Search for: molecular-biology
Total 45 records
Article Journal of Nanoparticle Research ; Volume 23, Issue 4 , 2021 ; 13880764 (ISSN) ; Nejat Pishkenari, H ; Mohammadi Moghaddam, M ; Sharif University of Technology
Springer Science and Business Media B.V 2021
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)...
Article IEEE Transactions on Industrial Electronics ; 2021 ; 02780046 (ISSN) ; Milimonfared, J ; Zolghadri, M. R ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc 2021
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) ; Shamloo, A ; Akbari, J ; Sharif University of Technology
Elsevier Ltd 2021
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...
Article ACS Applied Materials and Interfaces ; Volume 13, Issue 9 , 2021 , Pages 10796-10811 ; 19448244 (ISSN) ; Bagherzadeh, M ; Heidarian Haris, M ; Ghadiri, A. M ; Matloubi Moghaddam, F ; Fatahi, Y ; Dinarvand, R ; Jarahiyan, A ; Ahmadi, S ; Shokouhimehr, M ; Sharif University of Technology
American Chemical Society 2021
Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was...
Folic acid-functionalized niosomal nanoparticles for selective dual-drug delivery into breast cancer cells: An in-vitro investigation, Article Advanced Powder Technology ; Volume 31, Issue 9 , 2020 , Pages 4064-4071 ; Tavakkoli Yaraki, M ; Ahmadi, S ; Chiani, M ; Nourouzian, D ; Sharif University of Technology
Elsevier B.V 2020
In this study, a folic acid-functionalized niosome was formulated and loaded with letrozole and curcumin as a promising drug carrier system for chemotherapy of the breast cancer cells. The formulation process was optimized by varying the type of Span 80 and total lipid to drug ratio, where Span 80 and lipid to drug molar ratio of 10 resulted in the niosomes with maximum encapsulation of both drugs but minimum size. The developed niosomal formulation showed a great storage stability up to one month with the small changes in drug encapsulation efficiency and size during the storage. In addition, they showed a pH-dependent release behaviour with slow drug release at physiological pH (7.4) while...
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 ; Ramazani Saadatabadi, A ; Hadi, A ; Sharif University of Technology
Elsevier Ltd 2020
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...
Protein corona impact on nanoparticle-cell interactions: Toward an energy-based model of endocytosis, Article Journal of Physics Condensed Matter ; Volume 32, Issue 11 , 2020 ; Mehrafrooz, B ; Montazeri, A ; Naghdabadi, R ; Sharif University of Technology
Institute of Physics Publishing 2020
Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that...
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) ; Shamloo, A ; Sharif University of Technology
Elsevier B.V 2019
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...
Article Energy Sources, Part A: Recovery, Utilization and Environmental Effects ; Volume 41, Issue 22 , 2019 , Pages 2746-2756 ; 15567036 (ISSN) ; Ghasemi Dehkordi, M ; Sharif University of Technology
Taylor and Francis Inc 2019
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
An integrated analysis to predict micro-RNAs targeting both stemness and metastasis in breast cancer stem cells, Article Journal of Cellular and Molecular Medicine ; Volume 23, Issue 4 , 2019 , Pages 2442-2456 ; 15821838 (ISSN) ; Sharifi Zarchi, A ; Firouzi, J ; Azimi, M ; Zarghami, N ; Alizadeh, E ; Ebrahimi, M ; Sharif University of Technology
Blackwell Publishing Inc 2019
Several evidences support the idea that a small population of tumour cells representing self-renewal potential are involved in initiation, maintenance, metastasis, and outcomes of cancer therapy. Elucidation of microRNAs/genes regulatory networks activated in cancer stem cells (CSCs) is necessary for the identification of new targets for cancer therapy. The aim of the present study was to predict the miRNAs pattern, which can target both metastasis and self-renewal pathways using integration of literature and data mining. For this purpose, mammospheres derived from MCF-7, MDA-MB231, and MDA-MB468 were used as breast CSCs model. They had higher migration, invasion, and colony formation...
Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
Elsevier Inc 2018
Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated...
Article 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018, 21 April 2018 through 24 April 2018 ; Volume 10812 LNBI , 2018 , Pages 37-53 ; 03029743 (ISSN); 9783319899282 (ISBN) ; Shrestha, A ; Sharifi Zarchi, A ; Gallagher, S. R ; Sahinalp, S. C ; Chitsaz, H ; Sharif University of Technology
Springer Verlag 2018
Many problems in applied machine learning deal with graphs (also called networks), including social networks, security, web data mining, protein function prediction, and genome informatics. The kernel paradigm beautifully decouples the learning algorithm from the underlying geometric space, which renders graph kernels important for the aforementioned applications. In this paper, we give a new graph kernel which we call graph traversal edit distance (GTED). We introduce the GTED problem and give the first polynomial time algorithm for it. Informally, the graph traversal edit distance is the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals...
