Sharif Digital Repository

A familiarity with denaturation process is highly significant in understanding the DNA replication, manipulation, and interactions involving DNA double helix stability. We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. At each temperature, configurational entropy was estimated using the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we calculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat capacity for the atoms participating in the hydrogen bonding between two strands of DNA. Moreover, their temperature... 

We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T m) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There... 

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

We compute fractal dimension and permutation entropy for healthy and people who have experienced heart failure. Our result shows that permutation entropy is a suitable approach as well as detrend fluctuation analysis (DFA). The result of DFA shows that the fractal dimensions for healthy and heart failure are different as well as the permutation entropy result. The fluctuation value for permutation entropy for an individual who has experienced heart failure is bigger than for a healthy person. There is some specific change in the interbeat signal of a person who has experienced heart failure, but there is not previous trend for a healthy person  

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would... 

Molecular dynamics simulations are performed to obtain insight into the structural properties of hydrated Nafion using the sandwich model of the polymer membrane. It is shown that a larger distance between the sulfonate groups of a chain leads to the polymer forming a better inverted micelles structure. Water- and hydronium-polymer interfaces are investigated. Comparing our results with others indicates that, from the perspective of distance, the formation of shells of water and hydronium ions is independent of the model and monomer type, but depends on both if the coordination number is considered. The behaviour of water molecules and hydronium ions is also studied dynamically. Our survey... 

A method is developed to calculate the critical line of two dimensional (2D) anisotropic Ising model including nearest-neighbor interactions. The method is based on the real-space renormalization group (RG) theory with increasing block sizes. The reduced temperatures, Ks (where K=J/kBT and J, kB, and T are the spin coupling interaction, the Boltzmann constant, and the absolute temperature, respectively), are calculated for different block sizes. By increasing the block size, the critical line for three types of lattice, namely: triangular, square, and honeycomb, is obtained and found to compare well with corresponding results reported by Onsager in the thermodynamic limit. Our results also... 

To solve the controversy, regarding the existence of an analytic solution to the 1-D Ising model with nearest-neighbor (NN) and next-nearest-neighbor (NNN) interactions in the presence of a magnetic field, we apply the transfer matrix method to solve the 1-D Ising model in the presence of a magnetic field, taking both NN and NNN interactions into account. We show that it is possible to write a transfer matrix only if the number of sites is even. Even in such a case, it is impossible to diagonalize the transfer matrix in an analytic form. Therefore, we employ a numerical method to obtain the eigenvalues of the transfer matrix. Moreover, the heat capacity, magnetization, and magnetic... 

In this paper, we consider a zero error coordination problem wherein the nodes of a network exchange messages to be able to perfectly coordinate their actions with the individual observations of each other. While previous works on coordination commonly assume an asymptotically vanishing error, we assume exact, zero error coordination. Furthermore, unlike previous works that employ the empirical or strong notions of coordination, we define and use a notion of set coordination. This notion of coordination bears similarities with the empirical notion of coordination. We observe that set coordination, in its special case of two nodes with a one-way communication link is equivalent with the Hide... 

In this paper an optimized wind/PV hybrid system with battery and diesel backup is designed. As a result of this study the costs of the hybrid system will be minimized in its 20-year life time. The optimization is done by considering the annual load increase and fuel cost rise. This Optimization is subject to load covering and minimizing the total cost. The total cost entailed maintenance, equipment and diesel fuel consumption substitution. An advanced variation of individual particle optimization algorithm (IPO) is used to solve the optimization problem  

Four 5-, 10-, 20- and 30-story moment frames, representing low-, mid-, and two high-rise structures, were subjected to a great number of idealized directivity pulses. The amplitudes and periods of pulses vary from 0.02 g to 1.0 g and 0.5 to 12 sec, respectively. Over 1400 nonlinear dynamic analyses of low- to high-rise moment frames were performed which were feasible through using modified fish-bone model. The distribution of interstory drift along the height was studied and two applied contours were proposed: (i) the maximum interstory drift contour, and (ii) the critical story contour. These contours were demonstrated versus the ratio of natural period of the structure to the pulse period... 

