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... 

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... 

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... 

A general regularity has been found based on an effective pair potential of Lennard-Jones LJ (12, 6) for both dense nonmetallic and nonionic fluids and solids; namely, (Z-1)V2 linearly varies with respect to ρ2, this equation of state (EoS I) is known as LIR. The other equation of state (EoS II), according to wich the isotherm of (Z-1)V2 is linear in term of 1/ρ, wich gives a good description for the metallic and ionic fluids and solids. This equation of state was suggested based on an effective pair potential of LJ (6, 3). Unexpectedly, solid and liquid Ne indicates a significant deviations from EoS I. Recently, a general equation of state (EoS III) based on an effective near-neighbor pair... 

Ising model in nano systems are studied, in the presence of a magnetic field. For a one-dimensional(1-D) array of spins interacting via nearest-neighbor and next-nearest-neighbor interactions we calculated the heat capacity , the surface energy, the finite-size free energy, and bulk free energy per site. The heat capacity versus temperature exhibited a common wide peak for systems of any size. A small peak also appears at lower temperatures for small arrays when the ratio of magnetic field- spin interaction energy over the nearest-neighbour spin-spin interaction energy f is within and size. The peak becomes smaller for longer array and eventually vanishes for long arrays, disappearing when... 

In this research, a method based on the modified Enskog theory (MET) and some equations of state has been used to calculate the transport properties of some dense fluids. The main limitation to using the MET is the lack of experimental data for the co-volume, b0, that are substituted from the hard sphere (HS) theory, and the zero density transport properties that are substituted from the kinetic theory of gases for the HS in the MET expression, because of the fact that dense fluids behave more and less like a HS fluid. So a quadratic expression for both ηY/(√T ρ) and λY/(ρ√T) (C_(V,m)+ (9/4)R) in terms of Y at high densities (ρ > ρc) for each isotherm is expected, where Y = (T (∂p/∂T))/ρRT... 

In this thesis, we use two simple simulation models for ionic liquids, and the efficiency of the Lennard Jones equations and the state equation obtained from this potential were investigated. Then, using these models, the temperature-dependent coefficients were calculated in two equations at different temperatures, and then analytical expressions were reported to them. Given that ion fluid data is reported only in a small range of densities, these data were used to evaluate the equations used, using a model in a wider range of densities. For this purpose, simulation of molecular dynamics simulation data was simulated. In these two models, the relative size of cations and anions is different.... 

Prediction and calculation of shielding tensors of H, C, F and P nuclei of different molecules has been the subject of much research, because these nuclei have the greatest importance in NMR experiments. The optimum wave functions and calculation method were obtained using empirical models and factorial design. Based on preliminary experiences, the following four factors at two levels were selected: electron correlation, triple-ξ valence shell, diffuse function and polarization function. The wave functions for calculating gas phase 1H and 13C chemical shifts of various types of alcohols, amines and simple hydrocarbons were optimized using empirical model. The B3LYP/6-311+G wave function is... 

Long memory in assets return is important on the theoretical as well as the practical aspects and since it is a special form of nonlinear dynamics, in this study an ARFIMA model was used with the aim of considering the long memory in the return conditional average of automobile industry index. Then, due to the observation of ARCH effects, the simultaneous conditional average modeling and turbulences in the automotive industry index return using an ARFIMA-FIGARCH model was considered in the residuals of the best fitted model and results were that for modeling the returns and turbulences of automobile industry stocks which has a special long memory, FIGARCH will provide better and more... 

One of the recent studies in the field of humanoid robots is to achieve a robot gait close to the human-like gait. Therefore, using the foot equipped with passive or active toe joint is developed in case of robots. The results of several studies show that the segmented foot with a toe joint has several advantages compared to the rigid foot in: walking speed, range of joint angle and ability to kneel and climb higher steps. Both passive and active toe joints of humanoid robots are developed. Advantages of the passive toe joint is obvious; in terms of design, it is more simple and light. Moreover, in normal gait, when the robot is equipped with passive toe joint, body inertial causes an... 

Ion channels are present in all cell membranes which are the important part of the performances in regulating the flow across the membrane as well as the signaling. We have investigated the water permeation through carbon nanotube (CNT) membranes as a model for the synthetic ion channels, i.e. peptide nanotube channels (PNCs). The effect of different charge configured CNTs which tailored based on these ion channels on the water permeation has been studied. In addition, the temperature dependence of the permeation using statistical models such as continuous time random walk model (CTRW) via molecular dynamics simulation has been investigated. We have found that there is a jump in the... 

In this study, some properties of metallochlorophylls - compounds produced by replacing Mg2+ in tetrapyrrolic ring of chlorophyll b with divalent ions – of the forth period transit elements of the periodic table have been investigated. Using DFT/B3LYP method and DGDZVP basis set, structures of these compounds were optimized and the energy of electronic levels, Gibbs free energy of formation of complex, contribution of atomic orbitals to formation of molecular orbitals and partial charges in these molecules were computed. The results show that some properties of these complexes cannot be justified by the common theories of complexes. Among these properties is the negligible effect of... 

The expansion of technology and the increasing use of mobile devices and smartphones have aected various aspects of personal and social life. These include the use of personal mobile devices in enterprise environments called BYODs have a number of positive and negative eects. On the one hand, it would be more cost-eective for an organization or business environment for users to use their own devices, but on the other hand, it poses numerous security and information challenges that are important to manage. These include disrupting the user’s privacy or disseminating organization information to personal devices and thus violating the organization’s security policies. In this study, a model is...