Search for: molecules
Total 257 records
Probing the local bubble with diffuse interstellar bands, Article Proceedings of the International Astronomical Union ; Vol. 9, issue. S297 , February , 2014 , pp. 84-88 ; ISSN: 17439213 ; Khosroshahi, H. G ; Javadi, A ; Van Loon, J ; Sharif University of Technology
The Sun is located inside an enormous local cavity filled with a million degree, ionized hydrogen gas and surrounded by a wall of dense and cold gas, this cavity is known as the Local Bubble (LB). Since the tempreture of Local Bubble is high, the typical singly-ionized atoms or molecules can not survive at this high tempreture. To overcome this problem we should probe the Local Bubble using species which survive under this condition so we have done a whole sky survey in north hemisphere by observing absorptions in the Diffuse Interstellar Bands (DIBs) for sight-lines with distance >300 pc. We have done 30 nights observation and have observed 473 bright stars. We found that the correlations...
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
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
High-order harmonic generation of CO and N2 molecules under linearly- and bi circularly-polarized laser pulses by TD-DFT, Article Laser Physics ; Volume 28, Issue 7 , 2018 ; 1054660X (ISSN) ; Sadighi Bonabi, R ; Mohsen Nia, M ; Irani, E ; Sharif University of Technology
Institute of Physics Publishing 2018
We present a method for high-order harmonics generation of N2 and CO molecules under two-color circularly polarized counter-rotating laser pulses at frequencies of and 2. Pulse envelope in this investigation is sin-squared and the intensity of each laser beam is with ten-optical cycle (o.c.). We show that an isolated pulse with a pulse duration shorter than 20 attosecond from the superposition of several harmonics can be generated. Both two-color linearly- and bicircularly-polarized laser pulses are considered. Our results have also been compared with the outcomes of the previous theoretical works as well as experiment observations. It is found that for CO molecule, the...
Measurement and Characterization of Electric Current in Metallic-DNA Bundles, M.Sc. Thesis Sharif University of Technology ; Fardmanesh, Mahdi ; Hejazi, Mohammad Saeed
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...
Reactions of doubly deprotonated 2,6-naphthalenedicarboxylic acid with alcohols: Proton transfer versus solvation, Article International Journal of Mass Spectrometry ; 2016 ; 13873806 (ISSN) ; Meyer, M. M ; O'Hair, R. A. J ; Fattahi, A ; Schmidt, J ; Kass, S. R ; Sharif University of Technology
Elsevier B.V 2016
Electrospray ionization of 2,6-naphthalenedicarboxylic acid readily affords its doubly deprotonated dicarboxylate dianion (1 2-). This species clusters with background water and added alcohols in an ion trap at ∼10-3 Torr. Sequential solvation is observed to afford mono and dicoordinated ions. Surprisingly, the latter cluster (1 2- • 2TFE) is protonated by 2,2,2-trifluoroethanol (TFE) whereas 1 2-and 1 2- • TFE are not even though δHacid(TFE)=361.7±2.5kcalmol-1 (as given in the NIST website at http://webbook.nist.gov) and the B3LYP/6-31+G(d,p) proton affinities are 384.7 (1 2-), 377.6 (1 2- • TFE), and 362.7 (1 2- • 2TFE) kcal mol-1. That is, only the weakest base in this series, and the...
Reactions of doubly deprotonated 2,6-naphthalenedicarboxylic acid with alcohols: Proton transfer versus solvation, Article International Journal of Mass Spectrometry ; Volume 418 , 2017 , Pages 180-187 ; 13873806 (ISSN) ; Meyer, M. M ; O'Hair, R. A. J ; Fattahi, A ; Schmidt, J ; Kass, S. R ; Sharif University of Technology
Elsevier B.V 2017
Electrospray ionization of 2,6-naphthalenedicarboxylic acid readily affords its doubly deprotonated dicarboxylate dianion (12−). This species clusters with background water and added alcohols in an ion trap at ∼10−3 Torr. Sequential solvation is observed to afford mono and dicoordinated ions. Surprisingly, the latter cluster (12−• 2TFE) is protonated by 2,2,2-trifluoroethanol (TFE) whereas 12−and 12−• TFE are not even though ΔH°acid(TFE) = 361.7 ± 2.5 kcal mol−1 (as given in the NIST website at http://webbook.nist.gov) and the B3LYP/6-31+G(d,p) proton affinities are 384.7 (12−), 377.6 (12−• TFE), and 362.7 (12−• 2TFE) kcal mol−1. That is, only the weakest base in this series, and the dianion...
