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Prediction of Thermodynamic Parameters in Solutions with Similar Composition to Plasma or Blood
, Ph.D. Dissertation Sharif University of Technology ; Abdekhodaie, Mohammad Jafar (Supervisor) ; Ghotbi, Cyrus (Co-Advisor)
Abstract
Serum osmolality is an important physiological quantity that is directly related to health condition of human body. Glucose, urea, and NaCl are the main components which determine the value of serum osmolality. Besides, calcium and potassium are vital inorganic cations for the body. Thus, it is of high importance to investigate the interactions between these physiological solutes in aqueous solution. Thermodynamic quantities like osmotic and activity coefficients contain enthalpic and entropic information and thus are a direct measure of interactions in these complex systems. Thus, theoretical and experimental methods were applied to investigate these thermodynamic parameters in multi-solute...
Study of Biomolecules Imaging Using Molecular Dynamics Simulations
, Article Nano ; Volume 10, Issue 7 , October , 2015 ; 17932920 (ISSN) ; Nejat Pishkenari, H ; Moosavi, A ; Meghdari, A ; Sharif University of Technology
World Scientific Publishing Co. Pte Ltd
2015
Abstract
The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip-sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a...
Chemometrics comparison of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry Daphnia magna metabolic profiles exposed to salinity
, Article Journal of Separation Science ; Volume 41, Issue 11 , 2018 , Pages 2368-2379 ; 16159306 (ISSN) ; Garreta Lara, E ; Campos, B ; Barata, C ; Lacorte, S ; Tauler, R ; Sharif University of Technology
Wiley-VCH Verlag
2018
Abstract
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...
PH-Sensitive stimulus-responsive nanocarriers for targeted delivery of therapeutic agents
, Article Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology ; Volume 8, Issue 5 , 2016 , Pages 696-716 ; 19395116 (ISSN) ; Eslami, M ; Sahandi Zangabad, P ; Mirab, F ; Farajisafiloo, N ; Shafaei, Z ; Ghosh, D ; Bozorgomid, M ; Dashkhaneh, F ; Hamblin, M. R ; Sharif University of Technology
Wiley-Blackwell
2016
Abstract
In recent years miscellaneous smart micro/nanosystems that respond to various exogenous/endogenous stimuli including temperature, magnetic/electric field, mechanical force, ultrasound/light irradiation, redox potentials, and biomolecule concentration have been developed for targeted delivery and release of encapsulated therapeutic agents such as drugs, genes, proteins, and metal ions specifically at their required site of action. Owing to physiological differences between malignant and normal cells, or between tumors and normal tissues, pH-sensitive nanosystems represent promising smart delivery vehicles for transport and delivery of anticancer agents. Furthermore, pH-sensitive systems...
Noble metal nanoparticles in biosensors: Recent studies and applications
, Article Nanotechnology Reviews ; Volume 6, Issue 3 , 2017 , Pages 301-329 ; 21919089 (ISSN) ; Sahandi Zangabad, P ; Mirshekari, H ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
Walter de Gruyter GmbH
2017
Abstract
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...
Pattern recognition analysis of chromatographic fingerprints of Crocus sativus L. secondary metabolites towards source identification and quality control
, Article Analytical and Bioanalytical Chemistry ; Volume 408, Issue 12 , 2016 , Pages 3295-3307 ; 16182642 (ISSN) ; Sereshti, H ; Parastar, H ; Sharif University of Technology
Springer Verlag
2016
Abstract
Chromatographic fingerprinting is an effective methodology for authentication and quality control of herbal products. In the presented study, a chemometric strategy based on multivariate curve resolution-alternating least squares (MCR-ALS) and multivariate pattern recognition methods was used to establish a gas chromatography-mass spectrometry (GC-MS) fingerprint of saffron. For this purpose, the volatile metabolites of 17 Iranian saffron samples, collected from different geographical regions, were determined using the combined method of ultrasound-assisted solvent extraction (UASE) and dispersive liquid-liquid microextraction (DLLME), coupled with GC-MS. The resolved elution profiles and...