Article Biomedical Optics Express ; Volume 9, Issue 3 , 2018 ; 21567085 (ISSN) ; Babaei, M ; Azadbakht, A ; Pazoki Toroudi, H ; Mashaghi, A ; Moosavi Movahedi, A. A ; Seyed Reihani, .N ; Sharif University of Technology
OSA - The Optical Society 2018
Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America
Producing functional recombinant human keratinocyte growth factor in Pichia pastoris and investigating its protective role against irradiation, Article Enzyme and Microbial Technology ; Volume 111 , April , 2018 , Pages 12-20 ; 01410229 (ISSN) ; Kalhor, H. R ; Mowla, S. J ; Sharif University of Technology
Elsevier Inc 2018
Keratinocyte Growth Factor (KGF) is a paracrine-acting, epithelial mitogen that plays a prominent role in the regeneration of damaged epithelial tissues. In spite of different attempts to produce recombinant human KGF in many organisms, including bacteria, mammalian cells, plant cells and insect cells; production of recombinant form suffers from lower yields and recovery relative to other recombinant proteins of similar size and properties. Due to many advantages of Pichia pastoris expression systems for producing industrial enzymes and pharmaceutical proteins, in this study P. pastoris was chosen as a host for KGF expression. For preparing human KGF coding sequence, MCF-7 cell line was...
Application of hyperelastic models in mechanical properties prediction of mouse oocyte and embryo cells at large deformations, Article Scientia Iranica ; Volume 25, Issue 2B , March , 2018 , Pages 700-710 ; 10263098 (ISSN) ; Ahmadian, M. T ; Alizadeh, A ; Tarighi, S ; Sharif University of Technology
Sharif University of Technology 2018
Biological cell studies have many applications in biology, cell manipulation, and diagnosis of diseases such as cancer and malaria. In this study, Inverse Finite Element Method (IFEM) combined with Levenberg-Marquardt optimization algorithm has been used to extract and characterize material properties of mouse oocyte and embryo cells at large deformations. Then, the simulation results have been validated using data from experimental works. In this study, it is assumed that cell material is hyperelastic, isotropic, homogenous, and axisymmetric. For inverse analysis, FEM model of cell injection experiment implemented in Abaqus software has been coupled with Levenberg-Marquardt optimization...
Article Materials Science and Engineering C ; Volume 71 , 2017 , Pages 460-464 ; 09284931 (ISSN) ; Hashemi, E ; Akhavan, O ; Shamsara, M ; Hashemi, M ; Farmany, A ; Daliri Joupari, M ; Sharif University of Technology
Elsevier Ltd 2017
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...
Article Solar Energy Materials and Solar Cells ; Volume 157 , 2016 , Pages 55-64 ; 09270248 (ISSN) ; Sharif University of Technology
The potential for using Thermophotovoltaic (1TPV) generators as an alternative for recovering energy losses in steel production industry is assessed. A mathematical model for the assessment of the performance of TPV application in the iron and steel industry has been developed. In order to support the mathematical model, a sample TPV apparatus in laboratory scale based on an IR emitter has been designed and assembled. The key modeling parameters of TPV generator include: the open circuit voltage, the short circuit current density and fill factor of the TPV cell. These parameters have been considered in the model as functions of several variables such as: the emitter (hot steel slab)...
Article Journal of Micromechanics and Microengineering ; Volume 26, Issue 3 , 2016 ; 09601317 (ISSN) ; Selahi, Aa ; Madadelahi, M ; Sharif University of Technology
Institute of Physics Publishing 2016
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...
Article Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN) ; Mobasheri, H ; Nikouee, A ; Ejtehadi, M. R ; Sharif University of Technology
Elsevier B.V 2016
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...
Article Computers and Fluids ; Volume 132 , 2016 , Pages 19-31 ; 00457930 (ISSN) ; Farshchi, M ; Hejranfar, K ; Sharif University of Technology
Elsevier Ltd 2016
A new method of spatial filtering in high-order finite volume methods is presented and assessed. The base of this method is to filter face-averaged variables (fluxes) and then the recovery of cell-averaged ones. Two kinds of filtering method are proposed. The first kind is highly dissipative and appropriate for the numerical regions that need high dissipation, e.g. sponge zones. The second kind, on the other hand, is a precise method and hence is suitable for applying the high-order finite difference filters to the finite volume methods. Applying high-order finite difference filters directly to the high-order finite volume methods without using the proposed method causes stability problems...