Sharif Digital Repository

Milk is One of the most important source s of protein in the world. during the process of cheese the most of these protein remain in whey. There are different methods to separate these protein from whey. The one of advanced method is ultrafiltartion, this method is based on a permeable membranes, with different pore size. There are many research works in this field. In this project we have tried to study the effect ofpressure, temperature, concentration and resistance time on membrane porosity. In order to design the experiment and analyze the results tagochi L 16 methods is used. The PVC membranes were prepaid by gas anti solvent method, experiment showed that changes of temperature and... 

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... 

Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle–protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed Characterization studies of nanoparticle–protein complexes show that the structure and function are influenced by the... 

DNA is big protein molecule consisting of two strands intertwining each others. Recently DNA molecule has drawn attention of researchers to be used in electronic circuits and molecule electronic field. Therefore, many experiments have been carried out to measure DNA conductivity in different temperature in single molecule or bundle mode with varying size and shape. In this thesis, metallic bundle DNA at normal room temperature is studied and their resistance characteristic is obtained and compared. In order to improve DNA conductivity Metal Ions like zinc are adulterated to each of its structure period. DNAs with these metallic impurities are called metallic DNAs.
Thus, golden electrodes... 

The purpose of this reaserch is to create a context in production of Bone Morphogenetic Protein-2 with more effective properties in Bone healing in Iran. Because of demand Of this protein in medical field it could cause an evalution in bone healing. The first section of this reaserch was the Construction of new recombinant plasmid carrying bone morphogenetic protein gene that was title of this thesis. First total RNA was extracted from ostosarcoma cancer cell line MG-63 followed by cDNA synthesis.For amplifying of the mature region of protein a pair of primer with tow restriction site was designed. After Success in PCR and obtaining PCR product with size of 343bp it transferd to vector... 

In the present thesis, intracellular fluid flows have investigated for study cell motions. It is due to firmly relation between the cell motion and these flows. Generally, the cell firstly adheres to a surface, then, moves forward with the effects of the internal fluid flows. In this study, the cell structure is invided to two general parts; the front part of the cell and the cell body. The front part of the cell plays a essential roles in the cell motion, however, the cell body is considered as a extra cargo that is carried by the front of the cell. Therefor, in the present modellings, the front part is only considered. Here, using four different models for the front part of the cell, many... 

This research aims to develop a drug delivery system based on mesoporous silica nanoparticles (MSNPs) for hydrophobic drugs and evaluating their cytotoxicity. The internal environment of the body is aqueous, while most of effective drugs display poor aqueous solubility, resulting in insufficient bioavailability. Due to their several unique properties, such as a large surface area, tunable pore size, facile surface multi functionalization and excellent biocompatibility, MSNPs are recognized as promising and powerful tools to overcome this hurdle. In the present study, MSNPs were synthesized using template removing method and then were functionalized through grafting procedure. They were... 

The nanoparticles have been widely used in the field of physics, chemistry, electronics and mechanics because of their high surface area. One of their most important applications is in drug delivery systems as smart drug nanocarrier. Magnetic nanoparticles (including Fe2O3, Fe3O4) are the good candidates for this purpose. It is clear that, upon to entrance of nanoparticle into biological media (such as plasma), the surface of nanoparticles were covered by protein layers (protein corona). This layer is very stable and created new surface on the nanoparticles. The protein corona layer intracts with cellular receptors and determines the fate of nanoparticles. Protein corona covers the targeting... 

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... 

Axon is an important part of the neuronal cells and axonal microtubules are bundles in axons.In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded filamentous protein in the central nervous system. These proteins are responsible for cross-linking axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed between nearby microtubules creating bundles. Formation of bundles of microtubules causes their transverse reinforcement and has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain circumstances such as in... 

The increasing role of nanotechnology in our every-day-life, has aroused global concern regarding their hazardous potential, resulting in a demand for parallel risk assessment. Quatitative structure-activity relationships enable researches to use unique properties of nanoparticles as predictors for their toxicity or any other biological response. Extracting rational correlations between physicochemical properties of nanoparticles and their biological response, not only reveals the way that nanoparticles behave upon entering into biological media, but also leads to the design of safer and efficient nanoparticles for various applications of interest. This PhD dissertation presents QSAR tools... 

