Loading...
Search for:
molecules
0.007 seconds
Total 276 records
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; A molecular dynamics study
, Article Molecular Physics ; Volume 109, Issue 5 , Mar , 2011 , Pages 709-724 ; 00268976 (ISSN) ; Akbarzadeh, H ; Taherkhani, F ; Parsafar, G ; Sharif University of Technology
Abstract
Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would...
Design and Synthesis of Novel Polyglycerol Hybrid Nanomaterials for Potential Applications in Drug Delivery Systems
, Article Macromolecular Bioscience ; Volume 11, Issue 3 , NOV , 2011 , Pages 383-390 ; 16165187 (ISSN) ; Adeli, M ; Vossoughi, M ; Shokrgozar, M. A ; Sharif University of Technology
2011
Abstract
The synthesis of a new drug delivery system based on hybrid nanomaterials containing a β-CD core and hyperbranched PG is described. Conjugating PG branches onto β-CD not only increases its water solubility but also affects its host/guest properties deeply. It can form molecular inclusion complexes with small hydrophobic guest molecules such as ferrocene or FITC with reasonable release. In addition, the achievable payloads are significantly higher as for carriers such as hyperbranched PGs. Short-term in vitro cytotoxicity and hemocompatibility tests on L929 cell lines show that the hybrid nanomaterial is highly biocompatible. Due to their outstanding properties, β-CD-g-PG hybrid nanomaterials...
Vesicle deformations by clusters of transmembrane proteins
, Article Journal of Chemical Physics ; Volume 134, Issue 8 , 2011 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2011
Abstract
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters change the shapes of their host vesicles. The effects of depletion force and vesiculation on protein clustering are also investigated. By increasing the protein concentration, clusters are fragmented to smaller bundles, which are then redistributed to form more symmetric structures corresponding to lower bending energies. Big clusters and highly aspherical vesicles cannot be formed when the fraction of protein to lipid molecules is large
Simulation of imaging in tapping-mode atomic-force microscopy: A comparison amongst a variety of approaches
, Article Journal of Physics D: Applied Physics ; Volume 44, Issue 7 , February , 2011 ; 00223727 (ISSN) ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
2011
Abstract
Models capable of accurate simulation of microcantilever dynamics coupled with complex tip-sample interactions are essential for interpretation and prediction of the imaging results in amplitude modulation or tapping-mode atomic-force microscopy (AM-AFM or TM-AFM). In this paper, four approaches based on combinations of lumped and finite element methods for modelling of cantilever dynamics, and van derWaals and molecular dynamics for modelling of tip-sample interactions, are used to simulate the precise imaging by AM-AFM. Based on the simulated imaging and force determination, the efficiency of different modelling schemes is evaluated. This comparison is performed considering their...
Electrically rotating suspended films of polar liquids
, Article Experiments in Fluids ; Volume 50, Issue 2 , August , 2011 , Pages 419-428 ; 07234864 (ISSN) ; Amjadi, A ; Tonddast Navaei, A ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
Controlled rotation of a suspended soap water film, simply generated by applying an electric field, has been reported recently. The film rotates when the applied electric field exceeds a certain threshold. In this study, we investigate the phenomenon in films made of a number of other liquids with various physical and chemical properties. Our measurements show that the intrinsic electrical dipole moments of the liquid molecules seems to be vital for the corresponding film rotation. All the investigated rotating liquids have a molecular electric dipole moment of above 1 Debye, while weakly polar liquids do not rotate. However, the liquids investigated here cover a wide range of physical...
Recent progress in inorganic and composite coatings with bactericidal capability for orthopaedic applications
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 7, Issue 1 , Feb , 2011 , Pages 22-39 ; 15499634 (ISSN) ; Tamjid, E ; Pishbin, F ; Boccaccini, A. R ; Sharif University of Technology
Abstract
This review covers the most recent developments of inorganic and organic-inorganic composite coatings for orthopedic implants, providing the interface with living tissue and with potential for drug delivery to combat infections. Conventional systemic delivery of drugs is an inefficient procedure that may cause toxicity and may require a patient's hospitalization for monitoring. Local delivery of antibiotics and other bioactive molecules maximizes their effect where they are required, reduces potential systemic toxicity and increases timeliness and cost efficiency. In addition, local delivery has broad applications in combating infection-related diseases. Polymeric coatings may present some...
