Search for: molecular-analysis
Investigation into thermally activated migration of fullerene-based nanocars, Article Scientia Iranica ; Volume 25, Issue 3F , 2018 , Pages 1835-1848 ; 10263098 (ISSN) ; Meghdari, A ; Nejat Pishkenari, H ; Sohrabpour, S ; Sharif University of Technology
Sharif University of Technology 2018
The rotational and translational motions 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 (RBMD) method, an all-atom model and classic atomistic dynamics have been employed in this paper to achieve better accuracy. Our results demonstrated that the exibility of the chassis and its attachment to the gold surface played an important role in the motion of a nanocar. In fact, a heavier and more exible nanocar chassis reduces its speed compared to a nanotruck. In addition, the results...
Modeling vibrational behavior of silicon nanowires using accelerated molecular dynamics simulations, Article Scientia Iranica ; Volume 27, Issue 2 , 2021 , Pages 819-827 ; 10263098 (ISSN) ; Delafrouz, P ; Sharif University of Technology
Sharif University of Technology 2021
The classical methods utilized for modeling nano-scale systems are not practical because of the enlarged surface e ects that appear at small dimensions. Contrarily, implementing more accurate methods is followed by prolonged computations as these methods are highly dependent on quantum and atomistic models, and they can be employed for very small sizes in brief time periods. In order to speed up the Molecular Dynamics (MD) simulations of the silicon structures, Coarse-Graining (CG) models are put forward in this research. The procedure involves establishing a map between the main structure's atoms and the beads comprising the CG model and modifying the parameters of the system so that the...
Molecular dynamics simulation of melting, solidification and remelting processes of aluminum, Article Iranian Journal of Science and Technology - Transactions of Mechanical Engineering ; Volume 36, Issue M1 , 2012 , Pages 13-23 ; 22286187 (ISSN) ; Simchi, A ; Aashuri, H ; Sharif University of Technology
A molecular dynamics simulation study has been performed to investigate the solidification and remelting of aluminum using Sutton-Chen many body potential. Different numbers of atoms from 108 to 2048 atoms were considered to find an adequate size for the system. Three different cooling and heating rates, i.e. 10 12 K/s, 10 13 K/s and 10 14 K/s, were used. The structure of the system was examined using radial distribution function. The melting and crystallization temperatures of aluminum were evaluated by calculating the variation of heat capacity during the phase transformation. Additionally, Wendt-Abraham parameters were calculated to determine the glass transition temperature. It is shown...
Influence of quantum effect on deviation from linear isotherm regularity, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 555-560 ; 10263098 (ISSN) ; Parsafar, G. A ; Sharif University of Technology
A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well...
Ballistic molecular transport through two-dimensional channels, Article Nature ; Volume 558 , 20 June , 2018 , Pages 420-423 ; 00280836 (ISSN) ; Geim, A. K ; Janardanan, A ; Rooney, A. P ; Esfandiar, A ; Hu, S ; Dar, S. A ; Grigorieva, I. V ; Haigh, S. J ; Wang, F. C ; Radha, B ; Sharif University of Technology
Nature Publishing Group 2018
Gas permeation through nanoscale pores is ubiquitous in nature and has an important role in many technologies 1,2 . Because the pore size is typically smaller than the mean free path of gas molecules, the flow of the gas molecules is conventionally described by Knudsen theory, which assumes diffuse reflection (random-angle scattering) at confining walls 3-7 . This assumption holds surprisingly well in experiments, with only a few cases of partially specular (mirror-like) reflection known 5,8-11 . Here we report gas transport through ångström-scale channels with atomically flat walls 12,13 and show that surface scattering can be either diffuse or specular, depending on the fine details of the...
Mechanical differences between ATP and ADP actin states: A molecular dynamics study, Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) ; Shamloo, A ; Sharif University of Technology
Academic Press 2018
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed...
Conformation of gemcitabine: an experimental NMR and theoretical DFT study, Article Scientia Iranica ; Volume 25, Issue 3C , 2018 , Pages 1354-1363 ; 10263098 (ISSN) ; Tafazzoli, M ; Sharif University of Technology
Sharif University of Technology 2018
The structural and conformational behavior of gemcitabine (20; 20-diuoro cytidine) was investigated by advanced NMR experiments and a computational quantum mechanical method (DFT) using Potential Energy Scanning (PES) in gas and solution phases in the Polarizable Continuum Model (PCM). Three stable conformers (G1, G2, and G3) were predicted from minimum points in a potential energy diagram. In order to measure coupling constant values, a set of 2D spectra (H-H COSY, H-C HMQC, and H-C HMBC) was analyzed. Optimized structures and spin-spin coupling constant calculations in gas and solution phases were performed by B3LYP/6-311++G(d,p) method. Both energy and NMR parameters showed that G1-form...
Polymeric carbon nitride coupled with a molecular thiomolybdate catalyst: Exciton and charge dynamics in light-driven hydrogen evolution, Article Sustainable Energy and Fuels ; Volume 4, Issue 12 , 2020 , Pages 6085-6095 ; Akbarzadeh, E ; Li, C ; Mitoraj, D ; Krivtsov, I ; Adler, C ; Diemant, T ; Biskupek, J ; Kaiser, U ; Im, C ; Heiland, M ; Jacob, T ; Streb, C ; Dietzek, B ; Beranek, R ; Sharif University of Technology
Royal Society of Chemistry 2020
Solar hydrogen evolution from water is a necessary step to overcome the challenges of rising energy demand and associated environmental concerns. Low-cost photocatalytic architectures based on polymeric light absorbers coupled to highly efficient molecular catalysts might represent an attractive platform to address this issue. However, to-date, our mechanistic knowledge of these systems is still largely underdeveloped. In this study, a molecular molybdenum sulfide hydrogen evolving catalyst, [Mo3S13]2-, is loaded onto polymeric carbon nitride (CNx) photoabsorber by impregnation. The resulting composite shows enhanced photocatalytic activity for hydrogen evolution compared to pristine CNx...
Effects of physicochemical characteristics of magnetically recoverable biocatalysts upon fatty acid methyl esters synthesis from oils, Article Renewable Energy ; Volume 116 , 2018 , Pages 613-622 ; 09601481 (ISSN) ; Kazemeini, M ; Singh, G ; Arpanaei, A ; Sharif University of Technology
Elsevier Ltd 2018
This study reports the importance of physicochemical characteristics of the core-shell structured polymer-coated Fe3O4 cluster@SiO2 nanocomposite particles for designing the biocatalysts used for transesterification of soybean oil. To demonstrate this issue, two different types of polymer molecules such as polyethylenimine (PEI) and polyacrylic acid (PAA) each with two different molecular weights are employed. The highest fatty acid methyl esters (FAMEs) synthesis yield values are achieved by the lipases immobilized onto the low- and high-molecular-weight PEI-coated particles as compared to those of the low- and high-molecular-weight PAA-coated particles (i.e., ∼64.8% and ∼73.1% versus...