Sharif Digital Repository

Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper, we will introduce a new method for predicting the active sites that will use the spatial coordinates and the type of amino acids that contain the active sites. In order to increase the speed we use an approximate graph isomorphism algorithm. Furthermore, this algorithm allows us to find several... 

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

Liquid-liquid equilibrium (LLE) data, density, viscosity, and interfacial tension for the ternary system of toluene-acetic acid-water were measured at 298.15 K and 101.7 kPa. The Othmer-Tobias and the Hand correlations were used to check the reliability of the experimental tie-lines. Moreover, the distribution coefficient and the separation factor were explored. It was found from the experimental results that a maximum separation factor value happens at an acetic acid mass fraction of 0.02 in the organic phase. Density, viscosity, and interfacial tension were correlated using the appropriate correlations such that the predicted results have excellent agreement with the experimental data. The... 

Damage detection and structural health monitoring using the electromechanical impedance method has been accepted as an effective technique between various approaches of nondestructive evaluation. Many efforts have been made on experimental methods for obtaining the impedance of structures. However, expensive experimental methods encourage researchers to develop theoretical models. In this paper, a new theoretical model is developed for damage detection of L-shaped beams, which are basic components in frame structures, with an embedded piezoelectric wafer active sensor. For this purpose, a chirp signal of voltage is used to activate a piezoelectric patch for inducing local strains that lead... 

Pulsating heat pipes are complex heat transfer devices, and their optimum thermal performance is largely dependent on different parameters. In this paper, in order to investigate these parameters, first a closed-loop pulsating heat pipe (CLPHP) was designed and manufactured. The CLPHP was made of copper tubes with internal diameters of 1.8 mm. The lengths of the evaporator, adiabatic, and condenser sections were 60, 150, and 60 mm, respectively. Afterward, the effect of various parameters, including the working fluid (water and ethanol), the volumetric filling ratio (30%, 40%, 50%, 70%, 80%), and the input heat power (5 to 70 W), on the thermal performance of the CLPHP was investigated... 

A modified form of the UNIQUAC-NRF activity coefficient model was used to study the phase behaviour of the aqueous two-phase systems (ATPSs) of polyethylene glycol (PEG) and dextran (DEX) with different molecular weights at various temperatures. In the proposed model, a ternary interaction parameter was added to the expression for the excess Gibbs free energy and, in turn, to the corresponding activity coefficient rendered by the UNIQUAC-NRF model. The combinatorial part of the new model takes the same form as that of the original UNIQUAC model and the residual part considers the nonrandomness and also the binary and the ternary interactions among the molecules in mixtures of PEG, DEX, and... 

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned...