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configurational-entropy
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Calculation of melting temperature and transition curve for dickerson DNA dodecamer on the basis of configurational entropy, hydrogen bonding energy, and heat capacity: A molecular dynamics simulation study
, Article Journal of the Iranian Chemical Society ; Volume 8, Issue 3 , 2011 , Pages 708-716 ; 1735207X (ISSN) ; Parsafar, G. A ; Abroshan, H ; Akbarzade, H ; Sharif University of Technology
Abstract
A familiarity with denaturation process is highly significant in understanding the DNA replication, manipulation, and interactions involving DNA double helix stability. We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. At each temperature, configurational entropy was estimated using the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we calculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat capacity for the atoms participating in the hydrogen bonding between two strands of DNA. Moreover, their temperature...
Investigation of I the Stability of B-DNA Molecule: A Molecular Dynamics Simulation
, Ph.D. Dissertation Sharif University of Technology ; Parsafar, Gholam Abbas (Supervisor)
Abstract
In this thesis, the molecular dynamics simulation is used to investigate the melting transition of B-DNA molecule, via of configurational entropy, the fraction of broken hydrogen bonds (f-curve) and hydrogen bonding energy.We have performed molecular dynamics simulation on Drew-Dickerson oligomer with sequence of (CGCGAATTGCGC) at different temperatures, within the range of 280-400 K with the 20 K intervals. The simulation was done in two different mediums (pure water and 1 M NaCl), to see influences of water and salt in stabilizing the DNA molecule. At each temperature, configurational entropy is calculated by the Schlitter’s formula, using the Cartesian coordinate of all atoms. So, in each...
Denaturation of Drew-Dickerson DNA in a high salt concentration medium: Molecular dynamics simulations
, Article Journal of Computational Chemistry ; Volume 32, Issue 16 , September , 2011 , Pages 3354-3361 ; 01928651 (ISSN) ; Parsafar, G. A ; Abroshan, H ; Akbarzadeh, H ; Sharif University of Technology
2011
Abstract
We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T m) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There...
Effect of nitrogen doping on glass transition and electrical conductivity of [EMIM][PF6] ionic liquid encapsulated in a zigzag carbon nanotube
, Article Journal of Physical Chemistry C ; Volume 121, Issue 29 , 2017 , Pages 15493-15508 ; 19327447 (ISSN) ; Minofar, B ; Sharif University of Technology
Abstract
Molecular level understanding of the properties of ionic liquids inside nanopores is needed in order to use ionic liquids for many applications such as electrolytes for energy storage in electric double-layer capacitors and dye-sensitized solar cells for conversion of solar energy. In this study, classical molecular dynamics (MD) simulations have been performed to investigate the radial distribution, glass transition, ionic transfer number, and electrical conductivity of the ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate [EMIM][PF6] ionic liquid encapsulated in carbon nanotube (CNT). The effect of nitrogen as a doping element in CNT on these properties of [EMIM][PF6] was also...
Free energy, configurational and nonextensivity of Tsallis entropy with the size and temperature in colloidal silver nanoparticles in [EMim][PF6] ionic liquid
, Article Journal of Molecular Liquids ; Volume 249 , 2018 , Pages 1012-1019 ; 01677322 (ISSN) ; Taherkhani, F ; Sharif University of Technology
Elsevier B.V
2018
Abstract
Molecular dynamic simulation was performed to calculate the configurational entropy and the free energy for colloidal silver nanoparticles (Ag NPs) in 1-Ethyl-3-methylimidazolium Hexafluorophosphate [EMim][PF6] ionic liquid (IL). Furthermore, the density functional theory (DFT) was used to get the potential interaction between the metal surface and ion in IL. The effect of size and temperature on the configurational entropy and the free energy of colloidal Ag NPs were investigated. Then, it was compared with the gas phase. The Tsallis nonextensivity of entropy was investigated for different sizes of colloidal Ag NPs and it was shown that sub-extensivity of entropy occurs for colloidal Ag...
Protein corona impact on nanoparticle-cell interactions: Toward an energy-based model of endocytosis
, Article Journal of Physics Condensed Matter ; Volume 32, Issue 11 , 2020 ; Mehrafrooz, B ; Montazeri, A ; Naghdabadi, R ; Sharif University of Technology
Institute of Physics Publishing
2020
Abstract
Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that...