Sharif University of TechnologyScientia Iranica1026-309825320180601Plasmonic Circular Dichroism Study of Gold Nanorod-Quadruplex Nanobioconjugates17831788443110.24200/sci.2017.4431ENZeinab BagheriProtein Research Center, Shahid Beheshti University G.C., Velenjak Tehran, IranBijan RanjbarDepartment of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 154-14115 Tehran, IranAzadeh AziziDepartment of Bioscience and Biotechnology, Malik-Ashtar University of Technology, Tehran, IranHamid Latifi5- Laser and Plasma Research Institute, Shahid Beheshti University G.C., Velenjak Tehran. Iran.Mohammad Ismail Zibaii5- Laser and Plasma Research Institute, Shahid Beheshti University G.C., Velenjak Tehran. IranTahereh Tohidi MoghadamDepartment of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, 154-14115 Tehran, IranJournal Article20140801Circular dichroism spectroscopy is a simple way to study G-quadruplex structure and is very useful for monitoring the conformational changes in G-quadruplex structure induced by modifications of the environment. Plasmonic nanoparticles with localized surface plasmon resonance (LSPR) can create strong electromagnetic fields at the surface of plasmonic metals, which remarkably influence the optical properties of molecules. Plasmonic CD is a new CD signal which originates from the dipole–dipole interactions between surface plasmons of NPs and chiral biomolecules have received interest research in various fields of nanotechnology. In this paper we study the interaction between gold nanorods (GNR) and two types of G-quadruplex (parallel and antiparallel), to monitor the alterations in DNA conformation and plasmonic CD signal upon formation of GNR-quadruplex nanobioconjugate. The results from this study indicate the plasmonic CD signals in visible regions are more sensitive than Far-UV CD signals to detect the spatial conformational state of G-quadruplex-GNR nanobioconjugate. https://scientiairanica.sharif.edu/article_4431_0702d35f7b6ac2010ba967be6d688e9f.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Numerical Analysis of MHD Mixed Convection Flow in a Parallelogramic Porous Enclosure Filled with Nano Fluid and in Presence of Magnetic Field Induction178918072003410.24200/sci.2018.20034ENOmid GhaffarpasandDepartment of Physics, University of Isfahan, Isfahan, IranDariush FazeliDepartment of Physics, University of Isfahan, Isfahan, IranJournal Article20160415In the present study, the mixed convection Flow of nano Fluid in a lid-driven parallelogramic porous enclosure subjected to a magnetic Field is investigated numerically. Induced magnetic Field is also considered, in terms of the magnetic potential, in solving the magnetohydrodynamic (MHD) Flow and temperature equations. The Darcy-Brinkman-Forchheimer model with the Boussinesq approximation is adopted and the Finite volume method based on SIMPLE algorithm is utilized to solve the governing equations with the appropriate boundary conditions in an orthogonal computational domain. The governing equations in a non-orthogonal physical domain are transformed into a computational domain in an orthogonal co-ordinate by co-ordinate transformations. It has been shown that the Flow Field and heat transfer are sensible greatly to the skew angle variation. Magnetic potential circulates through the parallelogramic porous enclosure with either high either magnetic Reynolds number or magnetic permeability of the nano Fluid. Results also indicate that the influence of external magnetic Field on Fluid characteristics and heat transfer manifests variety fashions mainly depends on the effective area of the parallelogramic enclosure. Besides, the variation in rates of heat transfer while adding nanoparticles or applying magnetic Field are affected to some extent by porous medium permeability and Richardson number.https://scientiairanica.sharif.edu/article_20034_431e7a03207032ce0c36d5bffcc3f797.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Electrical conductivity of doped armchair graphene nanoribbon in the presence of gap parameter180818142010610.24200/sci.2018.20106ENH. RezaniaDepartment of Physics, Razi University, Kermanshah, P.O. Box 0786534239456 IranS. GoliDepartment of Physics, Razi University, Kermanshah, P.O. Box 0786534239456 IranA. JazidehDepartment of Physics, Razi University, Kermanshah, P.O. Box :0786534239456 IranJournal Article20161122We address the electronic properties of armchair graphene nanoribbon within tight binding model Hamiltonian. Specially we have investigated the behavior of density of states and electrical conductivity. The possible gap parameter effects, ribbon