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    Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation

    , Article Heliyon ; Volume 6, Issue 12 , December , 2020 Kordzadeh, A ; Ramazani Saadatabadi, A ; Hadi, A ; Sharif University of Technology
    Elsevier Ltd  2020
    Abstract
    A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. The... 

    Inferring Signaling Pathways from RNAi Data Using Machine Learning

    , M.Sc. Thesis Sharif University of Technology Mazloomian, Alborz (Author) ; Beigy, Hamid (Supervisor)
    Abstract
    One of the standing problems in Molecular Biology and Bioinformatics is uncovering signaling pathways. Discovering the causes of many cancer-like diseases and developing better treatments for them, requires a better understanding of the behavior of cellular processes. Understanding signaling pathways can help to realize cellular processes. Due to the fast increase of possible signaling pathways when the number of components increases, the problem seems to have an inherent complexity. One of the recent methods for generating data relating to such networks is RNA interference technique. In this thesis we use data which are provided by this method. We propose two methods to infer signaling... 

    Designing and modeling a centrifugal microfluidic device to separate target blood cells

    , Article Journal of Micromechanics and Microengineering ; Volume 26, Issue 3 , 2016 ; 09601317 (ISSN) Shamloo, A ; Selahi, Aa ; Madadelahi, M ; Sharif University of Technology
    Institute of Physics Publishing  2016
    Abstract
    The objective of this study is to design a novel and efficient portable lab-on-a-CD (LOCD) microfluidic device for separation of specific cells (target cells) using magnetic beads. In this study the results are shown for neutrophils as target cells. However, other kinds of target cells can be separated in a similar approach. The designed microfluidics can be utilized as a point of care system for neutrophil detection. This microfluidic system employs centrifugal and magnetic forces for separation. After model validation by the experimental data in the literature (that may be used as a design tool for developing centrifugo-magnetophoretic devices), two models are presented for separation of... 

    Toward chemical perfection of graphene-based gene carrier via ugi multicomponent assembly process

    , Article Biomacromolecules ; Volume 17, Issue 9 , 2016 , Pages 2963-2971 ; 15257797 (ISSN) Rezaei, A ; Akhavan, O ; Hashemi, E ; Shamsara, M ; Sharif University of Technology
    American Chemical Society 
    Abstract
    The graphene-based materials with unique, versatile, and tunable properties have brought new opportunities for the leading edge of advanced nanobiotechnology. In this regard, the use of graphene in gene delivery applications is still at early stages. In this study, we successfully designed a new complex of carboxylated-graphene (G-COOH) with ethidium bromide (EtBr) and used it as a nanovector for efficient gene delivery into the AGS cells. G-COOH, with carboxyl functions on its surface, in the presence of EtBr, formaldehyde, and cyclohexylisocyanide were participated in Ugi four component reaction to fabricate a stable amphiphilic graphene-EtBr (AG-EtBr) composite. The coupling reaction was... 

    OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

    , Article Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN) Haji Abdolvahab, R ; Mobasheri, H ; Nikouee, A ; Ejtehadi, M. R ; Sharif University of Technology
    Elsevier B.V  2016
    Abstract
    The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage... 

    Apoptotic and anti-apoptotic genes transcripts patterns of graphene in mice

    , Article Materials Science and Engineering C ; Volume 71 , 2017 , Pages 460-464 ; 09284931 (ISSN) Ahmadian, H ; Hashemi, E ; Akhavan, O ; Shamsara, M ; Hashemi, M ; Farmany, A ; Daliri Joupari, M ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    Recent studies showed that a large amount of graphene oxide accumulated in kidney and liver when it injected intravenously. Evaluation of lethal and apoptosis gene expression in these tissues, which are under stress is very important. In this paper the in vivo dose-dependent effects of graphene oxide and reduced graphene oxide nanoplatelets on kidney and liver of mice were studied. Balb/C mice were treated by 20 mg/kg body weight of nanoplatelets. Molecular biology analysis showed that graphene nanoplatelets injected intravenously lead to overexpression of BAX gene in both kidney and liver tissues (P ≥ 0.01). In addition these nanoparticles significantly increase BCL2 gene expression in both... 

