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Graphic: Graph-based hierarchical clustering for single-molecule localization microscopy
, Article 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021, 13 April 2021 through 16 April 2021 ; Volume 2021-April , 2021 , Pages 1892-1896 ; 19457928 (ISSN); 9781665412469 (ISBN) ; Aziznejad, S ; Unser, M ; Sage, D ; Sharif University of Technology
IEEE Computer Society
2021
Abstract
We propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitatively analyzing the biological particles of interest at different scales. It assumes a prior neither on the shape of particles nor on the background noise. Our multiscale clustering pipeline is built upon graph theory. At each scale, we first construct a weighted graph that represents the SMLM data. Next, we find clusters using spectral clustering. We then use the output of this clustering algorithm to build the graph in the next scale; in...
Structural and dynamical fingerprints of the anomalous dielectric properties of water under confinement
, Article Physical Review Materials ; Volume 5, Issue 2 , 2021 ; 24759953 (ISSN) ; Esfandiar, A ; Hassanali, A ; Ejtehadi, M. R ; Sharif University of Technology
American Physical Society
2021
Abstract
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms, which plays a crucial role in electrochemistry and biology. In this study, the dielectric, structural, and dynamical properties of confined water placed between two parallel graphene walls at different interdistances from the angstrom scale to a few tens of nanometer have been investigated using molecular dynamics. For the dielectric properties of water, we show that the dielectric constant of the perpendicular component of water drastically decreases under sub-2-nm spatial confinement. The dielectric constant data obtained through...
Structural and dynamical fingerprints of the anomalous dielectric properties of water under confinement
, Article Physical Review Materials ; Volume 5, Issue 2 , 2021 ; 24759953 (ISSN) ; Esfandiar, A ; Hassanali, A ; Ejtehadi, M. R ; Sharif University of Technology
American Physical Society
2021
Abstract
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms, which plays a crucial role in electrochemistry and biology. In this study, the dielectric, structural, and dynamical properties of confined water placed between two parallel graphene walls at different interdistances from the angstrom scale to a few tens of nanometer have been investigated using molecular dynamics. For the dielectric properties of water, we show that the dielectric constant of the perpendicular component of water drastically decreases under sub-2-nm spatial confinement. The dielectric constant data obtained through...
Electro-optical properties of APS and APhS linkers on silicon thin film: A DFT study
, Article Applied Surface Science ; Volume 605 , 2022 ; 01694332 (ISSN) ; Darvish, G ; Faez, R ; Sharif University of Technology
Elsevier B.V
2022
Abstract
APS (3-Aminopropyl) trimethoxysilane) and APhS (p-Aminophenyl) trimethoxysilane) are the most commonly used linkers on a silicon surface. We investigate the surface properties of the structures, including APS or APhS on a silicon substrate. The studied structures consist of APS or APhS linkers with one, two, or three bonds with a substrate, which is a thin layer of Si with crystal orientation 〈1 0 0〉 or 〈1 1 1〉. Using a first-principles study based on density functional theory (DFT), we investigated the electronic and optical properties of the silicon-linker interface, such as interface states, orbital location, dielectric function, and photon absorption. The effects of linker type, number...
Synthesis, Characterization and Voltametric Study of Single Molecule Magnet Hybrid Salts [Mn3O(O2CMe)6(Pyr)3][Keggin-Polyoxometalates]Type
,
M.Sc. Thesis
Sharif University of Technology
;
Mohammadi Boghaei, Davar
(Supervisor)
Abstract
Molecular nanomagnets, also known as Single Molecule Magnets (SMMs) are a class of molecules that at low temperature exhibit magnetic hysteresis of pure molecular origin and not related to a cooperative effect. In the past fifteen years they have attracted great interest for their potentiality to act as magnetic memory units and for the many quantum effects in the dynamics of their magnetization. Organization of SMM on surfaces is the first step in order to address the magnetic state of a single molecule or to connect the molecule to a conducting substrate. The complex nature of SMMs and the peculiar origin of their magnetic bistability have been representing for half a decade an obstacle to...
