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Peer-reviewedCC BYVirus research

Roughness-dependent retention of a reduced rabies-virus model in a platinum nanochannel: a molecular dynamics study.

  • Narinderjit Singh Sawaran Singh1
  • Murtaja Satea2
  • Ali Jawad Kadhum3
  • Ibrahm Mahariq4
  • Hemn A H Barzani5
  • Baydaa Abed Hussein6
  • Mina D Jumaah7
  • Mahmut Taner8
  • Soheil Salahshour9
  • A Rahimi10
10 affiliations
  1. 1Faculty of Data Science and Information Technology, INTI International University, Persiaran Perdana BBN, Putra Nilai, Nilai, 71800, Malaysia.
  2. 2College of Medicine, University of Warith Al-Anbiyaa, Karbala, 56001, Iraq.
  3. 3Department of Biology, College of Science, University of Al Maarif, Al Anbar, 31001, Iraq.
  4. 4University College, Korea University, Seoul, 02481, South Korea; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan. Electronic address: [email protected].
  5. 5Department of Medical Laboratory Science, College of Health Science, Lebanese French University, Erbil, Iraq.
  6. 6Department of pathological analyzes, University of Manara, Maysan, Iraq.
  7. 7College of Medicine, Misan University, Maysan, Iraq.
  8. 8Faculty of Engineering and Architecture, Istanbul Gelisim University, Istanbul, Türkiye.
  9. 9Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul, Türkiye; Faculty of Engineering and Natural Sciences, Bahcesehir University, Istanbul, Türkiye; Research Center of Applied Mathematics, Khazar University, Baku, Azerbaijan; Faculty of Science and Letters, Piri Reis University, Tuzla, Istanbul, Türkiye.
  10. 10Fast Computing Center, Shabihsazan Ati Pars, Tehran, Iran. Electronic address: [email protected].
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Abstract

Capturing nanoscale biological objects in nanochannels depends strongly on surface geometry and interfacial interactions. However, the spatial and temporal limitations of atomistic simulations prevent the direct representation of a complete rabies virion. In this study, we used molecular dynamics simulations to examine the force-driven retention of a reduced rabies-virus model with a characteristic size of approximately 4 nm in a water-filled platinum nanochannel with non-ideal surface roughness. The simulated construct was developed from reported rabies-virus structural information but did not reproduce the complete morphology, envelope, genomic content, or biological functionality of an intact virion. The atomic interactions were described using DREIDING and Universal Force Field parameters, the TIP3P water model, the embedded atom method for Pt-Pt interactions, and Lennard-Jones and Coulombic terms for interfacial interactions. After 10 ns of canonical equilibration at 300 K, the system underwent a 20 ns force-driven production stage. Roughness sizes of 35, 37, 40, and 43 Å were investigated. Among the four simulated configurations, the 40 Å roughness case produced the largest maximum density (0.187 atom/ų), the lowest maximum velocity (0.006 Å/ps), the largest retained surface-mesh volume (31,118 ų), and the most negative reduced-model-Pt interaction energy (-469.91 kcal/mol). The simulation-defined retained fraction for the reduced construct reached 95% at 20 ns. The weaker responses at 43 Å indicated a non-monotonic dependence on roughness size within this model and the investigated geometries. These results characterized the force-driven behavior of a specific 4-nm construct under the stated simulation conditions; they did not establish roughness-dependent capture behavior for intact rabies virions or predict experimental device performance.

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Cite

BibTeXRIS
BibTeX
@article{singh2026roughnessdependent,
  title = {{Roughness-dependent retention of a reduced rabies-virus model in a platinum nanochannel: a molecular dynamics study.}},
  author = {Narinderjit Singh Sawaran Singh and Murtaja Satea and Ali Jawad Kadhum and Ibrahm Mahariq and Hemn A H Barzani and Baydaa Abed Hussein and Mina D Jumaah and Mahmut Taner and Soheil Salahshour and A Rahimi},
  journal = {Virus research},
  year = {2026},
  month = oct,
  doi = {10.1016/j.virusres.2026.199816},
  url = {https://europepmc.org/article/MED/42849621},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Roughness-dependent retention of a reduced rabies-virus model in a platinum nanochannel: a molecular dynamics study.
AU  - Narinderjit Singh Sawaran Singh
AU  - Murtaja Satea
AU  - Ali Jawad Kadhum
AU  - Ibrahm Mahariq
AU  - Hemn A H Barzani
AU  - Baydaa Abed Hussein
AU  - Mina D Jumaah
AU  - Mahmut Taner
AU  - Soheil Salahshour
AU  - A Rahimi
PY  - 2026
DA  - 2026/10/08
JO  - Virus research
DO  - 10.1016/j.virusres.2026.199816
UR  - https://europepmc.org/article/MED/42849621
AB  - Capturing nanoscale biological objects in nanochannels depends strongly on surface geometry and interfacial interactions. However, the spatial and temporal limitations of atomistic simulations prevent the direct representation of a complete rabies virion. In this study, we used molecular dynamics simulations to examine the force-driven retention of a reduced rabies-virus model with a characteristic size of approximately 4 nm in a water-filled platinum nanochannel with non-ideal surface roughness. The simulated construct was developed from reported rabies-virus structural information but did not reproduce the complete morphology, envelope, genomic content, or biological functionality of an intact virion. The atomic interactions were described using DREIDING and Universal Force Field parameters, the TIP3P water model, the embedded atom method for Pt-Pt interactions, and Lennard-Jones and Coulombic terms for interfacial interactions. After 10 ns of canonical equilibration at 300 K, the system underwent a 20 ns force-driven production stage. Roughness sizes of 35, 37, 40, and 43 Å were investigated. Among the four simulated configurations, the 40 Å roughness case produced the largest maximum density (0.187 atom/ų), the lowest maximum velocity (0.006 Å/ps), the largest retained surface-mesh volume (31,118 ų), and the most negative reduced-model-Pt interaction energy (-469.91 kcal/mol). The simulation-defined retained fraction for the reduced construct reached 95% at 20 ns. The weaker responses at 43 Å indicated a non-monotonic dependence on roughness size within this model and the investigated geometries. These results characterized the force-driven behavior of a specific 4-nm construct under the stated simulation conditions; they did not establish roughness-dependent capture behavior for intact rabies virions or predict experimental device performance.
SN  - 0168-1702
SN  - 1872-7492
ER  -