    History matching of naturally fractured reservoirs based on the recovery curve method

    , Article Journal of Petroleum Science and Engineering ; Vol. 126, issue , February , 2015 , p. 211-221 ; ISSN: 09204105 Ghaedi, M ; Masihi, M ; Heinemann, Z. E ; Ghazanfari, M. H ; Sharif University of Technology
    Abstract
    The discrete fracture network (DFN) and Multiple-Continua concept are among the most widely used methods to model naturally fractured reservoirs. Each faces specific limitations. The recently introduced recovery curve method (RCM) is believed to be a compromise between these two current methods. In this method the recovery curves are used to determine the amount of mass exchanges between the matrix and fracture mediums. Two recovery curves are assigned for each simulation cell, one curve for gas displacement in the presence of the gravity drainage mechanism, and another for water displacement in the case of the occurrence of the imbibition mechanism. These curves describe matrix-fracture... 

    Force controlled manipulation of biological cells using a monolithic MEMS based nano-micro gripper

    , Article ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE) ; Volume 2 , 2012 , Pages 193-201 ; 9780791845189 (ISBN) Abbasi, A. A ; Ahmadian, M. T ; Sharif University of Technology
    2012
    Abstract
    Nano-micro grippers are able to pick-transport-place the micro or nanometer -sized materials, such as manipulation of biological cells or DNA molecules in a liquid medium. This paper proposes a novel monolithic nano-micro gripper structure with two axis piezoresistive force sensor which its resolution is under nanoNewton. The results of the study have been obtained by the simulation of the proposed gripper structure in Matlab software. Motion of the gripper arm is produced by a voice coil actuator. The behavior of the cell has been derived using the assumptions in the literatures. Moreover, two simple PID controllers, one for control of the gripper motion and another for control of the force... 

    Development of an aqueous TiO2 paste in terms of morphological manipulation of nanostructured photoanode electrode of dye-sensitized solar cells

    , Article Journal of Sol-Gel Science and Technology ; Volume 75, Issue 2 , August , 2015 , Pages 447-459 ; 09280707 (ISSN) Moradzaman, M ; Mohammadi, M. R ; Sharif University of Technology
    Kluwer Academic Publishers  2015
    Abstract
    Abstract: A novel simple synthetic procedure for improving cell efficiency and reducing the production cost of TiO2 dye-sensitized solar cells (DSSCs) by modification and optimization of homemade formulated paste is reported. This is achieved in terms of morphological manipulation of deposited monolayer TiO2 films by controlling three processing parameters of paste formulation. These parameters are tailored to obtain a paste with proper viscosity suitable for spin-coating technique and to achieve uniform, homogeneous, and crack-free films with good connections between TiO2 grains and porous structure. Photovoltaic measurements show that TiO2... 

    BLESS: A simple and efficient scheme for prolonging PCM lifetime

    , Article 53rd Annual ACM IEEE Design Automation Conference, DAC 2016, 5 June 2016 through 9 June 2016 ; Volume 05-09 , June-2016 , 2016 ; 0738100X (ISSN); 9781450342360 (ISBN) Asadinia, M ; Jalili, M ; Sarbazi Azad, H ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2016
    Abstract
    Limited endurance problem and low cell reliability are main challenges of phase change memory (PCM) as an alternative to DRAM. To further prolong the lifetime of a PCM device, there exist a number of techniques that can be grouped in two categories: 1) reducing the write rate to PCM cells, and 2) handling cell failures when faults occur. Our experiments confirm that during write operations, an extensive non-uniformity in bit ips is exhibited. To reduce this non-uniformity, we present byte-level shifting scheme (BLESS) which reduces write pressure over hot cells of blocks. Additionally, this shifting mechanism can be used for error recovery purpose by using the MLC capability of PCM and... 

    Inertial microfluidics: a method for fast prediction of focusing pattern of particles in the cross section of the channel

    , Article Analytica Chimica Acta ; Volume 1083 , 2019 , Pages 137-149 ; 00032670 (ISSN) Mashhadian, A ; Shamloo, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Inertial microfluidics is utilized as a powerful passive method for particle and cell manipulation, which uses the hydrodynamic forces of the fluid in the channel to focus particles in specific equilibrium positions in the cross section of the channel. To achieve high performance manipulation, knowledge of focusing pattern of particles in the cross section of channel is essential. In this paper, we propose a method to address this important issue. To this end, firstly inertial microfluidics is analyzed in rectangular cross section channels. The results indicate that fluid flow velocity and channel's cross-sectional profiles have great impacts on the forces exerted on particles. Next, these... 