Definition of the persistence length in the coarse-grained models of DNA elasticity, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 86, Issue 5 , November , 2012 ; 15393755 (ISSN) ; Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA
Tunneling properties of nonplanar molecules in a gas medium, Article Physical Review A - Atomic, Molecular, and Optical Physics ; Volume 84, Issue 6 , 2011 ; 10502947 (ISSN) ; Bassi, A ; Sharif University of Technology
We propose a simple, general, and accurate formula for analyzing the tunneling between classical configurations of a nonplanar molecule in a gas medium, as a function of the thermodynamic parameters of the gas. We apply it to two interesting cases: (i) the shift to zero frequency of the inversion line of ammonia, upon an increase in the pressure of the gas; and (ii) the destruction of the coherent tunneling of D 2S 2 molecules in a He gas. In both cases, we compare our analysis with previous theoretical and experimental results
DFT study of NH3(H2O) n=0,1,2,3 complex adsorption on the (8, 0) single-walled carbon nanotube, Article Computational Materials Science ; Volume 48, Issue 3 , 2010 , Pages 655-657 ; 09270256 (ISSN) ; Beheshtian, J ; Parsafar, G ; Hadipour, N. L ; Sharif University of Technology
Theoretical study of NH3(H2O) n=0,1,2,3 adsorption on (8, 0) carbon nanotube was performed at the X3LYP/6-31G* level of density functional theory (DFT). The tube-NH3 interaction was discussed in the terms of binding energy (EB), coupling energy (EC), charge density, molecular orbitals, and dipole moments. The results reveal that addition of water molecules to tube-NH3 system increases the interaction between tube and ammonia molecule
Selective photo-dissociative ionization of methane molecule with TDDFT study, Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 171 , 2017 , Pages 325-329 ; 13861425 (ISSN) ; Anvari, A ; Sadighi Bonabi, R ; Sharif University of Technology
Elsevier B.V 2017
Three dimensional calculation of control dynamics for finding the optimized laser filed is formulated using an iterative method and time-dependent density functional approach. An appropriate laser pulse is designed to control the desired products in the dissociation of methane molecule. The tailored laser pulse profile, eigenstate distributions and evolution of the efficient occupation numbers are predicted and exact energy levels of this five-atomic molecule is obtained. Dissociation rates of up to 78%, 80%, 90%, and 82% for CH2 +, CH+, C+ and C++ are achieved. Based on the present approach one can reduce the controlling costs. © 2016 Elsevier B.V
Generation of two-soliton and three-soliton molecules in a circular fiber array laser, Article Laser Physics ; Volume 28, Issue 4 , March , 2018 ; 1054660X (ISSN) ; Rooholamininejad, H ; Bahrampour, A ; Sharif University of Technology
Institute of Physics Publishing 2018
In this work, the generation of two-soliton and three-soliton molecules in a circular fiber array laser with an active optical central fiber is studied. Certain fibers of the array are excited by Gaussian and super-Gaussian pulses. The central fiber of the circular fiber laser is a rare-earth doped fiber. A circular fiber array is employed as a saturable absorber in a soliton mode locked fiber laser. Generation of two-soliton and three-soliton molecules are observed in our simulation. Numerical calculation of binding energy shows that the super-Gaussian pulse tends to be more stable, and therefore it would be a proper choice for the generation of soliton molecules in the circular fiber array...
Optomechanical heat transfer between molecules in a nanoplasmonic cavity, Article Physical Review A ; Volume 100, Issue 1 , 2019 ; 24699926 (ISSN) ; Malekfar, R ; Bahrampour, A. R ; Feist, J ; Sharif University of Technology
American Physical Society 2019
We explore whether localized surface plasmon polariton modes can transfer heat between molecules placed in the hot spot of a nanoplasmonic cavity through optomechanical interaction with the molecular vibrations. We demonstrate that external driving of the plasmon resonance indeed induces an effective molecule-molecule interaction corresponding to a heat transfer mechanism that can even be more effective in cooling the hotter molecule than its heating due to the vibrational pumping by the plasmon. This mechanism allows us to actively control the rate of heat flow between molecules through the intensity and frequency of the driving laser. © 2019 American Physical Society
The effect of chemical functional groups and salt concentration on performance of single-layer graphene membrane in water desalination process: A molecular dynamics simulation study, Article Journal of Molecular Liquids ; Volume 301 , 2020 ; Moosavi, A ; Bagheri Sarvestani, A ; Shariat, M ; Sharif University of Technology
Elsevier B.V 2020
In this study, the mechanisms of passing water and salt ions through nanoporous single-layer graphene membrane are simulated using classical molecular dynamics. The effects of functional groups placed in nanopores and feed water's salt concentration on water desalination are investigated. In order to understand the role of functional groups in desalination process, Methyl, Ethyl and a combination of Fluorine and Hydrogen molecules are distributed around the nanopores. In all cases, different number of functional molecules is employed in order to find an optimum distribution of the groups at hand. The results show that an appropriate distribution of Alkyl groups can properly stop the salt...