width and chemical potential on electrical conductivity are investigated. Us-<br />ing Green's function calculate the electrical conductivity and density of states of the system have been calculated. Based on the results, the band gap in density of states increases with gap parameter and decreases with ribbon width. The dependence of the electrical conductivity on temperature for various ribbon widths and chemical potentials has been found. Our results show a peak appears in temperature de-pendence of electrical conductivity for each value of chemical potential and ribbon width.https://scientiairanica.sharif.edu/article_20106_32ac2560bb6c9f94f606821d29a02ed1.pdfSharif University of TechnologyScientia Iranica1026-309825320180601A novel nano-composite scaffold for cartilage tissue engineering18151823459510.24200/sci.2017.4595ENM. Mehdikhani-NahrkhalajiDepartment of Biomedical Engineering, Faculty of Engineering, University of Isfahan, Isfahan, 8174613441, IranE. TavakoliDepartment of Biomedical Engineering, Faculty of Engineering, University of Isfahan, Isfahan, 8174613441, IranA. Zargar-KharaziDepartment of Biomaterials, Nanaotechnology and Tissue Engineering, School of Advanced technology in Medicine, Isfahan university of Medical sciences, Isfahan, 8174673461, IranB. Hashemi-BeniDepartment of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 8174673461, IranJournal Article20161212In this study, a hybrid Poly (lactic-co-glycolic acid) (PLGA)/ Hyaluronic acid (Ha)/ Fibrin/ 45S Bioactive Glass (45SBG) nanocomposite scaffolds seeded with human Adipose-Derived Mesenchymal Stem Cells (hADMSCs) were investigated as a construct for osteoarthritis (OA), articular cartilage (AC), and subchondral bone defects therapies. The bioactivity and biodegradation of the nanocomposite scaffolds were assessed in simulated body fluid (SBF) and phosphate buffer saline (PBS) solution, respectively. Furthermore, MTT analysis was performed in order to determine attachment and viability of hADMSCs. Ultimately, results indicated that bioactivity were increased in nanocomposite scaffolds as compared to the pure PLGA scaffold. As well as, biodegradation assay exhibited that the addition of Ha, fibrin, and 45SBG nanoparticles could modify the degradation rate of PLGA. The nanocomposite scaffolds were not showed any cytotoxicity and the hADMSCs were attached on the scaffolds and proliferate properly. According to our investigation, it was concluded that using natural and synthetic polymers along with BG nanoparticles may provide a suitable construct and could show a beneficial role in AC tissue engineering and OA therapy.https://scientiairanica.sharif.edu/article_4595_bb0a7fcf7ee20a4ffc81d3442fa8257c.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Realization of a reduced graphene oxide/ZnO nanorod photodetector, suitable for self-powered applications182418342014910.24200/sci.2018.20149ENL. ShafieiECE Department, Tarbiat Modares University, Jalal Ale. Ahmad Ave., Tehran, IranS. DarbariECE Department, Tarbiat Modares University, Jalal Ale. Ahmad Ave., Tehran, IranF. Dehghan NayeriECE Department, University of Tehran, North Kargar Str., Tehran, IranJournal Article20161221In this report, we propose a reduced graphene oxide (rGO) /ZnO nanorod hybrid structure, which benefits from high photosensitivity and piezoelectric properties of ZnO nanorods, beside excellent carrier mobility, high optical transparency and mechanical flexibility of the reduced graphene oxide sheets. Comparing with the pristine ZnO nanorod based structure; it is shown that the proposed hybrid photodetector exhibits improved output sensitivity to UV-illumination (ΔI/I=424). Also, by taking advantage of the coupled semiconducting/piezoelectric properties of ZnO nanorods, we demonstrate the application of the proposed hybrid rGO/ZnO nanorod structure as a photosensitive piezoelectric nanogenerator. In this regard, we have achieved enhanced open circuit voltage (1.5 V) and open circuit sensitivity (ΔV<sub>oc</sub>/V<sub>oc</sub>=-0.66 %), beside a faster photoresponse, for the realized rGO/ZnO hybrid structure in comparison with ZnO nanorod based counterpart. The observed enhancements are attributed to the presence of underlying reduced graphene oxide sheet, as an efficient carrier transport layer in the proposed hybrid structure.https://scientiairanica.sharif.edu/article_20149_32465bf353133cae521a27904e5ba900.