Sharif Digital Repository

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... 

Since the first observed case in December 2019, millions of people have been infected by Coronavirus disease 2019 (COVID-¬19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS¬-CoV-¬2). Located on the viral membrane, trimeric spike glycoprotein is one of the most crucial parts of the virus’ structure as it is responsible for the attachment and entry of the virus to host cells. The spike glycoprotein undergoes hinge-like conformational movements and its receptor¬binding domains (RBD) can be in either an accessible (up) state or an inaccessible (down) state to the host cell receptors, such as ACE2. Having performed Molecular Dynamics Simulations and Targeted Molecular... 

Ionic polymer metal nanocomposites (IPMNCs) are among the advance materials which have been widely used recently as smart materials. These nanocomposites, which are made of polymeric layers (Nafion) plated by metallic or non-metallic conductive electrodes, show large deformations under low applied voltages. The advance materials like these nanocomposites have resolved the problems of the conventional actuators and helped in producing accurate systems.
Several methods have been used to predict the behavior of IPMNCs which any of them consider some simplifying assumptions. In these materials physical phenomena happen at the molecular scale and deformations observed at the large scale.... 

Shape memory alloys (SMA) exhibit a number of features which are not easily explained by equilibrium thermodynamics, including hysteresis in the phase transformation and ‘‘reverse’’ shape memory in the high symmetry phase. Processing can change these features: repeated cycling can ‘‘train’’ the reverse shape memory effect, while changing the amount of hysteresis and other functional properties. These effects are likely to be due to formations of localised defects and these can be studied by atomistic methods. Here we present a molecular dynamics simulation study of such behaviour employing a two-dimensional, binary Lennard–Jones model. Our atomistic model exhibits a symmetry breaking,... 

Amyloid β (Aβ) peptide is believed to be associated with the progression of Alzheimer's disease. One of the main obstacles in developments of therapeutic agents to combat progression of Alzheimer's disease, is the presence of the blood–brain barrier (BBB), which prevents the penetration of the majority of drugs. However, nanoscale objects are able to cross the BBB at low concentrations. Therefore, it is worthwhile to study the interactions of these peptides at the interface of nanomaterials. In this work we have employed molecular dynamics, and weighted histogram analysis methods in order to study the dynamic behavior and affinity of Aβ25-35 peptide on metallic surfaces of different... 

Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

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... 

Iodine isotopes are among the most significant medical radioisotopes with a wide range of applications in therapy and diagnosis. The I-131 isotope is usually synthesized by irradiation of natural tellurium in atomic reactors. But there is an alternative route in which this isotopes is produced along with two other significant medical radioisotopes (i.e. Mo-99, Xe-131) by neutronic irradiation of uranium in the reactors. To separate iodine isotopes especially in the extraction process of fission fragments, it is necessary to be selective adsorption of iodine on a selective adsorbent. One of the most selective adsorbent for this application is copper. The aim of this study is to compare the... 

Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,... 

First atomistic simulation was used to study the deformation and fracture mechanisms of Ni-Si interfaces under tensile and shear loads dependent on the crystal structure of interface zone. Modified embedded atom method (MEAM) potential was utilized for molecular dynamics (MD) modeling. The simulation includes analysis of common neighbors, coordination number, least-square atomic local strain, and radial distribution function. The profound effect of interface crystallography on the tensile and shear deformation is shown. The highest tensile strength is obtained for interfaces with high plane density due to lowest atomic disorder while under shear loading planes with low density exhibit a high... 

Water plays an essential role in the daily lives of humans, plants, and animals. Due to the lack of safe water on the planet, in recent years there have been many challenges in the field of water treatment, which has made water desalination technology always one of the most advanced technologies. The most advanced technology in this field is the use of nanotechnology in water and wastewater treatment, especially the use of Membrane processes such as reverse osmosis. Unlike conventional reverse osmosis membranes, nanoporous membranes can ensure rapid water transfer during the displacement process. The purpose of this thesis is to introduce new monolayers that have an incredible performance in... 

In this thesis we try to find optimized parameters for imaging and manipulation of a biosample with AFM. For this we have prepared a numerous Molecular Dynamics simulation and find some reliable result. So, first we have focused on imaging process in Non contact mode (the less harmful mode). Then we headed into the manipulation process. The main problem about manipulating a biosample is the environment. In imaging section, the process of imaging a biomolecule by AFM is modeled using molecular dynamics simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the non-contact... 