Nano cobalt-copper ferrite catalyzed regioselective α-C(sp3)–H cyanation of amines: Secondary, tertiary, and drug molecules, Article Catalysis Communications ; Volume 149 , 2021 ; 15667367 (ISSN) ; Pourkaveh, R ; Heidarian, M ; Sharif University of Technology
Elsevier B.V 2021
Oxidative cyanation of sp3C–H bonds at the α position of amines was achieved using CoCuFe2O4 as a catalyst and NaCN as an inexpensive cyanide source at room temperature. CoCuFe2O4 was found to be an active catalyst for Csp -Csp coupling, efficiently delivering valuable α-aminonitriles from tertiary/secondary amines in good yields. The corresponding products were obtained with high selectivity toward α position. In addition, functional group tolerance offered the opportunity for application in late-stage functionalization of biologically active molecules. This transformation proceeds convenient on a gram-scale, and the catalyst can be reused for several runs with consistent catalytic...
Diffusion of Lipid and Protein Molecules in Cell Membranes, Ph.D. Dissertation Sharif University of Technology ; Jalali, Abbas
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...
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
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,...
Simultaneous versus sequential adsorption of β-casein/SDS mixtures. Comparison of water/air and water/hexane interfaces, Article ACS Symposium Series ; Volume 1120 , 2012 , Pages 153-178 ; 00976156 (ISSN) ; 9780841227965 (ISBN) ; Gochev, G ; Kotsmar, Cs ; Ferri, J. K ; Javadi, A ; Karbaschi, M ; Krägel, J ; Wüstneck, R ; Miller, R ; Sharif University of Technology
This chapter is dedicated to the surface properties of mixed protein/surfactant adsorption layers, formed by two different experimental approaches, i.e. by sequential and simultaneous adsorption, respectively. A special modification of a drop profile analysis tensiometer, consisting of a coaxial double capillary, provides a unique protocol for studies of mixed surface layers formed by sequential adsorption of the individual components in addition to the traditional simultaneous adsorption from their mixed solution. A CFD simulation allowed to optimize the drop exchange process performed with the special double capillary arrangement. The experiments show that properties of sequentially formed...
Searching for galactic hidden gas through interstellar scintillation: Results from a test with the NTT-SOFI detector, Article Astronomy and Astrophysics ; Volume 525, Issue 6 , 2010 ; 00046361 (ISSN) ; Moniez, M ; Ansari, R ; Rahvar, S ; Sharif University of Technology
Aims. Stars twinkle because their light propagates through the atmosphere. The same phenomenon is expected at a longer time scale when the light of remote stars crosses an interstellar molecular cloud, but it has never been observed at optical wavelength. In a favorable case, the light of a background star can be subject to stochastic fluctuations on the order of a few percent at a characteristic time scale of a few minutes. Our ultimate aim is to discover or exclude these scintillation effects to estimate the contribution of molecular hydrogen to the Galactic baryonic hidden mass. This feasibility study is a pathfinder toward an observational strategy to search for scintillation, probing...
Inhibition mechanisms of a pyridazine-based amyloid inhibitor: as a β-sheet destabilizer and a helix bridge maker, Article Journal of Physical Chemistry B ; Volume 121, Issue 32 , 2017 , Pages 7633-7645 ; 15206106 (ISSN) ; Jabbari, M. P ; Sharif University of Technology
Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ1−42 and Aβ1−40 pentamers, Aβ1−42 monomers, and double-horseshoe-like Aβ1−42. To set better parameters for the small molecule, experimental and computational log P values were obtained. In addition, an analogue of RS-0406 was also simulated...
Rydberg noisy dressing and applications in making soliton molecules and droplet quasicrystals, Article Physical Review Research ; Volume 3, Issue 3 , 2021 ; 26431564 (ISSN) ; Sharif University of Technology
American Physical Society 2021
The current advances in the field of ultracold atoms and atomic traps recall new controllable long-range interactions. These interactions are expected to extend the range of realizable quantum algorithms as well as provide new control mechanisms for the new types of quantum matters. This Letter presents special interatomic interactions between Rydberg-dressed atoms by manipulating the lasers' linewidth. The proposed interaction features a hybrid spatial profile containing plateaus and Gaussian peaks. Combined with dynamic control over the sign and strength of individual interaction elements, the Rydberg noisy-dressing (RnD) scheme provides a valuable interaction toolbox for quantum...