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    Characterization of Formation Damage Induced by Oil-Based Drilling Fluid and Proposing its Optimized Remedy

    , M.Sc. Thesis Sharif University of Technology Ahmadi, Amir (Author) ; Masihi, Mohsen (Supervisor) ; Tahmasbi, Koroush (Supervisor) ; Kalhor, Mojtaba (Co-Supervisor)
    Abstract
    During all operations in hydrocarbon reservoirs, there is a possibility of formation damage. These damages can reduce the production of fluids from reservoir. One of the major damages that can seriously affect the performance of a reservoir is the damage caused by drilling fluid. The main purpose of this research is to study the main mechanisms of formation damages when using oil-based drilling fluids and fixing or preventing these damages. Once the mechanisms are identified, it is tried to cure the damages but without acid-washing. The alternative method is surfactant-washing which is a surfactant-brine injection. This injection has been done for the first time. This study helps to industry... 

    Design, Manufacture and Evaluation of Water-Based Drilling Fluid Suitable for Onshore Wells in the Gorgan Plain

    , M.Sc. Thesis Sharif University of Technology Avatefi Anvar, Mehrdad (Author) ; Jamshidi, Saeed (Supervisor) ; Kalhor Mohammadi, Mojtaba (Co-Supervisor)
    Abstract
    The Southern Caspian Basin, which includes northern Iran, western Turkmenistan, and eastern Azerbaijan, is known as the Land of Fire due to its abundant gas springs. This region possesses unique geological features, including active mud volcanoes that are associated with the release of methane gas. These characteristics indicate a high potential for oil and gas exploration in the area. The Gorgan Plain, located in Golestan Province and bordered by the Alborz and Koupeh-Dagh mountain ranges and the southern Caspian Sea, witnesses several active and dormant mud volcanoes, which serve as indicators of energy resource presence in the region. The drilling problems faced in wells A and B in the... 

    Designing and Engineering of Lost Circulation Materials for Different Lost Circulation Scenarios

    , M.Sc. Thesis Sharif University of Technology Karimi Rad, Mohammad Saeed (Author) ; Goodarznia, Iraj (Supervisor) ; Tahmasebi, Korosh (Co-Advisor) ; kalhor, Mojtaba (Co-Advisor)
    Abstract
    Nowadays, one of the most major problems in drilling industry is Lost Circulation in different formations. Lost Circulation increases non-productive time, expenditures and environmental damages. Lost Circulation can happen in natural or induced fractures, cavernous formations and high permeable rocks and it can be subcategorized in seepage, medium, severe or complete type based on the severity of the problem. For addressing this issue, different methods are suggested. One of the most considered of these methods is using Lost Circulation Materials (LCM). In this thesis, it was tried to manage the situation with Designing and engineering of lost circulation materials for different lost... 

    Investigating the Challenges of Seabed Drilling in Deep Waters and Designing the Optimal Drilling Fluid

    , M.Sc. Thesis Sharif University of Technology Samadi, Samad (Author) ; Ghazanfari, Mohammad Hossein (Supervisor) ; Tahmasbi Nowtorki, Koorosh (Supervisor) ; Kalhor Mohammadi, Mojtaba (Co-Supervisor)
    Abstract
    With the development of technology and the increase in the global need for energy, the drilling of oil and gas wells moves towards deep and ultra-deep waters, and since the drilling fluid plays an important role in the drilling operations, it requires drilling fluid with the characteristics It is a suitable function to overcome the serious challenges of drilling, including low temperature rheology and borehole heat transfer problems in these areas.The purpose of carrying out this research on the design of water-based and emulsion-based protective fluids is to use laboratory materials and equipment and conduct appropriate tests in order to evaluate the observations and tests performed in... 

    Modeling and Laboratory Evaluation of Rheological Properties of Water based Mud for Horizontal Extended Reach Well

    , M.Sc. Thesis Sharif University of Technology Latifi Shirdar, Babak (Author) ; Taghikhani, Vahid (Supervisor) ; Ghazanfari, Mohammad Hossein (Supervisor) ; Tahmasbi Nowtarki, Koroush (Co-Supervisor) ; Kalhor, Mojtaba (Co-Supervisor)
    Abstract
    One of the most important challenges in drilling horizontal and directional wells is the optimization of hydraulics and hole cleaning and ECD management. In these wells, poor hole cleaning can lead to formation of cutting bed on the low side of the annulus and cause problems such as stuck pipe or increase in torque and drag. Also poor hydraulic design can lead to decrease in rate of penetration and thus, increase in costs. Mud weight should be placed inside the range of mud window (more than pore pressure and less than formation fracture pressure) in order to prevent kick of reservoir fluid or mud loss.In this thesis, the main goal is to optimize hydraulics and hole cleaning and manage ECD... 

    Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed... 

    Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Nature Research  2022
    Abstract
    DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of... 

    In silico design of novel anticancer drugs with amino acid and carbohydrate building blocks to inhibit PIM kinases

    , Article Molecular Simulation ; Volume 48, Issue 6 , 2022 , Pages 526-540 ; 08927022 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Taylor and Francis Ltd  2022
    Abstract
    PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to... 

    DNA Classification Using Optical Processing based on Alignment-free Methods

    , M.Sc. Thesis Sharif University of Technology Kalhor, Reza (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually... 

    Investigating One-pot Three Component Synthesis of ß-Amino Carbonyl Compounds Exploiting Hydrolases: Protein Splicing Enzyme and N-Acetylmuramide Glycanhydrolase

    , M.Sc. Thesis Sharif University of Technology Fathali, Yasaman (Author) ; Kalhor, Hamidreza (Supervisor)
    Abstract
    The application of biocatalysts in organic reactions refers to the use of enzymes, purified or crude, to increase the reaction rate. The usage of biocatalysts in organic reactions have many advantages, including biocompatibility, ease of separation, high yield, reusability without losing activity, high selectivity, and the use of water as the solvent. Furthermore, the carbon–carbon bond formation is one of the most important reactions in the synthesis of organic compounds, drugs, and biomolecules. Using enzymes in organic reactions can provide insightful information about the enzymes catalytic activities and paves the way for systematic investigation of their mechanisms. The enzymes... 

    Conversion of 3,6-O-dimethylfluorescein to fluorescein-based xanthylium derivative: characterization and covalent attachment to bovine serum albumin

    , Article ChemistrySelect ; Volume 4, Issue 36 , 2019 , Pages 10681-10687 ; 23656549 (ISSN) Kalhor, H. R ; Rezaei, M ; Sharif University of Technology
    Wiley-Blackwell  2019
    Abstract
    Xanthene dyes, such as fluorescein and rhodamine, have played crucial rules in biological sciences especially covalent attachment of these organic compounds to biomolecules. 3-O-methylfluorescein and 3,6-O-dimethylfluorescein were synthesized and purified using a facile procedure. 3,6-O-dimethylfluorescein, which lacks fluorescence, was treated with sodium hydroxide and sulfuric acid solutions, giving rise to yellow and green fluorescent compounds, respectively. In both basic and acidic conditions, donor-acceptor structures were formed. The reaction of 3,6-O-dimethylfluorescein with acids, in a reversible manner, emitted green fluorescence, whereas its reaction with hydroxide ion,... 

    Investigating reliable conditions for hewl as an amyloid model in computational studies and drug interactions

    , Article Journal of Chemical Information and Modeling ; Volume 59, Issue 12 , 2019 , Pages 5218-5229 ; 15499596 (ISSN) Kalhor, H. R ; Jabbary, M ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    A number of conformational diseases in humans have been associated with protein/peptide fibrillation known as amyloid. Although extensive studies have been conducted in understanding the molecular basis of amyloid formation, a detailed mechanism is still missing. Experimentally, HEWL (hen egg white lysozyme) has been exploited ubiquitously as a model protein for amyloid fibrillation and drug inhibition. However, computational studies investigating fibril formation of HEWL have been a difficult task to perform mainly due to high stability of lysozymes and the absence of crystal structures of HEWL fibril oligomers. In this study, we have examined various conditions of HEWL amyloid formation... 

    Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs

    , Article Phytochemistry ; Volume 140 , 2017 , Pages 134-140 ; 00319422 (ISSN) Kalhor, H. R ; Ashrafian, H ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as... 

    Investigating the effects of amino acid-based surface modification of carbon nanoparticles on the kinetics of insulin amyloid formation

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 176 , 2019 , Pages 471-479 ; 09277765 (ISSN) Kalhor, H. R ; Yahyazadeh, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only... 

    Probe into the molecular mechanism of ibuprofen interaction with warfarin bound to human serum albumin in comparison to ascorbic and salicylic acids: Allosteric inhibition of anticoagulant release

    , Article Journal of Chemical Information and Modeling ; Volume 61, Issue 8 , 2021 , Pages 4045-4057 ; 15499596 (ISSN) Kalhor, H. R ; Taghikhani, E ; Sharif University of Technology
    American Chemical Society  2021
    Abstract
    The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned... 

