Sharif Digital Repository

This paper addresses a conceptual study on different aspects of a novel smart treatment method for a relatively new challenge of saline water production from low permeability lenses of high flow gas wells. Selective sealing of such lenses along with minor effect on gas productivity usually faces practical difficulties due to the inherent permeability contrast. Engineered application of salt sensitive gellan biopolymer through a smart treatment scenario that includes a protective gas flow proved its ability for treating such challenge. This paper investigates the importance of the gel rigidity and its coverage in the smart treatment scenario through considering the brine salinity and the... 

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc. At low values of lp/Rc, the entropy of the linear chain leads to the... 

The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers... 

Abstract: In recent years, temporary skin grafts (TSG) based on natural biopolymers modified with carbon nanostructures have received considerable attention for wound healing. Developments are required to improve physico-mechanical properties of these materials to match to natural skins. Additionally, in-deep pre-clinical examinations are necessary to ensure biological performance and toxicity effect in vivo. In the present work, we show superior acute-wound healing effect of graphene oxide nanosheets embedded in ultrafine biopolymer fibers (60 nm) on adult male rats. Nano-fibrous chitosan-based skin grafts crosslinked by Genepin with physico-mechanical properties close to natural skins were... 

Rhamnolipids are the most common biosurfactants and P. aeruginosa strains are the most frequently studied microorganisms for the production of rhamnolipids. Eco-friendly advantages and promising applications of rhamnolipids in various industries are the major reasons for pursuing the economic production of these biosurfactants. This study shows that cultivation of P. aeruginosa MR01 in medium contained inexpensive soybean oil refinery wastes which exhibited similar levels and homologues of rhamnolipids. Mass spectrometry indicated that the Rha-C10-C10 and Rha-Rha-C10-C10 constitute the main rhamnolipids in different cultures of MR01 including one of oil carbon source analogues. Moreover,... 

Changing the wettability of reservoir rock towards strongly water-wet state is effective way to enhance oil recovery from fractured carbonate reservoirs which are typically oil-wet. Regarding this fact, the injection of surfactant and the bacterial solution as EOR agents is proposed in the current work as a potential method to alter the wettability of rock surface reservoir. Nevertheless, there is a definite lack of experimental data regarding this method and the synergistic effect of both chemical and bacterial solutions on this process. In this study, the sole and combined effects of the bacterial solution using an Enterobacter cloacae strain as a biosurfactant-producer are compared with... 

Owning to interesting properties of biosurfactants such as biodegradability and lower toxicity, they have broad application in the food industry, healthy products, and bioremediation as well as for oil recovery. The present study was aimed to develop a GA-ANFIS model for predicting the breakthrough curves for rhamnolipid adsorption over activated carbon. To that end, a set of 296 adsorption data points were utilized to train the proposed FIS structure. Different graphical and statistical methods were also used to evaluate the model's accuracy and reliability. Results were then compared to those of the previously reported Artificial Neural Network (ANN) and Group Method Data Handling (GMDH)... 

The performances of gas chromatography with mass spectrometry and of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry are examined through the comparison of Daphnia magna metabolic profiles. Gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with mass spectrometry were used to compare the concentration changes of metabolites under saline conditions. In this regard, a chemometric strategy based on wavelet compression and multivariate curve resolution–alternating least squares is used to compare the performances of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with... 

Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and... 

In the current study, a novel approach which takes into account the effectiveness of both convectional surfactants and biosurfactants was investigated. The biosurfactant produced by Enterobacter cloacae strain was utilized concomitant with conventional surfactant (sodium dodecyl benzene sulfonate (SDBS)) to evaluate its capability to reduce the SDBS adsorption on rock surface (biosurfactant acts as sacrificial agent) or synergistically enhance the effectiveness of the SDBS. In this regard, the wettability alteration and interfacial tension (IFT) measurements and calculation of spreading coefficient were performed considering two different scenarios. In the first scenario, SDBS was added to... 

