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Bidirectional water transport through non-straight carbon nanotubes
, Article Journal of Molecular Liquids ; Volume 276 , 2019 , Pages 39-46 ; 01677322 (ISSN) ; Moosavi, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Natural nanochannels and those used for applied purposes are often several nanometers in diameter and have lengths up to micrometer scales. Since normally no pressure gradient, mechanical force or electrical field is exerted on fluids in these situations, the fluid flow within them is not single-file and can be bidirectional. For this reason, studying the behavior of bidirectional flows in the channels is of paramount importance. In this study, a comprehensive investigation on the straight and non-straight bidirectional water transfer through carbon nanotubes is conducted via extensive molecular dynamics simulations. The results indicate that by changing the length, the diameter and the...
Bacteriorhodopsin as a superior substitute for hydrazine in chemical reduction of single-layer graphene oxide sheets
, Article Carbon ; Volume 81, Issue 1 , 2015 , Pages 158-166 ; 00086223 (ISSN) ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
Bacteriorhodopsin (bR) molecules were utilized as light-driven proton pumps for green as well as effective reduction of single-layer graphene oxide (GO) sheets. The bR molecules and graphene sheets were separated from each other in an aqueous environment by using a polytetrafluoroethylene membrane filter, in order to prevent their direct interactions (including attachment of the bR molecules onto the GO). Although reduction of GO using hydrazine or bR showed similar deoxygenation levels (based on X-ray photoelectron spectroscopy), the former resulted in formation of CAN bonds which can substantially decrease the electrical conductivity of the reduced sheets. The electrical characteristics of...
Bacterial receiver prototype for molecular communication using rhamnose operon in a microfluidic environment
, Article IEEE Transactions on Nanobioscience ; Volume 20, Issue 4 , 2021 , Pages 426-435 ; 15361241 (ISSN) ; Mashhadian, A ; Farahnak Ghazani, M ; Arjmandi, H. R ; Alsadat Rad, M ; Shamloo, A ; Vosoughi, M ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2021
Abstract
Bacterial populations are promising candidates for the development of the receiver and transmitter nanomachines for molecular communication (MC). A bacterial receiver is required to uptake the information molecules and produce the detectable molecules following a regulation mechanism. We have constructed a novel bacterial MC receiver using an inducible bacterial L-rhamnose-regulating operon. The proposed bacterial receiver produces green fluorescent protein (GFP) in response to the L-rhamnose information molecules following a quite fast regulation mechanism. To fabricate the receiver, the bacterial population has been transformed using a plasmid harboring L-rhamnose operon genes and gene...
Azahomofullerenes as new n-type acceptor materials for efficient and stable inverted planar perovskite solar cells
, Article ACS Applied Materials and Interfaces ; Volume 13, Issue 17 , 2021 , Pages 20296-20304 ; 19448244 (ISSN) ; Prochowicz, D ; Bończak, B ; Fiałkowski, M ; Tavakoli, M. M ; Yadav, P ; Patel, M. J ; Gupta, S. K ; Gajjar, P. N ; Hong, C. K ; Sharif University of Technology
American Chemical Society
2021
Abstract
Fullerene derivatives with a strong electron-accepting ability play a crucial role in enhancing both the performance and stability of perovskite solar cells (PSCs). However, most of the used fullerene molecules are based on [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which limits the device performance due to difficulties in preparing high-quality and uniform thin films. Herein, solution-processable azahomofullerene (AHF) derivatives (abbreviated as AHF-1 and AHF-2) are reported as novel and effective electron-transport layers (ETLs) in p-i-n planar PSCs. Compared to the control PCBM ETL-based PSCs, the devices based on AHFs exhibit higher photovoltaic performances, which is...
