Investigation of the effects of porosity and volume fraction on the atomic behavior of cancer cells and microvascular cells of 3DN5 and 5OTF macromolecular structures during hematogenous metastasis using the molecular dynamics method

Huanlei Wang; As'ad Alizadeh; Azher M Abed; Anahita Piranfar; Ghassan Fadhil Smaisim; Salema K Hadrawi; Hussein Zekri; Davood Toghraie; Maboud Hekmatifar

doi:10.1016/j.compbiomed.2023.106832

Investigation of the effects of porosity and volume fraction on the atomic behavior of cancer cells and microvascular cells of 3DN5 and 5OTF macromolecular structures during hematogenous metastasis using the molecular dynamics method

Comput Biol Med. 2023 May:158:106832. doi: 10.1016/j.compbiomed.2023.106832. Epub 2023 Apr 5.

Authors

Huanlei Wang¹, As'ad Alizadeh², Azher M Abed³, Anahita Piranfar⁴, Ghassan Fadhil Smaisim⁵, Salema K Hadrawi⁶, Hussein Zekri⁷, Davood Toghraie⁸, Maboud Hekmatifar⁹

Affiliations

¹ Department of Applied Engineering, Zhejiang Business College, Hangzhou, 310053, Zhejiang, China; Key Laboratory of Modern Acoustics (MOE), Department of Physics, Collaborative Innovation Centre of Advanced Microstructure, Nanjing University, Nanjing, 210093, Jiangsu, China. Electronic address: 00550@zjbc.edu.cn.
² Department of Civil Engineering, College of Engineering, Cihan University-Erbil, Erbil, Iraq.
³ Air Conditioning and Refrigeration Techniques Engineering Department, Al-Mustaqbal University College, Babylon 51001, Iraq.
⁴ Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran.
⁵ Department of Mechanical Engineering, Faculty of Engineering, University of Kufa, Iraq; Nanotechnology and Advanced Materials Research Unit (NAMRU), Faculty of Engineering, University of Kufa, Iraq.
⁶ Refrigeration and Air-conditioning Technical Engineering Department, College of Technical Engineering, The Islamic University, Najaf, Iraq; Computer Engineering Department, Imam Reza University, Mashhad, Iran.
⁷ College of Engineering, The American University of Kurdistan, Duhok, Kurdistan Region, Iraq; Department of Mechanical Engineering, College of Engineering, University of Zakho, Zakho, Kurdistan Region, Iraq.
⁸ Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Khomeinishahr, Iran. Electronic address: Toghraee@iaukhsh.ac.ir.
⁹ Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Khomeinishahr, Iran.

PMID: 37037148
DOI: 10.1016/j.compbiomed.2023.106832

Abstract

Background and objective: The molecular dynamics (MD) simulation is a powerful tool for researching how cancer patients are treated. The efficiency of many factors may be predicted using this approach in great detail and with atomic accuracy.

Methods: The MD simulation method was used to investigate the impact of porosity and the number of cancer cells on the atomic behavior of cancer cells during the hematogenous spread. In order to examine the stability of simulated structures, temperature and potential energy (PE) values are used. To evaluate how cell structure has changed, physical parameters such as gyration radius, interaction force, and interaction energy are also used.

Results: The findings demonstrate that the samples' gyration radius, interaction energy, and interaction force rose from 41.33 Å, -551.38 kcal/mol, and -207.10 kcal/mol Å to 49.49, -535.94 kcal/mol, and -190.05 kcal/mol Å, respectively, when the porosity grew from 0% to 5%. Also, the interaction energy and force in the samples fell from -551.38 kcal/mol and -207.10 kcal/mol to -588.03 kcal/mol and -237.81 kcal/mol Å, and the amount of gyration radius reduced from 41.33 to 37.14 Å as the number of cancer cells rose from 1 to 5 molecules. The strength and stability of the simulated samples will improve when the radius of gyration is decreased.

Conclusions: Therefore, high accumulation of cancer cells will make them resistant to atomic collapse. It is expected that the results of this simulation should be used to optimize cancer treatment processes further.

Keywords: Atomic behavior; Cancer; Molecular dynamics simulation; Porosity; Volume fraction.

MeSH terms

Humans
Molecular Docking Simulation
Molecular Dynamics Simulation*
Neoplasms*
Porosity