    The effect of nanoparticles on spontaneous imbibition of brine into initially oil-wet sandstones

    , Article Energy Sources, Part A: Recovery, Utilization and Environmental Effects ; Volume 41, Issue 22 , 2019 , Pages 2746-2756 ; 15567036 (ISSN) Sobhani, A ; Ghasemi Dehkordi, M ; Sharif University of Technology
    Taylor and Francis Inc  2019
    Abstract
    In this paper, the effect of silica nanoparticles on oil production due to the spontaneous imbibition of brine into oil-wet sandstones has been studied. The imbibed fluids were NaCl 3 wt. % solutions containing various concentrations of nanoparticles and the recovered oil for each solution was compared. The results revealed that nanoparticles yielded more oil recovery. Nanofluid was used after brine imbibition, and the oil recovery increased from 17.8% to 40% while in the case of using the same nanofluid as the first imbibed fluid the oil recovery was 53%. Also, the results indicated that the oil recovery depends on nanoparticle concentrations. © 2019, © 2019 Taylor & Francis Group, LLC  

    3D distributed modeling of trolling-mode AFM during 2D manipulation of a spherical cell

    , Article Journal of Nanoparticle Research ; Volume 23, Issue 4 , 2021 ; 13880764 (ISSN) Mohammadi, S.Z ; Nejat Pishkenari, H ; Mohammadi Moghaddam, M ; Sharif University of Technology
    Springer Science and Business Media B.V  2021
    Abstract
    In this study, a general 3D distributed modeling of Trolling-Mode AFM (TR-AFM) as a nanorobot is presented to analyze the 2D manipulation process of a spherical cell. To this aim, the analysis is categorized into 3 sections. In the first section, 6 deformations of TR-AFM are taken into account, and the standard model of the system is obtained. Moreover, the system is simulated in ANSYS Workbench. The results of modal and transient analyses of the system from both analytical and software methods reveal high agreement, which confirms the accuracy of the presented analytical model. In the second section, by utilizing the 3D derived model, displacement of a spherical yeast single cell (W303)... 

    A new modeling and control scheme for cascaded split-source converter cells

    , Article IEEE Transactions on Industrial Electronics ; 2021 ; 02780046 (ISSN) Montazeri, S. H ; Milimonfared, J ; Zolghadri, M. R ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2021
    Abstract
    Cascaded split-source inverter (CSSI) is a new single-stage modular multilevel topology. Each cell of this converter converts DC to AC power in the buck or boost operation mode without any additional power switch. This paper develops a design method based on a detailed model for CSSI. This model shows that energy storage elements experience double-fundamental frequency ripples besides high-frequency ones. It accurately calculates voltage gains and capacitor voltage and inductor current ripples. On the other hand, common carrier-based multilevel modulations have been modified in terms of both reference and carrier signals to control the inverter under symmetric and asymmetric conditions. With... 

    Design of two Inertial-based microfluidic devices for cancer cell separation from Blood: A serpentine inertial device and an integrated inertial and magnetophoretic device

    , Article Chemical Engineering Science ; 2021 ; 00092509 (ISSN) Nasiri, R ; Shamloo, A ; Akbari, J ; Sharif University of Technology
    Elsevier Ltd  2021
    Abstract
    The separation of cancer cells from a heterogeneous biological sample such as blood plays a vital role in cancer study and future treatments. In this paper, we designed and investigated two microfluidic devices for cancer cell separation, including a serpentine inertial device and an integrated inertial-magnetophoretic device. Firstly, numerical modeling was carried out to study the fluid flow, particles’ trajectories in the inertial device. Then the device was fabricated using soft photolithography and suspension of two types of microparticles with the size of 10 and 15 µm were injected into the microchannel separately to investigate the particles’ trajectories and focusing behavior at... 

