Sharif Digital Repository

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich  

Radial forging is an open forging process used for reducing the diameters of shafts, tubes, stepped shafts and axels, as well as for creating internal profiles for tubes such as rifling the gun barrels. The radial forging of tubes is usually performed over a mandrel to create an internal profile and/or size the internal diameter; but the process can also be used without a mandrel when workpiece geometry does not allow it or the internal surface quality is not critical. In some industrial applications, it may not be possible to use a mandrel inside the tubular workpiece, e.g., due to geometrical limitations of the workpiece. In this study, finite element modelling is applied to model the... 

Micro arc oxidation technique, as a facile and efficient process, was employed to grow sulfur doped titania porous layers. This research sheds light on the photocatalytic performance of the micro arc oxidized S-TiO2 nano-porous layers fabricated under pulse current. Morphological and topographical studies, performed by SEM and AFM techniques, revealed that increasing the frequency and/or decreasing the duty cycle resulted in formation of finer pores and smoother surfaces. XRD and XPS results showed that the layers consisted of anatase and rutile phases whose fraction was observed to change depending on the synthesis conditions. The highest anatase relative content was obtained at the... 

In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple... 

A sensitive fluorometric assay is described for the direct determination of the antibiotic sulfadiazine. Silver nanoparticles placed on graphene quantum dots (Ag NP-GQDs) were synthesized by reduction of AgNO3 with sodium borohydride in the presence of GQDs. The growth of Ag NPs on the surface of the GQDs causes quenching of the blue fluorescence of the GQDs with an emission maximum at 470 nm by surface-enhanced energy transfer. If sulfadiazine is added, it interacts with Ag NPs and fluorescence is restored. Under optimal conditions, the fluorescence increases linearly in the sulfadiazine concentration range of 0.04–22.0 μM. The detection limit is 10 nM with relative standard deviations of... 

Adsorption and desorption of methane by activated carbon (AC) at constant temperature and at various pressures were investigated. The effect of moisture was also studied. A volumetric method was used, up to 40 bar, at a temperature of 273.5 K. Results of a dry AC sample were compared with those obtained from a moist sample and two different ACs with different physical and surface properties were used. As expected, the results showed that the existence of moisture, trapped in the AC pores, could lead to a decrease in the amount of methane adsorbed and a decrease in the amount of methane delivered during desorption. To model the experimental results, a large variety of adsorption isotherms... 

Using whole cell as a catalyst of enzymatic transesterification is a method to produce biodiesel with fewer drawbacks and at a lower cost. In the present study, biodiesel was produced by the reaction of waste frying oil with methanol in the presence of Rhizopus oryzae PTCC 5174 in both immobilized and free forms. Effect of four influencing factors including temperature, methanol to oil molar ratio, amount of biomass, and shaking speed was investigated. Response surface methodology was used to find the optimum conditions of the transesterification reaction. Each factor was set at three levels and the yield of the biodiesel was considered as the response. A quadratic equation was well-fitted... 

Response surfaces express the behavior of responses and can be used for both single and multi-response problems. A common approach to estimate a response surface using experimental results is the ordinary least squares (OLS) method. Since OLS is very sensitive to outliers, some robust approaches have been discussed in the literature. Although there are many methods available in the literature for multiple response optimizations, there are a few studies in model building especially robust models. Assuming correlated responses, in this paper, a robust coefficient estimation method is proposed for multi response problem based on M-estimators. In order to illustrate the performance of the... 

We extend a hybrid DSMC/Navier-Stokes (NS) approach to unify the DSMC and the NS simulators in one framework capable of solving the mixed non-equilibrium and near-equilibrium flow regions efficiently. Furthermore, we use a one-way state-based coupling (Dirichlet-Dirichlet boundary-condition coupling) to transfer the required information from the continuum region to the rarefied one. The current hybrid DSMC-NS frame is applied to the hypersonic flows over nanoflat plate and microcylinder cases. The achieved solutions are compared with the pure DSMC and NS solutions. The results show that the current hybrid approach predicts the surface heat transfer rate and shear stress magnitudes very... 