    A low cost, efficient method for chip fabrication in cell analysis

    , Article 2016 23rd Iranian Conference on Biomedical Engineering and 2016 1st International Iranian Conference on Biomedical Engineering, ICBME 2016, 23 November 2016 through 25 November 2016 ; 2017 , Pages 93-96 ; 9781509034529 (ISBN) Rahmani, A ; Mohammadi, A ; Kalhor, H ; Sharif University of Technology
    2017
    Abstract
    in recent decades, DEP due to its high efficiency has been exploited widely in separation and manipulation of bioparticles. In the present work a simple, low-cost, and efficient procedure for fabrication of microfluidic chips applied in medicine and biochemistry has been presented. In this method, electrodes are not in direct contact with biological samples which results in elimination of conventional systems' cons. Efficacy of the designed system has been evaluated by injecting samples containing yeast and Ecoli cells into the system and analyzing their trajectory. Experimental results demonstrate that precise adjustment of voltage and frequency can lead to the desired separation in this... 

    Inhibition mechanisms of a pyridazine-based amyloid inhibitor: as a β-sheet destabilizer and a helix bridge maker

    , Article Journal of Physical Chemistry B ; Volume 121, Issue 32 , 2017 , Pages 7633-7645 ; 15206106 (ISSN) Kalhor, H. R ; Jabbari, M. P ; Sharif University of Technology
    2017
    Abstract
    Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ1−42 and Aβ1−40 pentamers, Aβ1−42 monomers, and double-horseshoe-like Aβ1−42. To set better parameters for the small molecule, experimental and computational log P values were obtained. In addition, an analogue of RS-0406 was also simulated... 

    An nnovative test bed for verification of attitude control system

    , Article IEEE Aerospace and Electronic Systems Magazine ; Volume 32, Issue 6 , 2017 , Pages 16-22 ; 08858985 (ISSN) Tavakoli, A ; Faghihinia, A ; Kalhor, A ; Sharif University of Technology
    2017
    Abstract
    A 3 DOF platform was constructed in the Georgia Institute of Technology to perform new control strategies in an experimental framework. Also in this simulator, there isn't any sensor used by a real satellite for attitude determination. The setup was structured on data transmitting and synchronization of distributed elements for ADCS tests. In such a plan, not only can different elements of the test bed be used individually, but also they can support an integrated hardware in the loop test. Accordingly, reusing the hardware sources causes a cost reduction of development. Furthermore the geometric interferences of different parts are minimized in this plan. So, the test bed can be developed... 

    Synthesis and structure activity relationship of pyridazine-based inhibitors for elucidating the mechanism of amyloid inhibition

    , Article Chemical Research in Toxicology ; Volume 31, Issue 10 , 2018 , Pages 1092-1104 ; 0893228X (ISSN) Kalhor, H. R ; Nazari Khodadadi, A ; Sharif University of Technology
    American Chemical Society  2018
    Abstract
    Conformational diseases, constituting a large number of diseases, have been connected with protein misfolding, leading to aggregation known as amyloid fibrils. Mainly due to the lack of detailed molecular mechanisms, there has not been an effective drug to combat amyloid-associated diseases. Recently, a small organic pyridazine-based molecule (RS-0406) has shown significant reductions in amyloid fibrils in both in vitro and in vivo animal studies. However, no information on molecular details of inhibition for the small molecule has been reported. In this work, we have decided to explore structure-activity relationship of pyridazine-based compounds to investigate structural parameters for... 

    Synthesis of Selected Pyridazine-based Organic Compounds and Investigation of Their Inhibitory Effects Against Amyloid Formation

    , M.Sc. Thesis Sharif University of Technology Ghasemi, Elham (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    At the molecular level, proteins control almost all the biochemical reactions in the cells. In order for proteins to function, they must be able to fold into their unique 3D structure. Deformation of protein structure due to some environmental phenomena such as pH, high temperature, and stress may cause unfolding of proteins and finally result in formation of protein fibrils called "amyloid". Amyloid has been found in a number of human diseases such as Alzheimer, type II diabetes, and Parkinson. Recently pyridazine has been under spotlight due to its unique chemical properties such as high dipole moment and higher solubility in biological solvents. In this study, we aim at using a...