Sharif Digital Repository

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... 

The physical characteristics of Pt nanoclusters with different sizes (256-8788 atoms) have been investigated via molecular dynamics simulations. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters are calculated at some temperatures. The melting point predicted by the various properties is consistent with each other and shows that the melting temperature increases with the particle size. We have calculated the Gibbs free energy for the Pt bulk and also for its nanoparticle. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its... 

In addition to chemical stability and biocompatibility, because of the characteristics of quantum dimensions, gold nanoparticles are used in detecting cancers, imaging and therapeutics .Atomic interactions between gold particles and bioparticles are influenced by the dimensions of gold particles .Therefore, in this project, after introduction of various water models and used potentials for modeling by the method of TIP3P, we studied gold clusters in different dimensions and densities, by using EAM potential in the aquatic environment .Then we can pave the way for studying proteins besides gold nanoparticles, in the future studies. Besides, gold particles were studied as colloid, so as to... 

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... 

Alzheimer’s disease (AD) is the most common type of dementia in the elderly. The neuropathology and treatment of AD is not precisely determined yet, but according to the pathological studies, AD is associated with presence of toxic soluble oligomers and insoluble senile plaques formed by amyloidosis of Amyloid Beta (Aβ) in neocortical region of brain. An attractive therapeutic approach to treat AD is to identify small ligands that are capable of binding to critical residues in order to inhibit or reverse Aβ amyloidosis process as source of neurotoxicity. In this area, therapeutic efforts designed various organic agents and most of them focused on the N-terminal sequence of Aβ. The aim of... 

In this study, the nano-scale deformation mechanism of cementite was investigated with aid of Molecular dynamics (MD) simulation using MEAM potential. For this purpose, flow localization was evaluated in various structures such as single crystal cementite, nanocrystalline (NC) cementite, and lamellar cementite at various temperatures and different stress conditions. In order to understand the deformation mechanism in the cementite single crystal, two cylindrical samples with 15 nm length and 5 nm diameter oriented along [001] and [011] were constructed. The result of tensile test simulation at 100 K, 300 K, 700 K and 1100 K revealed that the deformation mechanism in single crystal cementite... 

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... 

Mechanical properties such as Young's and bulk modulus and strength of material is improved by adding Nano fillers to polymer substrates. Hence by adding Nano fillers such as graphene and carbon nanotubes to polymer substrates it is possible to achieve better properties in resultant nano composites. The aim of this study is to investigate the improvement in polymer-based composites properties by adding graphene Nano fillers for shock absorption. In this study, molecular dynamics method is used to model the molecular behavior of the material. First, a sample cell that have the properties of the whole material, is modeled, then by applying impact loading in modeling software, the response of... 

In this study, a novel multiscale analysis is proposed to utilize atomistic properties of crystalline nano-materials as an input to continuum problems in the range of large deformation. The main purpose of presented work is investigating the capability of different hyperelasticity models based on molecular statics (MS) and molecular dynamics methods to attain proper hyperelastic strain energy density function to illustrate atomistic information under various types of deformation loadings. Also, the proficiency of hyperelastic model is investigated for nano-structure including different percentages of voids. The material parameters of hyperelastic strain energy density can be obtained from... 

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... 

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.
 

There is a need to achieve a capability for detailed modeling of the physical processes nano-robots at nano-scales that is driven by the growing demands of nanotechnology.. This is regime where behavior runs contrary to the familiar macroscopic world; optimized engineering design may well benefit from insight gained by emulating some of the multitude of architectures and mechanisms to be found in the biological world. Despite the fact that micro-robotics has long captured the imagination, practical implementations are only now starting to become feasible. One class of nano-robot with potential medical applications was considered that made of single wall carbon nanotube; however, long before... 

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,... 

In this work, structures of Cu-Zr bulk metallic glasses at atomic scale were studied by molecular dynamics simulation. Bulk metallic glasses have high glass form ability, which makes it possible to more effectively examine the relationship between structure and properties in glassy materials. Due to this reason, this family of materials has been selected in this research. Voronoi tessellation method, coordination number analysis, short-range order examination, glass transition temperature and pair distribution function have been selected to investigate the structure in atomic scale. Results show that full icosahedron (with the highest five-fold symmetry) and some distorted icosahedra have... 

Recent research suggests that the electrochemical deposition of cobalt-based binary alloys, such as cobalt-tungsten and cobalt-iron, can lead to the formation of amorphous structures in the coatings. Theoretical studies suggest that these structures are equivalent to structures created by the melt cooling of the alloy at speeds of about 〖10〗^10 Kelvin per second. The formation of a glass phase can significantly increase the abrasion resistance and corrosion resistance of these coatings. Empirical studies show that the ability of the glass to become glassy, or more precisely, the transition from crystalline to amorphous, is largely a function of the chemical composition. Simulation of... 

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... 

In this research, the behavior of surfactin at the presence of water, decane, and asphaltene is investigated. Decane is chosen instead of crude oil to simplify the model. In the first chapter, basic molecular structures are introduced. Furthermore, in the second chapter molecular dynamics simulation, as the main tool in these simulations, is introduced. In the third chapter, one of the most important quantities in chemical engineering, diffusion coefficient, is chosen to investigate the efficiency and accuracy of molecular dynamics simulation method to calculate such a quantity and results show that molecular dynamics simulation can present accurate quantities, more accurate than common... 

DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model... 

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, the molecular dynamics simulation is used to investigate the melting transition of B-DNA molecule, via of configurational entropy, the fraction of broken hydrogen bonds (f-curve) and hydrogen bonding energy.We have performed molecular dynamics simulation on Drew-Dickerson oligomer with sequence of (CGCGAATTGCGC) at different temperatures, within the range of 280-400 K with the 20 K intervals. The simulation was done in two different mediums (pure water and 1 M NaCl), to see influences of water and salt in stabilizing the DNA molecule. At each temperature, configurational entropy is calculated by the Schlitter’s formula, using the Cartesian coordinate of all atoms. So, in each...