Sharif Digital Repository

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was... 

A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. The... 

Understanding the adsorption dynamics of nanoparticles at solid-liquid interfaces is of paramount importance to engineer nanoparticles for a variety of applications. The nanoparticle surface chemistry is significant for controlling the adsorption dynamics. This study aimed to experimentally examine the adsorption of surface-modified round-shaped silica nanoparticles (with an average diameter of 12 nm), grafted with hydrophobic (propyl chains) and/or hydrophilic (polyethylene glycol chains) agents, at an aqueous solution-silica interface with spherical soda-lime glass beads (diameter of 3 mm) being used as adsorbents. While no measurable adsorption was observed for solely hydrophobic or... 

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with... 

Focused on the assessment of the diphenhydramine hydrochloride (DPH) capabilities as an alternative to conventional and harmful industrial corrosion inhibitors, electrochemical techniques were employed. The optimum concentration of 1000 ppm was determined by molecular simulation and validated through electrochemical experiments. The results acquired from the electrochemical impedance spectroscopy (EIS) study showed that DPH at a concentration of 1000 ppm has a corrosion efficiency of 91.43% after 6 h immersion. The DPH molecules' orientation on the surface was assessed based on EIS predicting horizontal adsorption on the surface. Molecular simulations were done to explore the adsorption... 

Background and objective:Doxorubicin (DOX) is a known anticancer drug which is widely used in cancer therapy. Carbon nanotubes (CNTs) are among the most promising platforms for smart drug delivery applications. However, due to the toxicity and their low sulubility their application is limited and their functionalization with wide range of biomolecules are suggested. Therefore, the functionalized carbon nanotubes (f-CNT) with carboxyl (CNT-COO) and folic acid (CNT-COO-FA) were investigated as drug-carrier. Methods: Molecular dynamics (MD) simulation along with the Density Functional Theory (DFT) methods are being used to study the drug loading process on functionalized carbon nanotubes.... 

In this study, the effect of heat shock on the cell membrane was investigated using molecular dynamics (MD) simulations. Specifically, we examined the structural and dynamic behavior of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer as it was exposed to increasing temperatures ranging from 310K to 340K. The results revealed a significant transition in membrane behavior as temperature increased, particularly at 330K and 340K, where the bilayer exhibited characteristics of a fluid disordered phase. This transition was marked by an increase in the area per lipid, a decrease in bilayer thickness, and a reduction in the deuterium order parameter (Scd), indicating... 

Estate administration involves managing and distributing a deceased individual’s assets to beneficiaries, as well as managing the liabilities. This process comprises legal, financial, and administrative tasks that ensure assets are transferred based on the deceased's wishes and in accordance with the law. In Southeast Asia countries such as Indonesia, Malaysia and Brunei where Muslims represents the majority of population, the Islamic law plays an integral part in the inheritance management as the process to be in line with the Islamic teachings and principle. The role of the syariah authority namely the syariah courts is prevalent and therefore, abidance to the rule under the syariah legal... 

A novel intelligent semi-active control system for an eleven degrees of freedom passenger car's suspension system using magnetorheological (MR) damper with neuro-fuzzy (NF) control strategy to enhance desired suspension performance is proposed. In comparison with earlier studies, an improvement in problem modeling is made. The proposed method consists of two parts: a fuzzy control strategy to establish an efficient controller to improve ride comfort and road handling (RCH) and an inverse mapping model to estimate the force needed for a semi-active damper. The fuzzy logic rules are extracted based on Sugeno inference engine. The inverse mapping model is based on an artificial neural network... 

Using CNG as an additive for gasoline is a proper choice due to higher octane number of CNG enriched gasoline with respect to that of gasoline. As a result, it is possible to use gasoline with lower octane number in the engine. This would also mean the increase of compression ratio in SI engines resulting in higher performance and lower gasoline consumption. Over the years, the use of simulation codes to model the thermodynamic cycle of an internal combustion engine have developed tools for more efficient engine designs and fuel combustion. In this study, a thermodynamic cycle simulation of a conventional four-stroke spark-ignition engine has been developed. The model is used to study the... 