Formation of Cyclobutane Pyrimidine Dimer (CPD), one of the most abundant types of damages in DNA double helices, is caused by UV radiation and plays a major role in causing skin cancer. DNA photolyase is an efficient enzyme that repairs this UV-induced damaged DNA-base. Previous studies have shown that the enzyme flips the dimer out of the DNA double helix into its binding pocket.
In this project, several nanoseconds of molecular dynamics simulations was performed to investigate the process of base flipping energetically. These simulations are consist of equilibration of repaired and damaged double strands for 3 and 8 nanoseconds respectively. All these simulations ran over NVT... 

SHP2 has been reported as a critical non-receptor phosphatase enzyme that plays crucial roles in numerous disorders like cancer. The previous studies on this enzyme showed that inhibiting the action of the enzyme comes as a way of controlling enzyme activity. SHP099 was discovered as an Allosteric inhibitor of the enzyme with the most inhibitory effect among all of the studied compounds. In this study we aimed to design novel dipeptide-and sugar-based inhibitors for the allosteric binding site of this enzyme with in-silico studies including docking, molecular dynamic simulation, and free binding energy analysis. Our novel designed drugs possess enough binding properties, low toxicity, and... 

Cyclin-dependent kinases 2 (CDK2) are one of the important proteins in cell cycle regulation and progression. In many human cancer cells, the activity of CDK2 kinases and their related subunits are deregulated, leading to tumor formation. Therefore, inhibition of this enzyme as an attractive therapeutic target can cause cancer cell death in glioblastoma and diffuse large B-cell lymphoma. Using new pharmaceutical structures based on sugar and amino acids is a new approach due to its greater efficacy and fewer side effects than old drugs. In this research, according to the structure of Flavopiridol as one of the CDK2 inhibitors, the active site of CDK2, and the structure of ATP molecule, 50... 

Malaria is one of the most important infectious diseases in the tropical and subtropical regions of the world and is caused in humans by the bite of the female Anopheles mosquito of five species of Plasmodium. According to the World Health Organization, about 229 million people worldwide were infected in 2019 by the disease, and 409,000 people died from the disease. Resistance of the parasite against drugs and resistance of vectors to insecticides and larvicides, which prevents the elimination and eradication of malaria, shows the need for new strategies, such as having an effective vaccine against this disease. In the second generation of vaccines, to develop malaria vaccines, recombinant... 

A Coiled Carbon Nanotube (CCNT) can be geometrically viewed as a graphene sheet whose rolled and twisted to form a helically coiled nanotube. It is the strongest material ever measured with strengthexceeding more than hundred times of steel.The strength of a CCNT iscritically influenced by temperature, tube diameter, strain rate and pitch angle. In this study,a Molecular Dynamics (MD) simulationis performed to understand the effect of temperature, strain rate, tube diameter and pitch angle on the mechanical properties of CCNTs. Results indicate thatexisting the stone-wales defects is necessaryfor thermodynamic stability of CCNTs.According to the stress-strain curves it was observed thatyield... 

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... 

With rising oil prices and predictions about the future of hydrocarbon reserves, issues of enhanced oil recovery and optimal production of existing reservoirs are of particular importance. In this study, molecular dynamics simulation was used to study the absorption of silica nanoparticles with surface groups at the interface of water and decane. The effect of surface chemistry of silica nanoparticles on the interface properties of water-decane with changing the surface groups was simulated. The initial surface factor of nanoparticle is hydroxyl (OH), which is called a hydrophilic surface agent. Nanoparticles were modified by methyl and ethyl surface agents to increase the hydrophobicity and... 

Formation of gas hydrates is a challenge in the oil and gas industry. Gas hydrate formation can be prevented by several methods. One of these methods is to utilize of inhibitor components. The gas hydrate inhibitors can affect hydrate formation from two aspects, i.e., thermodynamic or kinetic. In this work, thermodynamic and kinetic effects of [Emim][BF4] ionic liquid on growth and dissociation of methane hydrate crystal were investigated using molecular dynamics simulation. Molecular dynamics simulation is powerful tool to investigate the thermophysical, structural, and dynamic properties of methane hydrate and the formation, dissociation, and inhibition mechanisms at the molecular scale....