Efficient photo-dissociation of CH4 and H2CO molecules with optimized ultra-short laser pulses
, Article AIP Advances ; Volume 5, Issue 11 , 2015 ; 21583226 (ISSN) ; Irani, E ; Sadighi Bonabi, R ; Sharif University of Technology
American Institute of Physics Inc
2015
Abstract
The fragmentation dynamics of CH4 and H2CO molecules have been studied with ultra-short pulses at laser intensityof up to 1015Wcm-2. Three dimensional molecular dynamics calculations for finding the optimized laser pulses are presented based on time-dependent density functional theory and quantum optimal control theory. A comparison of the results for orientation dependence in the ionization process shows that the electron distribution for CH4 is more isotropic than H2CO molecule. Total conversion yields of up to 70% at an orientation angle of 30o for CH4 and 65% at 900 for H2CO are achieved which lead to enhancement of dissociation probability
Extreme bendability of DNA double helix due to bending asymmetry
, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
American Institute of Physics Inc
2015
Abstract
Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule...
Measurement and Characterization of Electric Current in Metallic-DNA Bundles
, M.Sc. Thesis Sharif University of Technology ; Fardmanesh, Mahdi (Supervisor) ; Hejazi, Mohammad Saeed (Supervisor)
Abstract
DNA is big protein molecule consisting of two strands intertwining each others. Recently DNA molecule has drawn attention of researchers to be used in electronic circuits and molecule electronic field. Therefore, many experiments have been carried out to measure DNA conductivity in different temperature in single molecule or bundle mode with varying size and shape. In this thesis, metallic bundle DNA at normal room temperature is studied and their resistance characteristic is obtained and compared. In order to improve DNA conductivity Metal Ions like zinc are adulterated to each of its structure period. DNAs with these metallic impurities are called metallic DNAs.
Thus, golden electrodes...
Thus, golden electrodes...
Influence of Intramolecular Hydrogen Bonding on Ability of Leaving Group in SN2 Reactions
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Alireza (Supervisor)
Abstract
Many of the significant reactions in chemistry and biology are related to bimolecular nucleophilic substitution (SN2) reactions which have been studied first by Hughes and Ingold in the 1930s. Afterward, many organic chemists have continued this work. Up to now, numerous experimental kinetic and theoretical researches have studied the mechanism of these reactions. Since most SN2 reactions occur in solution, a large number of these studies have been devoted to the solvent effects. One of these effects that has been examined extremely is H-bonding via protic solvents that lowers the energy of an anionic nucleophile relative to the transition state, in which the charge is more diffuse, and...
Diffusion of Lipid and Protein Molecules in Cell Membranes
, Ph.D. Dissertation Sharif University of Technology ; Jalali, Abbas (Supervisor)
Abstract
Lipid membranes are fundamental constituents of cell membranes and are now used in lap-on-a-chip technology. Membranes in living cells contain a significant fraction of proteins, which undergo lateral random movements due to thermal fluctuations and shear forces imposed by the solvent fluid. Prominent natural and biotechnological systems where membranes are highly sheared include the plasma membrane of endothelial cells, and membranes used in biosensors for high throughput screening of drug candidates, and in water purification devices. In these systems membrane is in direct contact with the mainstream suspension flow, which is driven by pressure gradients. The efficiency and function of...
On the capacity of level and type modulations in Molecular communication with ligand receptors
, Article IEEE International Symposium on Information Theory - Proceedings, 14 June 2015 through 19 June 2015 ; Volume 2015-June , 2015 , Pages 1951-1955 ; 21578095 (ISSN) ; 9781467377041 (ISBN) ; Mirmohseni, M ; Nasiri Kenari, M ; Fekri, F ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
In this paper, we consider the bacterial point-to-point communication problem with one transmitter and one receiver by considering the ligand receptor binding process. The most commonly investigated signalling model, referred to as the Level Scenario (LS), uses one type of a molecule with different concentration levels for signaling. An alternative approach is to employ multiple types of molecules with a single concentration level, referred to as the Type Scenario (TS). We investigate the trade-offs between the two scenarios for the ligand receptor from the capacity point of view. For this purpose, we evaluate the capacity using numerical algorithms. Moreover, we derive an upper bound on the...
Novel organic dyes with anchoring group of barbituric/thiobarbituric acid and their application in dye-sensitized solar cells
, Article Synthetic Metals ; Volume 209 , November , 2015 , Pages 1-10 ; 03796779 (ISSN) ; Salimi Beni, A ; Najafi Chermahini, A ; Ghahary, R ; Teimouri, A ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
Abstract New bi-anchoring donor-π-acceptor metal-free organic dyes based on diphenylamine as donor, and barbituric acid and thiobarbituric acid as the acceptor/anchor were synthesized, characterized and used in dye-sensitized solar cells applications. Among the fabricated dye sensitized solar cells, device based on the diphenylamine as donor, and barbituric acid as the acceptor exhibits a high power conversion efficiency of 1.53% with a short circuit current density of 3.71 mA cm-2, an open-circuit photo voltage of 0.55 V and a fill factor of 0.75% under AM 1.5 illumination (85 mW cm-2) compared to the other fabricated devices. The structure of synthesized dyes was optimized and their...
