fishes in rivers or along oceanic currents are some examples. Moreover, micro-organisms produce different collective behavior in the... 

Modern sensors consist of arrays of detectors specially arranged to enhance precision, capabilities, and field of view (FOV). Sensor arrays can have multiple functionalities such as the simultaneous detection of position and motion. We use a linear sensor model and develop an optimization method to design an array of photodiodes. Our objective function minimizes bias and variance estimations. We introduce a maximum likelihood technique to approximate and determine the bias caused by measurement errors, and verify our theory by statistically complete simulations. We apply our theory to design an optimal sun sensor. The sensor has a predefined conical FOV, and its accuracy is controlled by a... 

Solving Nematodynamic equations with Lattice Boltzmann method is presented.We have studid the effect of shear flow on the direction of Director in different boundary conditions and different geometries.we simulated the 2D Nematic Fluid in simple shear with tangential and perpendicular anchoring and We saw nonliner effects on velocity profile when the anchoring of Nematic and boundary was perpendicular to the boundary.also we have investigated and presented the effect of shear velocity magnitude on the overall direction of Director.Also the effect of shear flow have studid for the Nematic between two hegzagons  

In this thesis we study an unexpected reverse spiral turn in the final stage of the motion of rolling rings. Equations of motion for rolling rings have been derived in the framework of Newtonian and Lagrangian mechanics, and solved in the presence of air drag forces and torques. The rolling motions of ellipsoids and disks have been used to validate the governing equations of motion. Based on experimental tests, we have found that the center of mass of rings moves in an S-shape trajectory. This is in contrast to spinning disks and coins that follow a spiral path before they stop. To explain this behavior, we included the effect of air drag in the equations of motions and found that the escape... 

Spine column is the most important musculoskeletal structures. One of the serious health problems in societies, especially among aged population is osteoporosis. Loss of bone density in bone structures is called osteoporosis which increases the risk of fracture due to a decrease of bone stiffness and bone strength. Spine is the most common sites for osteoporosis-related fractures. Current assessment of osteoporosis status is based on bone densitometry tools like QCT (Quantitative Computed Tomography) or DEXA (Dual Energy X-ray absorptiometry). With these methods it is only possible to estimate density without any consideration the morphology of trabecular making parts like rods and plates.... 

Aggregation of membrane proteins plays a determinative role in many biological processes، such as signal transduction, cell division and endocytosis. In the present study, we have investigated the interaction between proteins in vesicles by means of coarse-grained molecular dynamics simulations. In the first step, a number of periodic lipid bilayers were simulated and their physical properties were calculated. Then, bilayers were immersed in water and converted into spherical vesicles via a selforganizing process . Finally two proteins were embedded into the vesicle and the potential of mean force (PMF) respect to the angle between them was obtained using umbrella sampling. This process was... 

Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with...