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Study and simulation of nanoparticle translocation through cell membrane
, Article Iranian Journal of Science and Technology - Transactions of Mechanical Engineering ; 2019 ; 22286187 (ISSN) ; Barzegar, M. R ; Taghibakhshi, A ; Sharif University of Technology
Springer International Publishing
2019
Abstract
In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the...
Study and Simulation of Nanoparticle Translocation Through Cell Membrane
, Article Iranian Journal of Science and Technology - Transactions of Mechanical Engineering ; Volume 45, Issue 4 , 2021 , Pages 939-960 ; 22286187 (ISSN) ; Barzegar, M. R ; Taghibakhshi, A ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2021
Abstract
In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the...
Nanomechanical properties of MscL α helices: A steered molecular dynamics study
, Article Channels ; Volume 11, Issue 3 , 2017 , Pages 209-223 ; 19336950 (ISSN) ; Bavi, O ; Vossoughi, M ; Naghdabadi, R ; Hill, A. P ; Martinac, B ; Jamali, Y ; Sharif University of Technology
Taylor and Francis Inc
2017
Abstract
Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during...