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Investigation into thermally activated migration of fullerene-based nanocars183518482032110.24200/sci.2018.20321ENAlireza NematiNano Robotics Laboratory, Center of Excellence in Design, Robotics, and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran, IranAli MeghdariNano Robotics Laboratory, Center of Excellence in Design, Robotics, and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran0000-0001-6009-3825Hossein Nejat PishkenariNano Robotics Laboratory, Center of Excellence in Design, Robotics, and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran, IranSaeed SohrabpourNano Robotics Laboratory, Center of Excellence in Design, Robotics, and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran, IranJournal Article20170423The rotational and translational motion of nanocars and nanotrucks as well as their motion regimes at different temperatures are investigated. In recent years, few similar types of molecular machines have been simulated. In contrast to previous studies which have used the Rigid-Body Molecular Dynamics (RB MD) method, an all-atom model and classic atomistic dynamics have been employed in this paper to achieve better accuracy. Our results demonstrated that the flexibility of the chassis and its attachment to the gold surface play important roles in the motion of a nanocar. In fact, a heavier and more flexible nanocar chassis reduces its speed compared to a nanotruck. In addition, simulations results are compared with available data from experimental studies done in recent years, and an acceptable agreement between the simulation results and experiments was observed. It was found that both molecules have three different regimes of motion, and the translational and rotational motion are not correlated. Results of this paper increase the knowledge and understanding of thermally-driven fullerene-based nanocars, and can be used to help design nanomachines with high controllability and maneuverability.https://scientiairanica.sharif.edu/article_20321_f360d862443de80bdff1565ffc18228a.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Controlling DNA translocation speed through graphene nanopore via plasmonic fields184918562041910.24200/sci.2018.20419ENBashir FotouhiDepartment of Electrical & Computer Engineering, Tarbiat Modares University, Tehran, Iran0000-0002-4164-510XVahid AhmadiDepartment of Electrical & Computer Engineering, Tarbiat Modares University, Tehran, IranMostafa AbasifardDepartment of Electrical & Computer Engineering, Tarbiat Modares University, Tehran, IranJournal Article20170713We propose a novel plasmonic-based method for controlling translocation speed of DNA molecule through graphene nanopore. Dynamic properties of a double-stranded DNA molecule passage through a graphene nanopore are investigated by employing molecular dynamics simulation. Also, the effect of plasmonic fields parallel to the graphene plane on the translocation speed of the DNA molecule is studied. The DNA translocation speed is calculated for different values of confinement, spectral width, and power of the plasmonic field. Results show the potential of the method for controlling translocation speed of DNA via surface plasmons in graphene nanopore. The plasmon field power, confinement depth, and spectral width can increase translocation time of DNA up to 107, 62 and 15 %. Also, strong plasmon field can trap the DNA molecule in the nanopore. The suggested method can be utilized to solve the fast-translocation challenge of the nanopore DNA sequencers.https://scientiairanica.sharif.edu/article_20419_bac2c3634f39ab0bb9b98122a247e654.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Fusarium oxysporum, a bio-Factory for Nano Selenium Compounds: Synthesis and Characterization185718632014710.24200/sci.2018.5301.1192ENFarnoush Asghari-PaskiabiDepartment of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, IranMohammad ImaniNovel Drug Delivery Systems Department, Iran Polymer and Petrochemical Institute, P.O. Box 14965/115, Tehran, IranMehdi Razzaghi-AbyanehDepartment of Mycology, Pasteur Institute of Iran, Tehran 13164, IranHashem Rafii-TabarDepartment of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, IranJournal Article20171002Selenium nanoparticles have received major consideration for their antimicrobial and anticancer properties. In the present study, a mycelia fungus named Fusarium oxysporum was employed as a cell factory for bio-production of selenium and selenium sulfide nanoparticles. Scanning Electron Microscope (SEM) micrographs displayed that the NPs were encompassed in medium and cells debris along with the presence of sulfur and selenium in the particles according to the energy-dispersive X-ray spectroscopy findings. The size of spherical NPs was measured between 34.32 