Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches

Jolfaei, Nitasha Adavoodi; Jolfaei, Niyusha Adavoodi; Hekmatifar, Maboud; Piranfar, Anahita; Toghraie, Davood; Sabetvand, Roozbeh; Rostami, Sara

doi:10.1016/j.cmpb.2019.105169

Cited by 82 publications

(21 citation statements)

References 56 publications

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“…Contrary to many studies, it is not known how the coronavirus interacts with the human environment, such as metallic structures. In this work, we study the coronavirus atomic interaction with metallic surfaces with MD [13][14][15][16][17][18]. Investigations are provided for the coronavirus and metallic…”

Section: Introductionmentioning

confidence: 99%

RETRACTED ARTICLE: Molecular dynamics performance for coronavirus simulation by C, N, O, and S atoms implementation dreiding force field: drug delivery atomic interaction in contact with metallic Fe, Al, and steel

Karimipour

Amini²,

Nouri³

et al. 2020

Comp. Part. Mech.

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Coronavirus causes some illnesses to include cold, COVID-19, MERS, and SARS. This virus can be transmitted through contact with different atomic matrix between humans. So, this atomic is essential in medical cases. In this work, we describe the atomic manner of this virus in contact with various metallic matrix such as Fe, Al, and steel with equilibrium molecular dynamic method. For this purpose, we reported physical properties such as temperature, total energy, distance and angle of structures, mutual energy, and volume variation of coronavirus. In this approach, coronavirus is precisely simulated by O, C, S, and N atoms and they are implemented dreiding force field. Our simulation shows that virus interaction with steel matrix causes the maximum removing of the virus from the surfaces. After 1 ns, the atomic distance between these two structures increases from 45 to 75 Å. Furthermore, the volume of coronavirus 14.62% increases after interaction with steel matrix. This atomic manner shows that coronavirus removes and destroyed with steel surface, and this metallic structure can be a promising material for use in medical applications.

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Section: Introductionmentioning

confidence: 99%

RETRACTED ARTICLE: Molecular dynamics performance for coronavirus simulation by C, N, O, and S atoms implementation dreiding force field: drug delivery atomic interaction in contact with metallic Fe, Al, and steel

Karimipour

Amini²,

Nouri³

et al. 2020

Comp. Part. Mech.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The gained outcomes express that the viscosity value was higher than that of nanofluids. In addition to experimental methods, theoretical approaches can be used to atomic study of various structures [21][22][23][24]. Molecular Dynamics (MD) approach is widely implemented in the atomic and thermal behavior of nanostructures [25][26][27][28][29].…”

Section: A Nanostructure Is a Materials Of Intermediate Size Between Mmentioning

confidence: 99%

Molecular Dynamics Study of Nanoparticles/argon Atoms Size Effects on Atomic Aggregation Phenomena in Ideal Platinum Nanochannel Affected by the External Magnetic Field

Karimipour

2021

Preprint

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In this paper, the computational method is used to describe the atomic behavior of Fe3O4 nanoparticles size effect on these nanoparticles aggregation phenomena in ideal platinum nanochannel and in the presence of outer magnetic major. In this work molecular dynamics (MD) method used and argon atoms described as base fluid. Technically, for the interaction between base fluid atoms, we used Lennard-jones (LJ) potential, while the nanochannel wall and nanoparticle structures are simulated. To calculate the atomic behavior of simulated systems, we report temperature, total energy, and distance of nanoparticles center of mass (COM) and time of aggregation phenomena. Our MD simulation results show the Fe3O4 nanoparticle size is an important factor in aggregation phenomenon occur. Numerically, by enlarging the Fe3O4 nanoparticle size, the aggregation time of Al2O3 nanoparticles changes from 1.41 ns to 1.29 ns. Further, the external magnetic field can be delayed this atomic phenomenon effectively.

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“…This research group reported the atomic interactions between histone molecule and 3LPT protein in other work [10] . Jolfaei et al [11] reported the thermal conductivity of Deoxyribonucleic acid molecules is essential for nanotechnology applications by using the MD approach.…”

Section: Introductionmentioning

confidence: 99%

The investigation of energy management and atomic interaction between coronavirus structure in the vicinity of aqueous environment of H2O molecules via molecular dynamics approach

Guo

Bajuri

Alrabaiah

et al. 2021

Journal of Molecular Liquids

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The coronavirus pandemic is caused by intense acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identifying the atomic structure of this virus can lead to the treatment of related diseases in medical cases. In the current computational study, the atomic evolution of the coronavirus in an aqueous environment using the Molecular Dynamics (MD) approach is explained. The virus behaviors by reporting the physical attributes such as total energy, temperature, potential energy, interaction energy, volume, entropy, and radius of gyration of the modeled virus are reported. The MD results indicated the atomic stability of the simulated virus significantly reduced after 25.33 ns. Furthermore, the volume of simulated virus changes from 182397 Å 3 to 372589 Å 3 after t=30 ns. This result shows the atomic interaction between various atoms in coronavirus structure decreases in the vicinity of H 2 O molecules. Numerically, the interaction energy between virus and aqueous environment converges to -12387 eV and -251 eV values in the initial and final time steps of the MD study procedure, respectively.

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Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches

Cited by 82 publications

References 56 publications

RETRACTED ARTICLE: Molecular dynamics performance for coronavirus simulation by C, N, O, and S atoms implementation dreiding force field: drug delivery atomic interaction in contact with metallic Fe, Al, and steel

RETRACTED ARTICLE: Molecular dynamics performance for coronavirus simulation by C, N, O, and S atoms implementation dreiding force field: drug delivery atomic interaction in contact with metallic Fe, Al, and steel

Molecular Dynamics Study of Nanoparticles/argon Atoms Size Effects on Atomic Aggregation Phenomena in Ideal Platinum Nanochannel Affected by the External Magnetic Field

The investigation of energy management and atomic interaction between coronavirus structure in the vicinity of aqueous environment of H2O molecules via molecular dynamics approach

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