A thermodynamically-consistent large deformation theory coupling photochemical reaction and electrochemistry for light-responsive gels
, Article Journal of the Mechanics and Physics of Solids ; Volume 116 , July , 2018 , Pages 239-266 ; 00225096 (ISSN) ; Zhang, H ; Naghdabadi, R ; Hu, Y ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
Gels are composed of crosslinked polymer network and solvent molecules. When the main chain network is incorporated with functional groups that can undergo photo-chemical reaction upon light irradiation, the gel becomes light-responsive. Under irradiation, the photosensitive groups may undergo photo-ionization process and generate charges that are attached to the main chain or diffuse into the solvent. The newly generated ions disturb the osmotic balance of the gel medium. As a result, water molecules and mobile ions are driven into or out of the network to compensate the osmotic imbalance, which eventually leads to macroscopic swelling or shrinking of the gel. In this work, we develop a...
A theoretical investigation into the effects of functionalized graphene nanosheets on dimethyl sulfoxide separation
, Article Chemosphere ; Volume 297 , 2022 ; 00456535 (ISSN) ; Alizadeh, M ; Hasanzadeh, A ; Khataee, A ; Azamat, J ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
The potential of carbon-based nanosheet membranes with functionalized pores is great as water treatment membranes. Using the molecular dynamic simulation technique, the dimethyl sulfoxide (DMSO) separation from the water/DMSO binary solution is investigated, and the functionalized graphene nanosheets are used as a membrane. This membrane was functionalized by –F (fluorine) and –H (hydrogen) functional groups. For the separation of DMSO, external hydrostatic pressures up to 100 MPa were applied to the considered systems. The separation mechanism was based on molecular size. Multiple analyses were done to study the capability of considered membranes for the separation of DMSO molecules from...
A temperature-calibrated continuum model for vibrational analysis of the fullerene family using molecular dynamics simulations
, Article Applied Mathematical Modelling ; Volume 80 , April , 2020 , Pages 115-125 ; Golzari, A ; Sharif University of Technology
Elsevier Inc
2020
Abstract
In the present study, a model was proposed to determine the elastic properties of the family of fullerenes at different temperatures (between 300 and 2000 K) using a combination of molecular dynamics simulation and continuum shell theory. The fullerenes molecules examined here are eight spherical fullerenes, including C60, C80, C180, C240, C260, C320, C500, and C720. First, the breathing mode frequency and the radius of gyration of the molecules were obtained at different temperatures by molecular dynamics simulations using AIREBO potential. Then, these data were used in a continuum model to obtain the elastic coefficients of these closed clusters of carbon in terms of temperature changes....
Asymmetric elastic rod model for DNA
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 80, Issue 1 , 2009 ; 15393755 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2009
Abstract
In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit. © 2009 The American Physical Society
Aptamer hybrid nanocomplexes as targeting components for antibiotic/gene delivery systems and diagnostics: a review
, Article International Journal of Nanomedicine ; Volume 15 , 2020 , Pages 4237-4256 ; Arab, Z ; Safarkhani, M ; Nasseri, B ; Rabiee, M ; Tahriri, M ; Webster, T. J ; Tayebi, L ; Rabiee, N ; Sharif University of Technology
Dove Medical Press Ltd
2020
Abstract
With the passage of time and more advanced societies, there is a greater emergence and incidence of disease and necessity for improved treatments. In this respect, nowadays, aptamers, with their better efficiency at diagnosing and treating diseases than antibodies, are at the center of attention. Here, in this review, we first investigate aptamer function in various fields (such as the detection and remedy of pathogens, modification of nanoparticles, antibiotic delivery and gene delivery). Then, we present aptamer-conjugated nanocomplexes as the main and efficient factor in gene delivery. Finally, we focus on the targeted co-delivery of genes and drugs by nanocomplexes, as a new exciting...
Application of sol-gel based molecularly imprinted xerogel for on-line capillary microextraction of fentanyl from urine and plasma samples
, Article Analytical Methods ; Volume 5, Issue 24 , 2013 , Pages 7096-7101 ; 17599660 (ISSN) ; Piri-Moghadam, H ; Bayat, P ; Balalaie, S ; Sharif University of Technology
2013
Abstract
A molecularly imprinted xerogel (MIX) for fentanyl was successfully prepared on the inner surface of a copper tube by sol-gel technology. Primarily, the tube was treated by self-assembly monolayers of 3-(mercaptopropyl) trimethoxysilane and then [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane was employed as a precursor for imprinting the template molecule in acidic conditions. During the sol-gel process influential parameters including volume and concentration of fentanyl were carefully investigated to obtain the most efficient and appropriate xerogel. In parallel, a non-imprinted xerogel (NIX) was synthesized in the absence of fentanyl. The extraction efficiencies achieved from MIX and NIX,...