Surface phenomena and dynamic interfacial properties plays a significant role in multiphase gas-liquid & liquid-liquid processes applied in different industrial applications. However, current laboratory equipment and represented methods for dynamic and unsteady state condition caused by motivation of interface of two phases (like rising bubble), in purpose of qualitative investigation of interphase properties are not satisfying enough. Also, common modeling methods are represented with lots of modified assumptions which are not validated properly with experimental results. In current thesis, with development of laboratory tools and applying the “rising bubble method” for investigating the... 

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... 

Diabetes has become the most prevalent disease all among the world. One of the complications of this disease is diabetic nephropathy. Diabetic nephropathy occurs when the kidney cells encounter high glucose concentration for long periods. Kidney cells use glucose as their energy supply. However, the excess glucose in the diabetics triggers specific gene pathways, gradually leading to diabetic nephropathy. As a result, proteins’ levels and the activity of transcription factors change during the disease progression. Diabetic nephropathy is characterized by excessive deposition of the proteins comprising the extracellular matrix in the mesangium, basement membrane of the glomerulus, and in the... 

These days, self-assembly is one of the most significant phenomena in chemistry and biology. Although There are some Experiments and Simulations which help us to understand self-assembly much more than before, their mechanism is poorly understood. As a result, Calculating Free-energy landscape could be a great development in this area.We use the Flat-histogram monte Carlo algorithm to calculate the density of states of a complex system. In this way, there is a comparison between the exact density of states of Ising Model and the same quantities that are obtained from Flat histogram Method. After that, there would be a combination of statistical thermodynamics and Graph theory toward drawing... 

Platelet Rich Plasma (PRP) is a blood-derived product containing concentrate of platelets, which are a rich source of autologous growth factors. PRP injection has been used clinically as a therapeutic method for cartilage repair. However, clinical efficiency of this method is unpredictable, maybe as a result of burst release of growth factors then fail cell-stimulating potential as most biomolecules are cleaned before they can exert a therapeutic effect. The aim of this project was to prepare a suitable scaffold for PRP delivery to regenerate cartilage injuries. In order to resemble polysaccharide-protein nature of the cartilaginous extracellular matrix, in this study, we developed an... 

Flagella is the organelle involved in motility of Salmonella and plays an important role in colonization of Salmonella. Flagellins is the structural subunits of flagellar filament that is known as an adjuvant. Recombinant production of flagellin of S. enteritidis is advantageous due to the removal of pathogenic microorganism from the production process and improved process safety. E.coli is an appropriate host for the expression of recombinant proteins. However, its major obstacle is the formation of inclusion bodies. Inclusion bodies are aggregated inactive proteins and the recovery of proteins in the active form from these aggregates usually has a low yield. Therefore, the objective of our... 

F-BAR protein is one of the Bin/Amphiphysin/Rvs (BAR) superfamily proteins which contributes in curvature generation and stabilization of lipid membranes. These proteins usualy form lattices on the membrane and can sculpt the membrane. In this project the interaction of F-BAR protein with a lipid membrane is modeled using coarse grained molecular dynamics approach. In order to describe the curvature generation and stabilization we would need an appropriate coarse grained model for the lipid membrane. In this project the proposed model for the membrane describes a membrane in liquid phase with a lateral diffusion in the lipid bilayer. Depth and width of the lipids potential is determined in... 

In novel drug delivery systems, once nanocarriers confront the biological milieu, their surface is rapidly covered with a layer of biomolecules (i.e., “protein corona”) which play an important role in their drug release rate. Various experimental studies have been done to elucidate the effect of nanoparticles properties on the drug release rate in different biological applications. The physical and geometrical properties of protein corona totally influence on the release profile. In this study, we proposed a suitable finite element model which contains the nanoparticles and the protein layer with their properties in the biological milieu. To this end, diffusion parameters including diffusion...