With the declining energy resources and increase of pollutant emissions, a great deal of efforts has been focused on the development of alternatives for fossil fuels. One of the promising alternative fuels to gasoline in the internal combustion engine is natural gas [1-5]. The application of natural gas in current internal combustion engines is realistic due to its many benefits. The higher thermal efficiency due to the higher octane value and lower exhaust emissions including CO2 as a result of the lower carbon to hydrogen ratio of the fuel are the two important feature of using CNG as an alternative fuel. It is well known that computer simulation codes are valuable economically as a cost... 

Gaining insight into possible vibratory responses of dynamical systems around their stable equilibria is an essential step, which must be taken before their design and application. The results of such a study can significantly help prevent instability in closed-loop stabilized systems by avoiding the excitation of the system in the neighborhood of its resonance. This paper investigates nonlinear oscillations of a rotary inverted pendulum (RIP) with a full-state feedback controller. Lagrange’s equations are employed to derive an accurate 2-DoF mathematical model, whose parameter values are extracted by both the measurement and 3D modeling of the real system components. Although the governing... 

A suction-controlled ring device has been developed to continuously measure the coefficient of lateral soil pressure in deformable unsaturated soil samples from the at-rest to the active condition under application of increasing vertical pressure and controlled matric suction. The device incorporates a thin aluminum specimen ring equipped with horizontal strain gages for recording the lateral soil strains. In addition, a sensor recording water volume changes is utilized to continuously monitor the degree of saturation of the soil sample during tests. The matric suction within the soil texture is controlled using the axis translation technique. In order to verify the performance of the ring... 

We introduce a new smooth, non-toxic, biocompatible method for cross-linking of gum tragacanth (GT), a polysaccharide of natural origin, in order to serve as a new supporting matrix for immobilization systems. The modified gum is used as a matrix for the catalysis of the conversion of benzyl penicillin to 6-aminopenicillanic acid (6-APA) by means of Escherichia coli ATCC11105 with penicillin G acylase (PGA) activity. The results show that GT beads can not only serve as a proper matrix for immobilization, but show enhanced hydrolysis rate and stability compared to other immobilization systems used for this reaction. This signifies the potential of GT as a biocompatible matrix for... 

The Class-E power amplifier has been widely studied and formulated in the literature. Although the majority of reported inductive coupling wireless power transfer (WPT) systems use a class-E power amplifier for driving the primary coil, still there is a lack of a comprehensive study on class-E circuit dedicated to WPT, providing a set of closed form design equations for proper class-E operation. This paper presents the required design equations needed to design a 'true' class-E circuit for WPT applications. Equations for the series-tuned secondary coil WPT system are presented, as well as two different design procedures for the parallel-tuned secondary coil. The derived equations have been... 

Pole Side Impact Tes is one out of three crash tests described by Euro NCAP standard for star rating of a vehicle and is required for assessing the Adult Occupant Protection. In this paper the goal is to determine the crashworthiness of side doors and B pillar in a Pole Side Impact Test based on Euro New Car Assessment Program (Euro-NCAP) using computer and simulation method. In this matter, a vehicle model has been prepared and meshed using Hypermesh and CATIA. The velocity of 29 km/h has been assigned to the vehicle which was on top of a cart while the pole has been assigned as a rigid static object based on Euro NCAP requirements specifically. Results show that different amounts of energy... 

To assess a car under the Euro New Car Assessment Program (Euro-NCAP), Adult Occupant Protection is one out of three parameters which need to be calculated with a weight factor of 50% while the other parameters, Child Occupant Protection and Pedestrian Occupant Protection, have a weight factor of 20%. The Pole Side Impact Test, beside two other tests, Side and Front Impact, is also required to calculate the Adult Occupant Protection. It shows how important the Pole Side Impact Test is and what an effective role it has in the car rating assessment. In this paper, the objective is to evaluate the effect of thickness on the energy absorbed by the side doors and the B pillar and its...