A bacterial strain was isolated and cultured from the oil excavation areas in tropical zone in southern Iran. It was affiliated with Pseudomonas. The biochemical characteristics and partial sequenced 16S rRNA gene of isolate, MR01, was identical to those of cultured representatives of the species Pseudomonas aeruginosa. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties. Compositional analysis revealed that the extracted biosurfactant was composed of high percentages lipid (∼65%, w/w) and carbohydrate (∼30%, w/w) in addition to a minor fraction of protein (∼4%, w/w). The best production of 2.1 g/l was obtained when the cells were grown on... 

In this article, a new group contribution model is suggested for obtaining the thermodynamic properties of biomolecules in aqueous solutions. Accordingly, a Freed-FV model has been applied for the combinatorial free-volume term. The activity coefficients, solubilities, densities, and vapor pressures of amino acids and simple peptides in aqueous solutions were correlated, using the proposed group contribution model. Group interaction parameters of the proposed model were obtained by use of experimental data from amino acids available in the literature. The results demonstrate that the group contribution model can accurately correlate activity coefficient, solubility, density, and vapor... 

A new local composition model was used to study the phase behavior of polymer-polymer and polymer-salt aqueous two-phase systems. The proposed model has three terms which account for the combinatorial, the long-range and the short-range effects in solution. The Flory-Huggins and the Debye-Hückel models were used for the combinatorial and long-range contributions. The interaction parameters of the model studied in this work can be regressed using a non-liner regression between the experimental data and those obtained from the proposed model. Also, this model was applied for modeling the partitioning of biomolecules in polymer-polymer and polymer-salt aqueous two-phase systems. The results... 

The bacterial strain MJ01 was isolated from stock tank water of one of the Iranian south oil field production facilities. The 16S rRNA gene of isolate, MJ01, showed 99% similarity to Bacillus subtilis. The results revealed that biosurfactant produced by this strain was lipopeptide-like surfactin based on FTIR analysis. Critical micelle concentration of produced surfactin in distilled water was 0.06 g/l. Wettability study showed that at zero salinity surfactin can change original oil-wet state to water-wet state, but in seawater salinity it cannot modify the wettability significantly. To utilize this biosurfactant in ex situ MEOR process, economical and reservoir engineering technical... 

In upstream oil industry, microorganisms arise some opportunities and challenges. They can increase oil recovery through microbial enhanced oil recovery (MEOR) mechanisms, or they can increase production costs and risks through reservoir souring process due to H2S gas production. MEOR is mostly known by bioproducts such as biosurfactant or processes such as bioclogging or biodegradation. On the other hand, when it comes to treatment of reservoir souring, the only objective is to inhibit reservoir souring. These perceptions are mainly because decision makers are not aware of the effect microorganisms’ cell can individually have on the wettability. In this work, we study the individual effect... 

The ever-increasing growth of nano-technology has elevated the necessity for development of new computational methods that are capable of evaluating large systems at nano-scale. The existing techniques, such as the molecular dynamics, lack the ability to simulate large systems of practical size and time scales. In order to provide a realistic simulation of large models, the multi-scale methods such as coarse-graining, have therefore become very popular. The coarse-grained models have mostly been used to simulate large biomolecules, such as proteins, lipids, DNA and polymers. In this paper, the Iterative Boltzmann Inversion (IBI) coarse-graining technique is applied to FCC nano-crystals; the... 

The primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives... 

We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the... 

Metabolomics is the science of studying small molecules (metabolites) in biological systems with the aim of getting insight into cells, biofluids and organisms. Chemometric methods are powerful tools to address data problems generated in metabolomic studies and to extract valuable information. This review focuses mainly on a range of chemometric methods used for processing of metabolomics data generated from gas chromatography-mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS). Herein, essential skills used for preprocessing of raw data, multivariate resolution, pattern recognition, variable selection and identification of... 

The ultimate goal of new food packaging technologies, in addition to maintaining the quality and safety of food for the consumer, is to consider environmental concerns and reduce its impacts. In this regard, one of the solutions is to use eco-friendly biopolymers instead of conventional petroleum-based polymers. However, the challenges of using biopolymers in the food packaging industry should be carefully evaluated, and techniques to eliminate or minimize their disadvantages should be investigated. Many studies have been conducted to improve the properties of biopolymer-based packaging materials to produce a favorable product for the food industry. This article reviews the structure of...