Search for: biomolecules
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    Thermodynamic properties of aqueous glucose-urea-salt systems

    , Article Journal of Solution Chemistry ; Volume 43, Issue 6 , June , 2014 , Pages 1110-1131 ; ISSN: 00959782 Sadeghi, M ; Held, C ; Ghotbi, C ; Abdekhodaie, M. J ; Sadowski, G ; Sharif University of Technology
    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... 

    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) Pazuki, G. R ; Taghikhani, V ; Vossough, M ; Sharif University of Technology
    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... 

    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 Sharafdini, R ; Mohammadpour, M ; Ramazani, S ; Jamshidi, Z ; Sharif University of Technology
    John Wiley and Sons Ltd  2020
    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... 

    Noble metal nanoparticles in biosensors: Recent studies and applications

    , Article Nanotechnology Reviews ; Volume 6, Issue 3 , 2017 , Pages 301-329 ; 21919089 (ISSN) Malekzad, H ; Sahandi Zangabad, P ; Mirshekari, H ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Walter de Gruyter GmbH  2017
    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... 

    Recent advances in silicon nanowire biosensors: Synthesis methods, properties, and applications

    , Article Nanoscale Research Letters ; Volume 11, Issue 1 , 2016 ; 19317573 (ISSN) Namdari, P ; Daraee, H ; Eatemadi, A ; Sharif University of Technology
    Springer New York LLC 
    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... 

    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) Ahmadi, A ; Reihani, S. N. S ; Sharif University of Technology
    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  

    Comparison and modification of models in production of biosurfactant for Paenibacillus alvei and Bacillus mycoides and its effect on MEOR efficiency

    , Article Journal of Petroleum Science and Engineering ; Volume 128 , April , 2015 , Pages 177-183 ; 09204105 (ISSN) Najafi, A. R ; Roostaazad, R ; Soleimani, M ; Arabian, D ; Moazed, M. T ; Rahimpour, M. R ; Mazinani, S ; Sharif University of Technology
    Elsevier  2015
    Biosurfactant production from two indigenous consortia has already been investigated in two previous studies. In this study, comparison and modification of those models for having as much biosurfactant as possible was conducted. After characterization of bacteria by biochemical tests and 16S ribotyping, a fully modification on the final models was presented. Response surface methodology has the ability to investigate the liability of the parameters and models by the help of Desirability mode and R2 coefficient in Design Expert software. Our models in the previous works follow the style of (y=f(A,B,. . .)) and two Desirability of 0.968 and 0.996 for Paenibacillus alvei ARN63 and Bacillus... 

    Prediction of Thermodynamic Parameters in Solutions with Similar Composition to Plasma or Blood

    , Ph.D. Dissertation Sharif University of Technology Sadeghi, Masoud (Author) ; Abdekhodaie, Mohammad Jafar (Supervisor) ; Ghotbi, Cyrus (Co-Advisor)
    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... 

    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) Pishkenari, H. N ; Mahboobi, S. H ; Mahjour, M. A ; Meghdari, A ; Sharif University of Technology
    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) Abbasi, A. A ; Ahmadian, M. T ; Sharif University of Technology
    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... 

    Disease-related metabolites affect protein-nanoparticle interactions

    , Article Nanoscale ; Volume 10, Issue 15 , 2018 , Pages 7108-7115 ; 20403364 (ISSN) Tavakol, M ; Montazeri, A ; Naghdabadi, R ; Hajipour, M. J ; Zanganeh, S ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2018
    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... 

    Manipulation of biomolecules: A molecular dynamics study

    , Article Current Applied Physics ; Volume 14, Issue 9 , September , 2014 , Pages 1216-1227 ; ISSN: 15671739 Mahdjour Firouzi, M. A ; Nejat Pishkenari, H ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
    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 Fathi, F ; Kasmaee, L. M ; Sohrabzadeh, K ; Nejad, M. R ; Tafazzoli, M ; Oskouie, A. A ; Sharif University of Technology
    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... 

    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) Safian Boldaji, M ; Shahri, M. P ; Zargartalebi, M ; Arabloo, M ; Sharif University of Technology
    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... 

    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) Fathi, F ; Kyani, A ; Darvizeh, F ; Mehrpour, M ; Tafazzoli, M ; Shahidi, G ; Sharif University of Technology
    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... 

    Study of Biomolecules Imaging Using Molecular Dynamics Simulations

    , Article Nano ; Volume 10, Issue 7 , October , 2015 ; 17932920 (ISSN) Kheirodin, M ; Nejat Pishkenari, H ; Moosavi, A ; Meghdari, A ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2015
    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... 

    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) Ziaee, H ; Arabloo, M ; Ghazanfari, M. H ; Rashtchian, D ; Sharif University of Technology
    Institution of Chemical Engineers  2015
    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... 

    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) Esmaeili, E ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
    Royal Society of Chemistry  2016
    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... 

    Topology of polymer chains under nanoscale confinement

    , Article Nanoscale ; Volume 9, Issue 33 , 2017 , Pages 12170-12177 ; 20403364 (ISSN) Satarifard, V ; Heidari, M ; Mashaghi, S ; Tans, S ; Ejtehadi, M. R ; Mashaghi, A ; Sharif University of Technology
    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... 

    ANFIS modeling of rhamnolipid breakthrough curves on activated carbon

    , Article Chemical Engineering Research and Design ; Volume 126 , 2017 , Pages 67-75 ; 02638762 (ISSN) Baghban, A ; Sasanipour, J ; Haratipour, P ; Alizad, M ; Vafaee Ayouri, M ; Sharif University of Technology
    Institution of Chemical Engineers  2017
    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)...