In this article singular points of a parallel manipulator are obtained based on a novel geometrical method. Here we introduce the constrained plain method (CPM) and some of its application in parallel mechanism. Given the definition of constraint plane (CP) and infinite constraint plane (ICP) the dependency conditions of constraints is achieved with the use of a new theorem based on the Ceva geometrical theorem. The direction of angular velocity of a body is achieved by having three ICPs with the use of another theorem. Finally, with the use of the above two novel theorems singularities of the 3UPF_PU mechanism are obtained. It should be emphasized that this method is completely geometrical,... 

An analytical model is proposed to study the effect of particle size on melting enthalpy and entropy of metallic nanoparticles (NPs). The Mott's and Regel's equations for melting entropy in the combination of core average coordination number (CAC) and surface average coordination number (SAC) of freestanding NPs are considered. Clusters of icosahedral (IC), body centered cubic (BCC), and body centered tetragonal (BCT) structure without any vacancies and defects are modeled. Using the variable coordination number made this model to be in good agreement with experimental and molecular dynamic (MD) results of different crystal structures. The model predicts melting entropy and enthalpy of... 

Grinding is widely used for manufacturing of components that require fine surface finish and good dimensional accuracy. In this study a thermo-mechanical finite element analysis is conducted to find out how grinding parameters can affect temperature and residual stress distribution in the workpiece. Results of parametric study presented in this work indicate, by carefully selecting the grinding parameters, minimum thermal and mechanical damage can be achieved. Higher workpiece velocities produce higher surface residual stress. By increasing depths of cut, depth of tensile residual stresses increases. Convection heat coefficient does not have any considerable effect on surface residual stress... 

Adaptive Noise Cancellation (ANC) is a well-known technique for background noise reduction in automobile and vehicular environments. The noise fields in automobile and other vehicle interior obey the diffuse noise field model closely. On the other hand, the ANC does not provide sufficient noise reduction in the diffuse noise fields. In this paper, a new multistage post-filter is designed for ANC as a solution to diffuse noise conditions. The designed post-filter is a single channel Linear Prediction (LP) based speech enhancement system. The LP is performed by an adaptive lattice filter and attempts to extract speech components by using intermediate ANC signals. The post-filter has no... 

Self-Compacting Concrete (SCC) is a unique type of concrete that can flow and fill spaces without the need for vibrating compaction, resulting in a dense and uniform material. This article focuses on estimating the compressive strength of SCC utilizing Artificial Neural Networks. Specifically, the study employs multilayer perceptrons with back-propagation learning algorithms, which are commonly used in various problem-solving scenarios. The study covers essential components such as structure, algorithm, data preprocessing, over-fitting prevention, and sensitivity analysis in MLPs. The input variables considered in the research include water, fine aggregate, super-plasticizer, fly ash, coarse... 

Seismic retrofits can significantly reduce the vulnerability of masonry buildings. Multiple seismic retrofit alternatives are often available for a given building. Estimating the cost of each candidate action is essential to selecting and implementing the appropriate seismic retrofit initiatives. This research harnesses the capabilities of various regression models for cost estimation. A dataset from 167 retrofit projects for masonry school buildings was used to develop models. Three main retrofit actions were taken into consideration: shotcrete, steel belt and fiber-reinforced polymer. Various regression methods, including multiple linear regression, ridge regression, lasso regression, and... 

Shot peening is widely used to improve the fretting fatigue strength of critical surfaces. Fretting fatigue occurs in contacting parts that are subjected to fluctuating loads and sliding movements at the same time. This paper presents a sequential finite element simulation to investigate the shot peening effects on normal stress, shear stress, bulk stress and slip amplitude, which are considered to be the controlling parameters of fretting damage. The results demonstrated that among the modifications related to shot peening, compressive residual stress has a dominant effect on the fretting parameters  

One-dimensional (1D) MgO structures were successfully synthesized via carbothermic reduction of mechanically activated mixture of MgO and graphite. Mechanical activation of source materials before carbothermic reduction can substantially enhance the formation of MgO products at a temperature (1000 °C) relatively lower than that required in previous approaches (≥1200 °C). However, the morphology of MgO formed is dependent on the degree of mechanical activation and the condition of the subsequent carbothermic reduction. Two distinctive morphologies were found for MgO products synthesized using our method: single crystalline nanorods with rectangular cross-sections whose diameters range from 50...