Application of perturbation theory to elastic models of DNA
, Article Proceedings of the 13th Regional Conference on Mathematical Physics, Antalya, Turkey ; October , 2013 , Pages 241-253 ; 9789814417525 (ISBN) ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy
An ultrasensitive and selective turn-off fluorescent nanoprobe for the detection of copper ions
, Article Analytical Methods ; Volume 7, Issue 12 , 2015 , Pages 5067-5073 ; 17599660 (ISSN) ; Taghipour, M ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
In this study, a novel approach for sensitive and extremely selective detection of copper ions has been developed based on fluorescence resonance energy transfer (FRET) between AuNPs as an acceptor and fluorescein isothiocyanate (FITC) as a donor. Initially, the fluorescence of the FITC molecule turns-off due to adsorption to the AuNPs surface. However, the fluorescence of the FITC-AuNPs system was switched to turn-on by adding d-Pencillamine (d-PC) to the solution mixtures as FITC molecules are released upon displacement by d-PC on the NPs surface. The higher affinity of d-PC toward the surface of AuNPs was further evidenced by controlling the fluorescence intensity enhancement of the...
A novel model for complex permittivity of glass for propagation modeling in millimeter-wave band
, Article Mediterrannean Microwave Symposium, MMS 2009 ; 2009 ; 9781424446643 (ISBN) ; Shishegar, A. A ; Sharif University of Technology
Abstract
In radio channels modelings, the phases and amplitudes of the rays undergo some modifications when they are reflected from or transmitted through a particular material. These reflection and transmission coefficients make use of the electrical properties of the materials, thus, it is essential to know the values of the relative dielectric constant and of the conductivity or the loss tangent of the materials that appear in the propagation environments. In this paper, a theoretical model based on the inter-molecule interactions, has been developed and used to estimate the dielectric parameters of glass. ©2009 IEEE
A note on the synergistic effect of surfactants and nanoparticles on rising bubble hydrodynamics
, Article Chemical Engineering and Processing - Process Intensification ; Volume 155 , 2020 ; Bastani, D ; Lotfi, M ; Sharif University of Technology
Elsevier B.V
2020
Abstract
Various mixtures of surfactants and nanosilica particles were investigated to assess their influence on rising bubble hydrodynamics. For this purpose, local velocities of rising bubbles were measured experimentally. Also, the effects of concentration of three types of surface-modified silica nanoparticles on density, viscosity, and surface tension of surfactant solutions were determined. Experimental results revealed that the simultaneous presence of nanoparticles and surfactant molecules led to the decrease of local velocities of rising bubbles. The presence of nanoparticles in surfactant solutions leads to a more reduction of bubble local velocity. This could be caused by the formation of...
A new proof of the molecular Hamiltonian in Radau coordinates for triatomic molecules based on tensor form
, Article Molecular Physics ; Volume 106, Issue 5 , 2008 , Pages 643-648 ; 00268976 (ISSN) ; Tafazzoli, M ; Sharif University of Technology
2008
Abstract
A generalized coordinates molecular Hamiltonian for polyatomic molecules has been obtained. Using this Hamiltonian in Radau coordinates as the orthogonal coordinates, the molecular Hamiltonian is derived for tri-atomic molecules. An exact derivation is presented of the molecular Hamiltonian in different axis embedding such as bond embedding, bisector embedding, and the linear combination of Radau vector coordinates. In addition, the symmetrized Radau coordinates are considered as an example for this general formulation. This new approach is greatly simplified. Also presented are simple and explicit expressions without cross-terms in Radau coordinates as vibrational variables
A new approach to flexible humidity sensors using graphene quantum dots
, Article Journal of Materials Chemistry C ; Volume 5, Issue 35 , 2017 , Pages 8966-8973 ; 20507534 (ISSN) ; Iraji Zad, A ; Ghiass, M. A ; Fardindoost, S ; Hatamie, S ; Sharif University of Technology
Abstract
Highly sensitive flexible humidity sensors based on graphene quantum dots (GQDs) were developed. The GQDs were prepared using a facile hydrothermal method and characterized considering morphological, structural, and compositional experiments. Then, their humidity sensing properties in correlation with flexibility characteristics were investigated. Good selectivity and response (∼390 for a RH change of 99%), broad detection range (1-100% RH), rather short response and recovery times (12 and 43 s, respectively) as well as flexibility were obtained, demonstrating that the GQD sensors have potential for application in wearable electronics and RH monitoring. Detection of hydrogen (H2) gas by the...