Equation of State for Dense Systems of Light Molecules in Fluid and Solid States
, M.Sc. Thesis Sharif University of Technology ; Parsafar, Gholam Abbas (Supervisor)
Abstract
A general regularity has been found based on an effective pair potential of Lennard-Jones LJ (12, 6) for both dense nonmetallic and nonionic fluids and solids; namely, (Z-1)V2 linearly varies with respect to ρ2, this equation of state (EoS I) is known as LIR. The other equation of state (EoS II), according to wich the isotherm of (Z-1)V2 is linear in term of 1/ρ, wich gives a good description for the metallic and ionic fluids and solids. This equation of state was suggested based on an effective pair potential of LJ (6, 3). Unexpectedly, solid and liquid Ne indicates a significant deviations from EoS I. Recently, a general equation of state (EoS III) based on an effective near-neighbor pair...
Molecular structure and character of bonding of mono and divalent metal cations (Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and cu +) with guanosine: AIM and NBO analysis
, Article Structural Chemistry ; Volume 23, Issue 3 , June , 2012 , Pages 613-626 ; 10400400 (ISSN) ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
2012
Abstract
The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA....
Influence of the water molecules (n 5 1-6) on the interaction between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue
, Article Structural Chemistry ; Volume 23, Issue 3 , 2012 , Pages 857-865 ; 10400400 (ISSN) ; Nasiri, M ; Fattahi, A ; Vafaeezadeh, M ; Sharif University of Technology
2012
Abstract
Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the...
Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2'-deoxythymidine with different anions
, Article Structural Chemistry ; Volume 23, Issue 1 , July , 2012 , Pages 17-28 ; 10400400 (ISSN) ; Fattahi, A ; Sharif University of Technology
2012
Abstract
Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory...
Directed motion of C60 on a graphene sheet subjected to a temperature gradient
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 83, Issue 4 , 2011 ; 15393755 (ISSN) ; Neek Amal, M ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
Nonequilibrium molecular dynamics simulations are used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors
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...
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
Study of self-association of water in supercritical CO2 by Monte Carlo simulation: Does water have a specific interaction with CO2?
, Article Fluid Phase Equilibria ; Volume 267, Issue 2 , 2008 , Pages 181-187 ; 03783812 (ISSN) ; Khanlarkhani, A ; Sharif University of Technology
2008
Abstract
The extent of the self-association of water in supercritical CO2 has been investigated in a wide range of density and temperature by the test particle insertion technique. The results show that the association constant for water decreases with temperature and weakly depends on CO2 density. This weak density dependence provides evidence for the lack of a strong specific CO2-water interaction. Comparing calculated association constants with its gas-phase values shows that the association constant is at most ca. 38% lower than its gas-phase value in the high density-low temperature region. Inspection of the simulated radial distribution functions revealed that forming modest water-CO2 complexes...
The vibration-rotation kinetic energy operator for sequentially bonded tetra-atomic molecules in internal coordinates
, Article Molecular Physics ; Volume 105, Issue 17-18 , 2007 , Pages 2269-2278 ; 00268976 (ISSN) ; Tafazzoli, M ; Sharif University of Technology
2007
Abstract
An exact vibration-rotation kinetic energy operator for polyatomic molecules has been obtained. Using this Hamiltonian for sequentially bonded tetra-atomic molecules, all rovibrational terms have been derived with internal coordinates as the vibrational variables. The present approach is greatly simplified with less algebra compared with conventional methods. Also, simple and explicit expressions for the vibration-rotation coupling terms in internal coordinates are presented
Theoretical study of kinetics and mechanism of reactions of hydroxylamine and amineoxide anion with methyl iodide in gas and aqueous phases
, Article Progress in Reaction Kinetics and Mechanism ; Volume 32, Issue 1 , 2007 , Pages 29-50 ; 14686783 (ISSN) ; Irani, M ; Gholami, M. R ; Sharif University of Technology
Science Reviews Ltd
2007
Abstract
The kinetics and mechanism of the reactions of hydroxylamine and aminoxide anion with methyl iodide were studied with ab initio calculations, Monte-Carlo and QM/MM simulations in gas and aqueous phases. Geometrical parameters and charge calculations show that these reactions proceed through the SN2 (bimolecular nucleophilic displacement) mechanism only. The solvent effects on these reactions were studied by inserting water molecules in reaction media, Onsager model, Monte-Carlo and QM/MM simulations. Activation parameters indicate the expected variation in activation energy and rate coefficient in aqueous phase in comparison to the gas phase. The shift of potential energy barrier through the...