A close look at the motion of C60 on gold
,
Article
Current Applied Physics
;
Volume 15, Issue 11
,
November
,
2015
,
Pages 1402-1411
;
15671739 (ISSN)
; Nemati, A
; Meghdari, A
; Sohrabpour, S
;
Sharif University of Technology
Elsevier
2015
Abstract
In this paper, we have studied the motion of buckminsterfullerene (C60 ) on a gold surface by analyzing its potential energy and using classical molecular dynamics method. The results can be employed to investigate the motion of C60 -based nanocars which have been made in recent years. For this purpose, we have studied the translational and rotational motions of C60 molecule independently. First, we have calculated the potential energy of a C60 molecule on a gold surface in different orientations and positions and employed this data to predict fullerene motion by examining its potential energy. Then we have simulated the motion of C60 at...
Optimal control of dissociation of nitrogen molecule with intense ultra-short laser pulse shaping
, Article Journal of Molecular Structure ; Volume 1083 , March , 2015 , Pages 121-126 ; 00222860 (ISSN) ; Irani, E ; Sadighi Bonabi, R ; Sharif University of Technology
Elsevier
2015
Abstract
(GraphPresented) The quantum optimal control theory in conjunction with time dependent density functional theory is used to optimize the laser pulse shape for dissociation of nitrogen molecule. For several initial peak intensities and frequency ranges, the optimum shapes are produced and compared to determine the most efficient pulse. Ehrenfest molecular dynamics model is also used to test the dissociation process. The corresponding snapshots of density and time dependent electron localization function are presented. It is noticed that when the frequency ranges of laser pulses are doubled, it leads to 60% faster dissociation of N2 molecule
Smulation of Hydrogen Production by the Process of Thermal Decomposition of Methane
, M.Sc. Thesis Sharif University of Technology ; Saboohi, Yadollah (Supervisor)
Abstract
Different disadvantages associated with using fossil fuels as the main energy source including crisis of wells’ depletion and serious environmental problems, causing by the emission of large quantities of greenhouse gases (GHG), especially carbon dioxide (CO2), has increased attention to replacing them with renewable and clean fuels such as wind, solar, and geothermal energy sources. Hydrogen, as a clean energy carrier, is one of the best fuels in terms of the environment and cost. So, it is recently receiving increasing attention and it may one day replace fossil fuels for various applications such as in automobiles and power stations. The main subject of this thesis was surveying 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...
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...
Morphology transition control of polyaniline from nanotubes to nanospheres in a soft template method
, Article Polymer International ; Volume 64, Issue 1 , June , 2015 , Pages 88-95 ; 09598103 (ISSN) ; Ghorbani, M ; Shojaei, A ; Sharif University of Technology
John Wiley and Sons Ltd
2015
Abstract
A soft template route is reported for the fabrication of polyaniline nanospheres via the oxidative polymerization of aniline in the presence of β-naphthalenesulfonic acid (β-NSA) as both surfactqant and dopant, and ammonium persulfate as oxidant at 2-5°C. Control over the morphology and size of the nanoparticles was achieved by changing the reaction medium via addition of an organic cosolvent (i.e. ethanol or ethylene glycol) and by controlling the concentrations of aniline and β-NSA and the molar ratio of β-NSA to aniline. By this means the size of the β-NSA-aniline micelles and the way that aniline monomer interacts with the micelles were controlled. In fact the lower dielectric constant...
Amine-functionalized magnetic nanocomposite particles for efficient immobilization of lipase: effects of functional molecule size on properties of the immobilized lipase
, Article RSC Advances ; Volume 5, Issue 42 , Apr , 2015 , Pages 33313-33327 ; 20462069 (ISSN) ; Kazemeini, M ; Singh, G ; Arpanaei, A ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
A cost-effective design of reusable enzyme-functionalized particles with better catalytic activity is of great scientific interest due to their applications in a wide range of catalytic reactions in several industrial processes. In this work, a systematic approach for preparing amine-functionalized magnetic nanocomposite particles through the surface modification of core/shell type Fe3 O4 cluster@SiO2 particles by the small molecules of 3-(2-aminoethyl)aminopropyltrimethoxysilane (AAS) or the large molecules of polyethyleneimine (PEI) with two different molecular weights, as the support materials for enzyme immobilization, has been demonstrated. The functional...