Isolation and screening of Bacillus subtilis MJ01 for MEOR application: biosurfactant characterization, production optimization and wetting effect on carbonate surfaces
, Article Journal of Petroleum Exploration and Production Technology ; Volume 9, Issue 1 , 2019 , Pages 233-245 ; 21900558 (ISSN) ; Ganji Azad, E ; Deihimi, T ; Niazi, A ; Ayatollahi, S ; Sharif University of Technology
Springer Verlag
2019
Abstract
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...
Temporary skin grafts based on hybrid graphene oxide-natural biopolymer nanofibers as effective wound healing substitutes: pre-clinical and pathological studies in animal models
, Article Journal of Materials Science: Materials in Medicine ; Volume 28, Issue 5 , 2017 , 73 ; 09574530 (ISSN) ; Eslahi, N ; Mehdipour, A ; Mohammadi, M ; Akbari, M ; Samadikuchaksaraei, A ; Simchi, A ; Sharif University of Technology
Springer New York LLC
2017
Abstract
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...
Recent advances in silicon nanowire biosensors: Synthesis methods, properties, and applications
, Article Nanoscale Research Letters ; Volume 11, Issue 1 , 2016 ; 19317573 (ISSN) ; Daraee, H ; Eatemadi, A ; Sharif University of Technology
Springer New York LLC
Abstract
The application of silicon nanowire (SiNW) biosensor as a subtle, label-free, and electrical tool has been extensively demonstrated by several researchers over the past few decades. Human ability to delicately fabricate and control its chemical configuration, morphology, and arrangement either separately or in combination with other materials as lead to the development of a nanomaterial with specific and efficient electronic and catalytic properties useful in the fields of biological sciences and renewable energy. This review illuminates on the various synthetic methods of SiNW, with its optical and electrical properties that make them one of the most applicable nanomaterials in the field of...
Microorganisms’ effect on the wettability of carbonate oil-wet surfaces: implications for MEOR, smart water injection and reservoir souring mitigation strategies
, Article Journal of Petroleum Exploration and Production Technology ; Volume 10, Issue 4 , 2020 , Pages 1539-1550 ; Ayatollahi, S ; Sharif University of Technology
Springer
2020
Abstract
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...
Dual improvement of DNA-directed antibody immobilization utilizing magnetic fishing and a polyamine coated surface
, Article RSC Advances ; Volume 6, Issue 112 , 2016 , Pages 111210-111216 ; 20462069 (ISSN) ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
Royal Society of Chemistry
2016
Abstract
The present study is aimed at the development of a novel approach based on the magnetic improvement of DNA-directed antibody immobilization to prepare a highly efficient sensing platform. Magnetic nanoparticle substrates with high surface area capture the dual DNA-conjugated antibodies in a solution. This allows overcoming the typical mass transport limitation of the surface-based antibody immobilization. Antibody-magnetic nanoparticle conjugation is based on a robust hybridization between a DNA tether (attached to the antibody) and its complementary sequence (immobilized on the nanoparticle). Conventional antibody immobilization for the detection of proteins is often insignificant for the...
Disease-related metabolites affect protein-nanoparticle interactions
, Article Nanoscale ; Volume 10, Issue 15 , 2018 , Pages 7108-7115 ; 20403364 (ISSN) ; Montazeri, A ; Naghdabadi, R ; Hajipour, M. J ; Zanganeh, S ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
Royal Society of Chemistry
2018
Abstract
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...
Theoretical simulation of surface-enhanced resonance Raman spectroscopy of cytosine and its tautomers
, Article Journal of Raman Spectroscopy ; Volume 51, Issue 1 , 2020 , Pages 55-65 ; Mohammadpour, M ; Ramazani, S ; Jamshidi, Z ; Sharif University of Technology
John Wiley and Sons Ltd
2020
Abstract
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...
Evaluation of a recycling bioreactor for biosurfactant production by Pseudomonas aeruginosa MR01 using soybean oil waste
, Article Journal of Chemical Technology and Biotechnology ; Volume 91, Issue 5 , 2016 , Pages 1368-1377 ; 02682575 (ISSN) ; Ebadipour, N ; Roostaazad, R ; Sharif University of Technology
John Wiley and Sons Ltd
Abstract
This study deals with the large-scale production of biosurfactant from soybean oil soapstock by Pseudomonas aeruginosa MR01. The production of biosurfactant was carried out in a newly designed bioreactor equipped with recycling flow under three operational conditions. Kinetic studies were conducted at both shake flask and 5-L bioreactor scales during fermentation in a soapstock medium. Mathematical equations were developed to model the kinetic patterns at both scales. RESULT: Statistical analyses demonstrated the goodness of fit, with regression r-squared, R2, between 0.97and 0.99 for different models. Furthermore, biosurfactant concentration in the bioreactor including the recycling flow,...
