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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...
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...
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...
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...
Recent progress in inorganic and composite coatings with bactericidal capability for orthopaedic applications
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 7, Issue 1 , Feb , 2011 , Pages 22-39 ; 15499634 (ISSN) ; Tamjid, E ; Pishbin, F ; Boccaccini, A. R ; Sharif University of Technology
Abstract
This review covers the most recent developments of inorganic and organic-inorganic composite coatings for orthopedic implants, providing the interface with living tissue and with potential for drug delivery to combat infections. Conventional systemic delivery of drugs is an inefficient procedure that may cause toxicity and may require a patient's hospitalization for monitoring. Local delivery of antibiotics and other bioactive molecules maximizes their effect where they are required, reduces potential systemic toxicity and increases timeliness and cost efficiency. In addition, local delivery has broad applications in combating infection-related diseases. Polymeric coatings may present some...
Evaluating the effects of different plasticizers on mechanical properties of starch/ clay nanocomposites
, Article Advanced Materials Research ; Volume 829, 2014 , 2014 , Pages 279-283 ; ISSN: 10226680 ; ISBN: 9783037859070 ; Mousavi, S. M. A ; Emam Djomeh, Z ; Bagheri, R ; Sharif University of Technology
Abstract
Nano-biocomposites are a new class of hybrid materials composed of nano-sized filler (nanofiller) incorporated into a bio-based matrix. Such an association between eco-friendly biopolymers and nano-objects, with the aim to obtain synergic effects, is one of the most innovating routes to enhance the properties of these bio-matrices. In recent years, there has been an increasing interest in Starch as an inexpensive and renewable source has been used as a filler for environmentally friendly plastics for about two decades. However, the poor mechanical properties of starch based biopolymers, leads to use of nanoparticles as reinforcing materials. In the present study, the influence of a...
On the importance of gel rigidity and coverage in a smart water shutoff treatment in gas wells
, Article Journal of Natural Gas Science and Engineering ; Volume 31 , 2016 , Pages 808-818 ; 18755100 (ISSN) ; Escrochi, M ; Riazi, M ; Ayatollahi, S ; Sharif University of Technology
Abstract
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...
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...
Interaction of cations with 2′-deoxythymidine nucleoside and analysis of the nature and strength of cation bonds
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 2 , JAN , 2012 , Pages 153-161 ; 08943230 (ISSN) ; Fattahi, A ; Jamshidi, Z ; Sharif University of Technology
2012
Abstract
Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate...
Topology of polymer chains under nanoscale confinement
, Article Nanoscale ; Volume 9, Issue 33 , 2017 , Pages 12170-12177 ; 20403364 (ISSN) ; Heidari, M ; Mashaghi, S ; Tans, S ; Ejtehadi, M. R ; Mashaghi, A ; Sharif University of Technology
Abstract
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...
Modification of rock/fluid and fluid/fluid interfaces during MEOR processes, using two biosurfactant producing strains of Bacillus stearothermophilus SUCPM#14 and Enterobacter cloacae: A mechanistic study
, Article Colloids and Surfaces B: Biointerfaces ; Vol. 117 , May , 2014 , pp. 457-465 ; ISSN: 09277765 ; Zeinolabedini Hezave, A ; Mohammadi, S ; Niazi, A ; Ayatollahi, S ; Sharif University of Technology
Abstract
During any microbial enhanced oil recovery process, both cells and the metabolic products of bacteria govern the tertiary oil recovery efficiency. However, very accurate examination is needed to find the functionality of these tiny creatures at different reservoir conditions. In this regard, the effect of cell structure on ultimate microbial recovery efficiency which is the most dominant mechanism based on the microorganism types (gram-negative or gram-positive) was systematically investigated. At the first stage, possible different active mechanisms using Bacillus stearothermophilus SUCPM#14 strain were tested using specially designed injection protocol, in situ and ex situ core flooding...
Investigating the efficiency of MEOR processes using Enterobacter cloacae and Bacillus stearothermophilus SUCPM#14 (biosurfactant-producing strains) in carbonated reservoirs
, Article Journal of Petroleum Science and Engineering ; Volume 113 , January , 2014 , Pages 46-53 ; ISSN: 09204105 ; Niazi, A ; Oboodi, V ; Ravanbakhsh, M ; Hezave, A. Z ; Ayatollahi, S ; Raeissi, S ; Sharif University of Technology
Abstract
Microbial enhanced oil recovery (MEOR) process is divided into two main categories, namely in-situ and ex-situ techniques. It utilizes reservoir microorganisms or specially selected bacteria to use their metabolites for more oil recovery from depleted oil reservoirs. In the present study, the potential of two biosurfactant-producing strains of Enterobacter cloacae and Bacillus stearothermophilus SUCPM#14 were investigated on tertiary oil recovery efficiency in carbonated cores using different designed injection protocols. The required operational time, process cost and proper selection of bacterial formulation during the MEOR process were the main objectives of this study. The results of...
New surfactant extracted from Zizyphus Spina-Christi for enhanced oil recovery: Experimental determination of static adsorption isotherm
, Article Journal of the Japan Petroleum Institute ; Volume 56, Issue 3 , 2013 , Pages 142-149 ; 13468804 (ISSN) ; Shahri, M. P ; Zargartalebi, M ; Arabloo, M ; Sharif University of Technology
2013
Abstract
A fundamental chemical enhanced oil recovery (EOR) process is surfactant flooding in which the key mechanism is to reduce interfacial tension between oil and the displacing fluid and hence mobilizing the trapped oil. Surfactant loss by adsorption is one of the most important criteria that governs the economics of the surfactant flooding methods. In addition to this, detrimental effects and high price of currently used surfactants cause EOR process so expensive and unfeasible. This study is aimed to introduce a novel kind of plant based surfactant which is extracted from Zizyphus Spina-Christi tree. In addition, equilibrium adsorption behavior of this novel biosurfactant in aqueous solution...