In this research, data on liquid-liquid extraction of platinum from commercial spent catalysts by trioctylphosphine oxide (TOPO) in toluene were experimentally obtained. Alkaline metal salts were used to optimize the separation process. Best Salting-out effect was obtained by KCl which extracted up to 90% of platinum utilizing TOPO. Furthermore, extraction percentages of Pt and Al depending upon different factors were investigated. It was observed that the extraction process was kinetically fast and achieving the equilibrium time took less than 30 seconds. Optimized points obtained utilizing response surface methodology (RSM) by the "Design Expert" software in order to minimize the... 

We study the fractal properties of the two-dimensional (2D) discrete scale-invariant (DSI) rough surfaces. The contour lines of these rough surfaces show clear DSI. In the appropriate limit the DSI surfaces converge to the scale-invariant rough surfaces. The fractal properties of the 2D DSI rough surfaces apart from possessing the discrete scale-invariance property follow the properties of the contour lines of the corresponding scale-invariant rough surfaces. We check this hypothesis by calculating numerous fractal exponents of the contour lines by using numerical calculations. Apart from calculating the known scaling exponents, some other new fractal exponents are also calculated  

Among innovations and improvements that occurred in the past two decades on the techniques and tools used for statistical process control (SPC), adaptive control charts have shown to substantially improve the statistical and/or economical performances. Variable sampling intervals (VSI) control charts are one of the most applied types of the adaptive control charts and have shown to be faster than traditional Shewhart control charts in identifying small changes of concerned quality characteristics. While in the designing procedure of the VSI control charts the data or measurements are assumed independent normal observations, in real situations the validity of these assumptions is under... 

A heterogeneous recoverable catalyst was prepared via the complexation of palladium onto the surface of magnetic nanoparticles coated by a poly(1-vinyl imidazole) brush. The stable, active and reusable catalyst was proven to be highly active in aerobic oxidation of primary and secondary alcohols with excellent yields. Only 0.1 mol% of the catalyst was used to oxidize 1 mmol of primary and secondary alcohols. The catalyst was readily recovered and reused up to 10 times under the described reaction conditions without significant loss of activity  

Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and... 

The dielectric constant e of interfacial water has been predicted to be smaller than that of bulk water (e ≈ 80) because the rotational freedom of water dipoles is expected to decrease near surfaces, yet experimental evidence is lacking. We report local capacitance measurements for water confined between two atomically flat walls separated by various distances down to 1 nanometer. Our experiments reveal the presence of an interfacial layer with vanishingly small polarization such that its out-of-plane e is only ~2. The electrically dead layer is found to be two to three molecules thick. These results provide much-needed feedback for theories describing water-mediated surface interactions and... 

Conjugated linoleic acid (CLA) is one of the most physiological active fatty acids due to its positive effect on prevention of diseases such as obesity, hyperlipidemia, atherosclerosis and cancer. The aim of this study was to optimize the production of conjugated linoleic acid (CLA)% in alkali isomerization of safflower oil including 71% linoleic acid (LA) using response surface methodology (RSM). The effect of three reaction variables such as temperature, reaction time and amount of KOH on CLA production was investigated using design-expert software. The optimal condition determined at this point, 72% total CLA with the yield of 84% temperature reaction time and the amount of KOH were 187.6... 

The star graph, as an interesting network topology, has been extensively studied in the past. In this paper, we address some of the combinatorial properties of the star graph. In particular, we consider the problem of calculating the surface area and volume of the star graph, and thus answering an open problem previously posed in the literature. The surface area of a sphere with radius i in a graph is the number of nodes in the graph whose distance from a given node is exactly i. The volume of a sphere with radius i in a graph is the number of nodes within distance i from the given node. In this paper, we derive explicit expressions to calculate the surface area and volume in the star graph.... 

A resource investment problem with discounted cash flows (RIPDCF) is a project-scheduling problem in which (a) the availability levels of the resources are considered decision variables and (b) the goal is to find a schedule such that the net present value of the project cash flows optimizes. In this paper, the RIPDCF in which the activities are subject to generalized precedence relations is first modeled. Then, a genetic algorithm (GA) is proposed to solve this model. In addition, design of experiments and response surface methodology are employed to both tune the GA parameters and to evaluate the performance of the proposed method in 240 test problems. The results of the performance...