and 231.98 nm in SEM micrographs and 81.9 nm in DLS analysis. Fourier-transform infrared spectroscopy spectra supported selenium compounds production and also exposed that proteins are associated with the particles. The presence of primary and secondary amine band was demonstrated by the peaks at 1090-1020 and 1650-1580 cm-1 and also at 1580-1490 cm-1 in FTIR spectra. UV/VIS spectrophotometry analysis showed that maximum absorbance for the test was at 217 nm. The strongest Bragg’s reflection in the X-ray diffractograms peaks revealed the closest match with SeS, SeS2 and Se according to standard JCPDS cards. To conclude Fusarium oxysporum is able to produce selenium compounds nanoparticles in a safe and cost effective aerobic green approach.https://scientiairanica.sharif.edu/article_20147_fd5158daa17b2f5fd8e5f67d62ee74d1.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Isogeometric Vibration Analysis of Small-Scale Timoshenko Beams Based on the Most Comprehensive Size-Dependent Theory186418782042910.24200/sci.2018.5267.1177ENAmir NorouzzadehDepartment of Mechanical Engineering, University of Guilan, P.O. Box 3756, Rasht, IranReza AnsariDepartment of Mechanical Engineering, University of Guilan, P.O. Box 3756, Rasht, Iran0000-0002-6810-6624Hessam RouhiDepartment of Engineering Science, Faculty of Technology and Engineering, East of Guilan, University of Guilan, P.C. 44891-63157, Rudsar-Vajargah, IranJournal Article20171021By taking the nonlocal and strain gradient effects into account, the vibrational behavior of Timoshenko micro- and nano-beams is studied in this paper based on a novel size-dependent model. The nonlocal effects are captured using both differential and integral formulations of Eringen’s nonlocal elasticity theory. Moreover, the strain gradient influences are incorporated into the model according to the most general form of strain gradient theory which can be reduced to simpler strain gradient-based theories such as modified strain gradient and modified couple stress theories. Hamilton’s principle is employed to derive the variational form of governing equations. The isogeometric analysis (IGA) is then utilized for the solution approach. Comprehensive results for the effects of small scale and nonlocal parameters on the natural frequencies of beams under various types of boundary conditions are given and discussed. It is revealed that using the differential nonlocal strain gradient model for computing the fundamental frequency of cantilevers leads to paradoxical results, and one must recourse to the integral nonlocal strain gradient model to obtain consistent results.https://scientiairanica.sharif.edu/article_20429_c496baaf58d00980b70ce12e45c25f68.pdfSharif University of TechnologyScientia Iranica1026-309825320180601Molecular Dynamics Simulation: the Effect of Graphene on the Mechanical Properties of Epoxy Based Photoresist: SU8187918902043510.24200/sci.2018.5697.1432ENFaraz Mohammadzadeh HonarvarDepartment of Polymer Engineering, Nanostructured Materials Research Centre, Sahand University of Technology, Sahand New Town, Tabriz, Iran.Behzad PourabbasDepartment of Polymer Eng., Sahand University of TechnologyMahdi Salami HosseiniInstitute of Polymeric Materials, Department of Polymer Engineering, Sahand University of ‎Technology, SUT, P.O. Box 51335-1996, Tabriz, Iran‎Mahsa KharaziDepartment of Mechanical Engineering, Sahand University of Technology, Sahand New Town, Tabriz, Iran.Hamid Erfan-NiyaDepartment of Chemical and Petroleum Engineering, University of Tabriz, Tabriz, IranJournal Article20171205SU8 is an epoxy-Novolac resin, which is used as photo initiator in micro- and nano- fabrication techniques. From literature, graphene has been proved that results in significant improvement in the properties of the composites. However, due to nanometer size of the graphene layers there is no any experimental tool to obtain insight of the fillers inside the resin especially when the materials are under mechanical deformations where simulation techniques work well. Therefore, SU8 and SU8-graphene nanocomposites as the model compounds were taken to be investigated from atomistic molecular dynamic approach to demonstrate the effect of graphene layers. This leads to mechanical property enhancement such as Young’s, bulk and shear modules being affected by the aspect ratio of the graphene layers high aspect ratio graphene in SU8 leads to an 81% improvement in Young’s, 100% in bulk and 83% in shear moduli in addition to higher density and less graphene wrinkling.https://scientiairanica.sharif.edu/article_20435_872e51a5913e5f58abaeaff4fb1d9a22.pdf