Thermodynamic properties of aqueous glucose-urea-salt systems
, Article Journal of Solution Chemistry ; Volume 43, Issue 6 , June , 2014 , Pages 1110-1131 ; ISSN: 00959782 ; Held, C ; Ghotbi, C ; Abdekhodaie, M. J ; Sadowski, G ; Sharif University of Technology
Abstract
In this work, the thermodynamic behavior of aqueous solutions containing the solutes NaCl, glucose, and/or urea is investigated. These substances are vital components for living bodies and further they are main components of blood serum. Osmotic coefficients were determined by cryoscopic measurements in single-solute and multi-solute aqueous solutions containing salts (NaCl, KCl, CaCl2), glucose, and/or urea. The results show that NaCl determines the osmotic coefficients in the urea/glucose/NaCl/water system. Investigation of the effect of different salts on osmotic coefficients revealed ion-specific effects. At physiologically important solute concentrations in typical blood serum...
Core flooding tests to investigate the effects of IFT reduction and wettability alteration on oil recovery during MEOR process in an Iranian oil reservoir
, Article Applied Microbiology and Biotechnology ; Volume 97, Issue 13 , July , 2013 , Pages 5979-5991 ; 01757598 (ISSN) ; Sharifinik, M ; Niazi, A ; Hashemi, A ; Ayatollahi, S ; Sharif University of Technology
2013
Abstract
Microbial enhanced oil recovery (MEOR) refers to the process of using bacterial activities for more oil recovery from oil reservoirs mainly by interfacial tension reduction and wettability alteration mechanisms. Investigating the impact of these two mechanisms on enhanced oil recovery during MEOR process is the main objective of this work. Different analytical methods such as oil spreading and surface activity measurements were utilized to screen the biosurfactant-producing bacteria isolated from the brine of a specific oil reservoir located in the southwest of Iran. The isolates identified by 16S rDNA and biochemical analysis as Enterobacter cloacae (Persian Type Culture Collection (PTCC)...
Simulation of biomanipulation using molecular dynamics
, Article ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE) ; Volume 9, Issue PARTS A AND B , 2012 , Pages 137-143 ; 9780791845257 (ISBN) ; Mahboobi, S. H ; Mahjour, M. A ; Meghdari, A ; Sharif University of Technology
2012
Abstract
In this paper, the simulation of biomolecules manipulation using molecular dynamics (MD) is studied. In order to investigate the manipulation behavior, we have used the ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a two-layer graphene sheet as substrate. Along this line, a series of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between the tip and substrate, initial orientation of protein, and the tip position with respect to the biomolecule
Prediction of the partition coefficients of biomolecules in polymer-polymer aqueous two-phase systems using the artificial neural network model
, Article Particulate Science and Technology ; Volume 28, Issue 1 , 2010 , Pages 67-73 ; 02726351 (ISSN) ; Taghikhani, V ; Vossoughi, M ; Sharif University of Technology
Abstract
In this work, an artificial neural network model was used to obtain the partition coefficients of biomolecules in polymer-polymer aqueous two-phase systems. In the artificial neural network, the partition coefficient of a biomolecule depends on the difference between concentrations of poly (ethylene glycol), dextran in the top and bottom phases, temperature and molecular weights of poly (ethylene glycol), dextran, and the biomolecule. The network topology is optimized and the (6-1-1) architecture is found using optimization of an objective function with sequential quadratic programming (SQP) method for 450 experimental data points. The results obtained from the neural network of the...
Modeling of aqueous biomolecules using a new free-volume group contribution model
, Article Industrial and Engineering Chemistry Research ; Volume 48, Issue 8 , 2009 , Pages 4109-4118 ; 08885885 (ISSN) ; Taghikhani, V ; Vossoughi, M ; Sharif University of Technology
2009
Abstract
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...
Modeling process partitioning of biomolecules in polymer-polymer and polymer-salt aqueous two-phase systems (ATPS) using an extended excess gibbs energy model
, Article Zeitschrift fur Physikalische Chemie ; Volume 223, Issue 3 , 2009 , Pages 263-278 ; 09429352 (ISSN) ; Taghikhani, V ; Vossough, M ; Sharif University of Technology
2009
Abstract
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...
Management of soybean oil refinery wastes through recycling them for producing biosurfactant using Pseudomonas aeruginosa MR01
, Article World Journal of Microbiology and Biotechnology ; Volume 29, Issue 6 , June , 2013 , Pages 1039-1047 ; 09593993 (ISSN) ; Lotfabad, T. B ; Roostaazad, R ; Bahmaei, M ; Tayyebi, S ; Sharif University of Technology
2013
Abstract
Biosurfactant production through a fermentation process involving the biodegradation of soybean oil refining wastes was studied. Pseudomonas aeruginosa MR01 was able to produce extracellular biosurfactant when it was cultured in three soybean oil refinement wastes; acid oil, deodorizer distillate and soapstock, at different carbon to nitrogen ratios. Subsequent fermentation kinetics in the three types of waste culture were also investigated and compared with kinetic behavior in soybean oil medium. Biodegradation of wastes, biosurfactant production, biomass growth, nitrate consumption and the number of colony forming units were detected in four proposed media, at specified time intervals....