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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...
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...
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...
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...
Manipulation of biomolecules: A molecular dynamics study
, Article Current Applied Physics ; Volume 14, Issue 9 , September , 2014 , Pages 1216-1227 ; ISSN: 15671739 ; Nejat Pishkenari, H ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
Abstract
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...
The Differential Diagnosis of Crohn's Disease and Celiac Disease Using Nuclear Magnetic Resonance Spectroscopy
, Article Applied Magnetic Resonance ; Volume 45, Issue 5 , May , 2014 , Pages 451-459 ; Kasmaee, L. M ; Sohrabzadeh, K ; Nejad, M. R ; Tafazzoli, M ; Oskouie, A. A ; Sharif University of Technology
Abstract
Crohn's disease and celiac disease belong to a group of autoimmune conditions that affect the digestive system, specifically the small intestine. They both attack the digestive tract and share many symptoms. Thus, the discovery of proper methods would be a major step toward differentiating celiac disease from Crohn's disease. The aim of this study was to search for the metabolic biomarkers to differentiate between these two diseases. Proton nuclear magnetic resonance spectroscopy (1H NMR) was employed as the metabolic profiling method to look for serum metabolites that differentiate between celiac disease and Crohn's disease. Classification of celiac disease and Crohn's disease was done...
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...
Investigation of wettability alteration through relative permeability measurement during MEOR process: A micromodel study
, Article Journal of Petroleum Science and Engineering ; Vol. 120, issue , 2014 , p. 10-17 ; Mahmoodi, M ; Biria, D ; Ayatollahi, S ; Sharif University of Technology
Abstract
Microbial Enhanced Oil Recovery (MEOR) as a tertiary process employs microorganisms and their metabolites to reduce the residual oil saturation of the reservoir mainly through interfacial tension (IFT) reduction and wettability alteration. In spite of its great potential and the mentioned advantages, application of MEOR has been limited because of the lack of practical convincing experimental results. In this study, the effects of MEOR process on wettability changes and the reduction of residual oil saturation have been examined by providing microscopic visualization of two phase flow in transparent glass micromodels. Biosurfactant producing bacterial strain (Enterobacter cloacae) was...
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...
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)...
Application of biosurfactants to wettability alteration and IFT reduction in enhanced oil recovery from oil-wet carbonates
, Article Petroleum Science and Technology ; Volume 31, Issue 12 , Jul , 2013 , Pages 1259-1267 ; 10916466 (ISSN) ; Maghsoudi, E ; Roostaazad, R ; Sharif University of Technology
2013
Abstract
To obtain potentially applicable microorganisms to an effective in situ microbial enhanced oil recovery operation, bacteria that were compatible with the harsh conditions of a petroleum reservoir were isolated from a crude oil sample. The application of an oil spreading technique showed that all of the isolates were capable of producing biosurfactants from both the glucose and crude oil as carbon sources. The secreted biosurfactants could at least reduce the surface tension 20 mN/m and for one of the isolates; the surface tension value dropped below 40 mN/m. In addition, the contact angle measurements revealed that the produced biosurfactants could effectively alter the wettability of the...
Relationship between serum level of selenium and metabolites using 1hnmr-based metabonomics in parkinson's disease
, Article Applied Magnetic Resonance ; Volume 44, Issue 6 , January , 2013 , Pages 721-734 ; 09379347 (ISSN) ; Kyani, A ; Darvizeh, F ; Mehrpour, M ; Tafazzoli, M ; Shahidi, G ; Sharif University of Technology
2013
Abstract
Parkinson's disease (PD) is a neurodegenerative disease, which is not easily diagnosed using clinical tests and the discovery of proper methods would be a major step towards a successful diagnosis. In the present study, we employed metabolic profiling using proton nuclear magnetic resonance spectroscopy to find metabolites in serum, which are helpful for the diagnosis of PD. Classification of PD and healthy subject was done using random forest. Serum levels of selenium measured by atomic absorption spectrometry in PD group were lower than the serum selenium levels in the control group. The metabolites causing selenium changes in PD patients were identified using random forest, and a model...
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....
Axial potential mapping of optical tweezers for biopolymer stretching: The bead size matters
, Article Optics Letters ; Volume 38, Issue 5 , 2013 , Pages 685-687 ; 01469592 (ISSN) ; Reihani, S. N. S ; Sharif University of Technology
2013
Abstract
Optical tweezers (OT) are widely used for pico (and femto)-Newton range force measurements. The appropriate choice of the bead size is not well understood for biopolymer stretching applications of OT. We have shown, both by theory and experiment, that wrong choice of the bead size could cause errors as large as 295% in the measured force. We provide a simple map for correct choice of the bead size and the direction of pulling for such applications. There is a good agreement between our theoretical and experimental results
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
Adaptive neural fuzzy inference (ANFI) modeling technique for production of marine biosurfactant
, Article Proceedings of the ASME Design Engineering Technical Conference ; Volume 2, Issue PARTS A AND B , 2012 , Pages 47-52 ; 9780791845011 (ISBN) ; Ahmadian, M. T ; Sharif University of Technology
2012
Abstract
In this study; a Sugeno type ANFI model which describes the relationship between the bio surfactant concentration as a model output and the critical medium components as its inputs has been constructed. The critical medium components are glucose, urea,SrCl2 and MgSo4 .The experimental data for training and testing capability of the model obtained by a statistical experimental design which have been captured from literatures. Six generalized bell shaped membership function have been selected for each of input variables and based on the training data ANFI model has been trained using the hybrid learning algorithm. The yielded biosurfactant concentration values from the model prediction shows...
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...
Influence of metal complexation on acidity of cytosine nucleosides: Part I, Li +, Na + and K + cation
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 535-545 ; 10263098 (ISSN) ; Fattahi, A ; Pourjavadi, A ; Sharif University of Technology
2012
Abstract
Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been...
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...
Salep-g-poly(sodium acrylate)/alumina as an environmental-sensitive biopolymer superabsorbent composite: Synthesis and investigation of its swelling behavior
, Article Advances in Polymer Technology ; Volume 31, Issue 1 , 2012 , Pages 41-51 ; 07306679 (ISSN) ; Pourjavadi, A ; Soleyman, R ; Ghavami, S ; Sharif University of Technology
Abstract
A novel kind of a biopolymer-based superabsorbent composite, salep-g-poly(sodium acrylate)/alumina, was prepared from salep, sodium acrylate, and alumina by aqueous polymerization, using N,N'-methylenebisacrylamide (MBA) as a cross-linker and ammonium persulfate (APS) as an initiator. The reaction parameters [i.e., acrylic acid (AA), MBA, APS amounts, and neutralization percentage of AA as well as alumina/salep weight ratio] affecting the water absorbency of the hydrogel composite were optimized using systematic method to achieve a composite with high swelling capacity as possible. The swelling behavior of optimum superabsorbent composite was measured in various pH solutions. In addition,...