    PH-Responsive chitosan-adorned niosome nanocarriers for co-delivery of drugs for breast cancer therapy

    , Article ACS Applied Nano Materials ; Volume 5, Issue 7 , 2022 , Pages 8811-8825 ; 25740970 (ISSN) Karimifard, S ; Rezaei, N ; Jamshidifar, E ; Moradi Falah Langeroodi, S ; Abdihaji, M ; Mansouri, A ; Hosseini, M ; Ahmadkhani, N ; Rahmati, Z ; Heydari, M ; Vosough, M ; Akbarzadeh, I ; Mostafavi, E ; Sharif University of Technology
    American Chemical Society  2022
    Abstract
    Breast cancer incidence has increased in recent decades. In the present study, an optimum formulation of chitosan (CS)-adorned niosome-based nanocarriers for co-delivery of doxorubicin (DOX) and vincristine (VIN) was developed for the treatment of breast cancer to reduce drug doses and overcome multidrug resistance. The three-level Box-Behnken method was utilized to optimize the particles in terms of size, polydispersity index (PDI), entrapment efficacy (EE (%)), and percent of drug release (%). The release rate of two drugs from CS-adorned nanoparticles (DOX+VIN/Nio/CS) in acidic and physiological pH is less than uncoated niosome (DOX+VIN/Nio). In addition, acidic pH increases the release... 

    Design of two Inertial-based microfluidic devices for cancer cell separation from Blood: A serpentine inertial device and an integrated inertial and magnetophoretic device

    , Article Chemical Engineering Science ; Volume 252 , 2022 ; 00092509 (ISSN) Nasiri, R ; Shamloo, A ; Akbari, J ; Sharif University of Technology
    Elsevier Ltd  2022
    Abstract
    The separation of cancer cells from a heterogeneous biological sample such as blood plays a vital role in cancer study and future treatments. In this paper, we designed and investigated two microfluidic devices for cancer cell separation, including a serpentine inertial device and an integrated inertial-magnetophoretic device. Firstly, numerical modeling was carried out to study the fluid flow, particles’ trajectories in the inertial device. Then the device was fabricated using soft photolithography and suspension of two types of microparticles with the size of 10 and 15 µm were injected into the microchannel separately to investigate the particles’ trajectories and focusing behavior at... 

    On the natural aging behavior of Aluminum 6061 alloy after severe plastic deformation

    , Article Materials Science and Engineering A ; Volume 580 , 2013 , Pages 202-208 ; 09215093 (ISSN) Farshidi, M. H ; Kazeminezhad, M ; Miyamoto, H ; Sharif University of Technology
    2013
    Abstract
    Natural aging behavior of the aluminum 6061 alloy after a novel Severe Plastic Deformation process called Tube Channel Pressing (TCP) was studied. For this purpose, Vickers microhardness test was used to investigate the changes of mechanical properties while TEM and XRD observations were utilized in order to characterize microstructural evolution during natural aging. Results show that Si-enriched precipitates appear and coarsen rapidly in the first few days of natural aging of TCPed aluminum 6061 alloy which causes consecutive increase and decrease of Vickers microhardness, respectively. Similarly, other alloying elements such as Cu and Fe lead to formation of coarse precipitates during... 

    A new genetic algorithm for multiple sequence alignment

    , Article International Journal of Computational Intelligence and Applications ; Volume 11, Issue 4 , December , 2012 ; 14690268 (ISSN) Narimani, Z ; Beigy, H ; Abolhassani, H ; Sharif University of Technology
    2012
    Abstract
    Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use very complicated, problem specific and time consuming mutation operators. In this paper, we propose a... 

    Deformation prediction of mouse embryos in cell injection experiment by a feedforward artificial neural network

    , Article Proceedings of the ASME Design Engineering Technical Conference, 28 August 2011 through 31 August 2011 ; Volume 2, Issue PARTS A AND B , August , 2011 , Pages 543-550 ; 9780791854792 (ISBN) Abbasi, A. A ; Ahmadian, M. T ; Vossoughi, G. R ; Sharif University of Technology
    2011
    Abstract
    In this study, neural network models have been used to predict the mechanical behaviors of mouse embryos. In addition, sensitivity analysis has been carried out to investigate the influence of the significance of input parameters on the mechanical behavior of mouse embryos. In order to reach these purposes two neural network models have been implemented. Experimental data earlier deduced-by [Flückiger, M. (2004). Cell Membrane Mechanical Modeling for Microrobotic Cell Manipulation. Diploma Thesis, ETHZ Swiss Federal Institute of Technology, Zurich, WS03/04]-were collected to obtain training and test data for the neural network. The results of these investigations show that the correlation...