Electrocatalytic oxidation of methanol on a nickel electrode modified by nickel dimethylglyoxime complex in alkaline medium
, Article Journal of Power Sources ; Volume 144, Issue 1 , 2005 , Pages 21-27 ; 03787753 (ISSN) ; Shahrokhian, S ; Asgari, M ; Ghannadi Maragheh, M ; Irannejad, L ; Khanchi, A ; Sharif University of Technology
2005
Abstract
Electrocatalytic oxidation of methanol on a nickel disc electrode coated with nickel dimethyglyoxime complex (NiDMG), conditioned by potential recycling in a potential range of 100-700 mV (versus SCE) is studied by cyclic voltammetry in alkaline medium (0.10 M NaOH). The results show that the NiODMG layer formed at the surface of electrode behaves as an efficient electrocatalyst for the oxidation of methanol in alkaline medium via Ni(III) species with the cross exchange reaction occurring through out the layer at a low concentration of methanol. A plausible mechanism was proposed for catalytic oxidation of methanol at this modified electrode. Moreover, the effects of various parameters such...
Classification, Similarity Analysis and Modeling of Drug Activities Using Chemometric Techniques: Introduction of Classical Relativity in Chemical Space
, Ph.D. Dissertation Sharif University of Technology ; Jalali-Heravi, Mehdi (Supervisor)
Abstract
The present research devoted to the application, development and implementation of clustering, classification and regression techniques for modeling of the biological activity of different drug and drug-like molecules. At first, the prediction ability of Bayesian regression techniques was evaluated for describing and predicting the inhibition behavior of Integrin antagonists. As a next step, the complementary local search techniques have been used for improving the performances of Bayesian regularized genetic neural network (BRGNN) algorithm. The results indicated that the pattern search algorithm has a great potential to be used as a feature selection method in Chemoinformatics. In line...
Methane molecule over the defected and rippled graphene sheet
, Article Solid State Communications ; Volume 152, Issue 15 , August , 2012 , Pages 1493-1496 ; 00381098 (ISSN) ; Neek Amal, M ; Sharif University of Technology
Elsevier
2012
Abstract
Adsorption of a methane molecule (CH 4) onto a defected and rippled graphene sheet is studied using ab initio and molecular mechanics calculations. The optimal adsorption position and orientation of this molecule on the graphene surface (motivated by the recent realization of graphene sensors to detect individual gas molecules) is determined and the adsorption energies are calculated. In light of the density of states, we used the SIESTA code. It is found that (i) classical force field yields adsorption energy comparable with experimental result and ab initio calculation; (ii) the periodic nature of the van der Waals potential energy stored between methane and perfect sheet is altered due to...
Mixed protein-surfactant adsorption layers formed in a sequential and simultaneous way at water-air and water-oil interfaces
, Article Soft Matter ; Volume 8, Issue 22 , 2012 , Pages 6057-6065 ; 1744683X (ISSN) ; Kotsmar, C ; Ferri, J. K ; Javadi, A ; Karbaschi, M ; Krägel, J ; Wüstneck, R ; Miller, R ; Sharif University of Technology
2012
Abstract
Mixed protein-surfactant adsorption layers can be built up in two different ways. The classical way is when all components adsorb simultaneously from a mixed solution. Alternatively, the components adsorb one after another, i.e. in a sequential way. In the present work, the formation of such surface layers has been studied with the random coil protein β-casein in the presence of added anionic surfactant SDS and compared for two different interfaces: the water-air (W-A) and water-hexane (W-H) interfaces. The used experimental technique is a drop profile analysis tensiometer PAT-1 specially equipped with a coaxial double capillary for drop volume exchange during the experiments. The results...
Simulation of heat transfer in nanoscale flow using molecular dynamics
, Article ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels Collocated with 3rd Joint US-European Fluids Engineering Summer Meeting, ICNMM2010, 1 August 2010 through 5 August 2010, Montreal, QC ; Issue PARTS A AND B , 2010 , Pages 1563-1568 ; 9780791854501 (ISBN) ; Abbasi, H. R ; Sabouri, M ; Khaledi Alidusti, R ; Sharif University of Technology
2010
Abstract
We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the...