Trends and challenges of biopolymer-based nanocomposites in food packaging
, Article Comprehensive Reviews in Food Science and Food Safety ; Volume 20, Issue 6 , 2021 , Pages 5321-5344 ; 15414337 (ISSN) ; YousefniaPasha, H ; Tabatabaeekoloor, R ; Pesaranhajiabbas, E ; Sharif University of Technology
John Wiley and Sons Inc
2021
Abstract
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...
Efficient biodegradation of naphthalene by a newly characterized indigenous achromobacter sp. FBHYA2 isolated from Tehran oil refinery complex
, Article Water Science and Technology ; Volume 66, Issue 3 , March , 2012 , Pages 594-602 ; 02731223 (ISSN) ; Borghei, S. M ; Hassani, A. H ; Yakhchali, B ; Ardjmand, M ; Zeinali, M ; Sharif University of Technology
IWA Pub
2012
Abstract
A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30°C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals...
Herschel-Bulkley rheological parameters of lightweight colloidal gas aphron (CGA) based fluids
, Article Chemical Engineering Research and Design ; Volume 93 , 2015 , Pages 21-29 ; 02638762 (ISSN) ; Arabloo, M ; Ghazanfari, M. H ; Rashtchian, D ; Sharif University of Technology
Institution of Chemical Engineers
2015
Abstract
The proper understanding of rheological characteristics of CGA based fluids is of crucial importance in determining the performance of the fluid, in order to maintain the most effective fluid properties for safe, efficient, and economical drilling operation. This paper presents a concise investigation on the effect of concentration of the three main components of a novel environmentally friendly lightweight CGA based drilling fluid, i.e., xanthan gum biopolymer, starch, and biosurfactant, to the Herschel-Bulkley rheological model parameters. The three parameters of Herschel-Bulkley model, i.e., yield stress, fluid consistency, and fluid flow index were calculated by fitting the experimental...
ANFIS modeling of rhamnolipid breakthrough curves on activated carbon
, Article Chemical Engineering Research and Design ; Volume 126 , 2017 , Pages 67-75 ; 02638762 (ISSN) ; Sasanipour, J ; Haratipour, P ; Alizad, M ; Vafaee Ayouri, M ; Sharif University of Technology
Institution of Chemical Engineers
2017
Abstract
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)...
Carbon nanotubes part II: A remarkable carrier for drug and gene delivery
, Article Expert Opinion on Drug Delivery ; Volume 12, Issue 7 , 2015 , Pages 1089-1105 ; 17425247 (ISSN) ; Solati, N ; Ghasemi, A ; Estiar, M. A ; Hashemkhani, M ; Kiani, P ; Mohamed, E ; Saeidi, A ; Taheri, M ; Avci, P ; Aref, A. R ; Amiri, M ; Baniasadi, F ; Hamblin, M. R ; Sharif University of Technology
Informa Healthcare
2015
Abstract
Introduction: Carbon nanotubes (CNT) have recently been studied as novel and versatile drug and gene delivery vehicles. When CNT are suitably functionalized, they can interact with various cell types and are taken up by endocytosis.Areas covered: Anti-cancer drugs cisplatin and doxorubicin have been delivered by CNT, as well as methotrexate, taxol and gemcitabine. The delivery of the antifungal compound amphotericin B and the oral administration of erythropoietin have both been assisted using CNT. Frequently, targeting moieties such as folic acid, epidermal growth factor or various antibodies are attached to the CNT-drug nanovehicle. Different kinds of functionalization (e.g., polycations)...
Two schemes for production of biosurfactant from Pseudomonas aeruginosa MR01: Applying residues from soybean oil industry and silica sol–gel immobilized cells
, Article Colloids and Surfaces B: Biointerfaces ; Volume 152 , 2017 , Pages 159-168 ; 09277765 (ISSN) ; Ebadipour, N ; Roostaazad, R ; Partovi, M ; Bahmaei, M ; Sharif University of Technology
Elsevier B.V
2017
Abstract
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,...