Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

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Effect of temperature on properties of aluminum/single-walled carbon nanotube nanocomposite by molecular dynamics simulation

Proceedings of the Institution of Mechanical Engineers Part C Journal of Mechanical Engineering Science ◽

10.1177/0954406219878760 ◽

2019 ◽

Vol 234 (2) ◽

pp. 635-642 ◽

Cited By ~ 1

Author(s):

Mohsen Motamedi ◽

AH Naghdi ◽

SK Jalali

Keyword(s):

Mechanical Properties ◽

Molecular Dynamics ◽

Carbon Nanotube ◽

Molecular Dynamics Simulation ◽

Young’S Modulus ◽

Young's Modulus ◽

Strain Curve ◽

Dynamics Simulation ◽

Effect Of Temperature ◽

Metal Composite

Composite materials have become popular because of high mechanical properties and lightweight. Aluminum/carbon nanotube is one of the most important metal composite. In this research, mechanical properties of aluminum/carbon nanotube composite were obtained using molecular dynamics simulation. Then, effect of temperature on stress–strain curve of composite was studied. The results showed by increasing temperature, the Young’s modulus of composite was decreased. More specifically increasing the temperature from 150 K to 620 K, decrease the Young’s modulus to 11.7%. The ultimate stress of composite also decreased by increasing the temperature. A continuum model of composite was presented using finite element method. The results showed the role of carbon nanotube on strengthening of composite.

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Transport Properties of the Ionic Liquid 1-Ethyl-3-Methylimidazolium Chloride from Equilibrium Molecular Dynamics Simulation. The Effect of Temperature

The Journal of Physical Chemistry B ◽

10.1021/jp0680746 ◽

2006 ◽

Vol 110 (32) ◽

pp. 16157-16157 ◽

Cited By ~ 4

Author(s):

Carlos Rey-Castro ◽

Lourdes F. Vega

Keyword(s):

Molecular Dynamics ◽

Ionic Liquid ◽

Molecular Dynamics Simulation ◽

Transport Properties ◽

Dynamics Simulation ◽

Effect Of Temperature

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Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

Canadian Journal of Chemistry ◽

10.1139/cjc-2014-0371 ◽

2015 ◽

Vol 93 (3) ◽

pp. 348-361 ◽

Cited By ~ 2

Author(s):

C. Izanloo

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Double Helix ◽

Melting Process ◽

Minor Groove ◽

Dynamics Simulation ◽

Transition Curve ◽

Water Molecules ◽

Major Groove ◽

Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

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Thermal Rectification in Silicon Nanowires With Mass Gradients

ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels ◽

10.1115/icnmm2008-62240 ◽

2008 ◽

Cited By ~ 1

Author(s):

Shuai-Chuang Wang ◽

Xin-Gang Liang ◽

Xiang-Hua Xu

Keyword(s):

Molecular Dynamics ◽

Heat Flux ◽

Molecular Dynamics Simulation ◽

Silicon Nanowires ◽

Dynamics Simulation ◽

Effect Of Temperature ◽

Phonon Density ◽

Phonon Density Of States ◽

Thermal Rectification ◽

Axial Mass

Thermal rectification as a new phenomenon is attracting great attention. Thermal rectification in silicon nanowires with axial mass gradient is investigated by molecular dynamics simulation. The results of the simulations show that the thermal conductivities are different for the heat flux with opposite directions. The rectification efficiency becomes larger when the mass gradient increases. The effect of temperature gradient on the thermal rectification is also considered. The phonon density of states is calculated to explain the phenomenon. It is found that the interface is responsible to the thermal rectification.

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The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207322666191022142629 ◽

2019 ◽

Vol 22 (8) ◽

pp. 546-554

Author(s):

Mohadeseh Bazoobandi ◽

Mohammad R. Bozorgmehr ◽

Ali Mahmoudi ◽

Ali Morsali

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Low Temperatures ◽

Simulation Method ◽

Dynamics Simulation ◽

Effect Of Temperature ◽

Quadruplex Structure ◽

G Quadruplex ◽

The Stability ◽

Increasing Temperature

Aim and Objective: The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C. Materials and Methods: RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues. Results: The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated. Conclusion: The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.

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