An atomistic insight into interfacial properties of brine nanofilm confined between calcite substrate and hydrocarbon layer
, Article Applied Surface Science ; Volume 490 , 2019 , Pages 89-101 ; 01694332 (ISSN) ; Badizad, M. H ; Ayatollahi, S ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Molecular dynamics simulation was applied in this study to scrutinize the interfacial properties of water nano-film confined between calcite mineral and hydrocarbon layer, as two intrinsically different media. Such system resembles the environment experienced by water molecules in the pore spaces of underground carbonate reservoirs. The interplay between water film and confining phases, oil and mineral, strongly influences hydrocarbon production process; however, there is a lack of detailed understanding of the involved interactions. MD simulations indicate development of several layers with different water densities in the confined brine. Water molecules form well-ordered structure in three...
Analysis of impedance stabilization of natural and metallic DNA molecules
, Article 2012 19th Iranian Conference of Biomedical Engineering, ICBME 2012 ; 2012 , Pages 139-142 ; 9781467331302 (ISBN) ; Khakestar, A. S ; Hejazi, M. S ; Fardmanesh, M ; Sharif University of Technology
2012
Abstract
In this work, we used λ-DNA to produce metallic DNA samples and we investigated the stabilization time of their impedances. This is in order to show that the DNA molecules can possibly be utilized as a frame for assembling the nanocircuits and as an electronic element as well, in nanoelectric devices. It has been shown that metallic DNA has lower stabilization time than natural DNA. As expected, it is shown that making the bundled DNA oriented, impacts their impedance stabilization. In order to find the characteristic impedance of the DNA molecules under direct current, we designed and made patterned electrodes to make electrical connections between the DNAs and the used current source. The...
An alternative mechanism for the formation of high density lipoprotein in peripheral tissue
, Article Scientia Iranica ; Volume 23, Issue 2 , 2016 , Pages 600-608 ; 10263098 (ISSN) ; Saidi, M. S ; Rismanian, M ; Firoozabadi, B ; Amininasab, M ; Sharif University of Technology
Sharif University of Technology
2016
Abstract
High Density Lipoprotein (HDL) is a lipid-protein complex responsible for transporting cholesterol and triglyceride molecules, as these compounds are unable to dissolve in aqueous environments such as a bloodstream. Among the most well-known possible structures, the belt-like structure is the most common shape proposed for this vital bimolecular complex. In this structure, the protein scaffold encompasses the lipid bilayer and a planar circular structure is formed. Several HDL simulations with embedded components in the lipid section were performed. Here, we applied a series of molecular dynamic simulations using the MARTINI coarse grain force field to investigate an HDL model, with pores of...
An adaptive pulse-width modulation for limited molecule production and storage
, Article 2018 Iran Workshop on Communication and Information Theory, IWCIT 2018, 25 April 2018 through 26 April 2018 ; 2018 , Pages 1-6 ; 9781538641491 (ISBN) ; Mirmohseni, M ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2018
Abstract
The nature of molecular transmitter imposes some limitations on the molecule production process and its storage. As these molecules act the role of the information carriers, their limitation affect the transmission process and the system performance considerably. In this paper, we focus on these limitations at the transmitter, the limited production rate and finite storage capacity. We consider a time-slotted communication where the transmitter opens its outlet and releases the stored molecules for a time duration to send bit '1' and remains silent to send bit '0'. By changing the duration molecules are released, we propose an adaptive pulse-width modulation. The objective is to find the...