Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Dynamics of polymer packaging.

I Ali1, D Marenduzzo, J M Yeomans

  • 1Rudolf Peierls Centre for Theoretical Physics, Oxford University 1 Keble Road, Oxford OX1 3NP, United Kingdom. issam@squ.edu.om

The Journal of Chemical Physics
|October 30, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Modelling transcriptional silencing and its coupling to 3D genome organisation.

Soft matter·2025
Same author

Biomechanical strength of triceps tendon repairs: systematic review and meta-regression analysis of human cadaveric studies.

Musculoskeletal surgery·2024
Same author

Halogens engineering-based design of agonists for boosting expression of frataxin protein in Friedreich's ataxia.

European review for medical and pharmacological sciences·2023
Same author

Revolutionizing treatment for toxic shock syndrome with engineered super chromones to combat antibiotic-resistant Staphylococcus aureus.

European review for medical and pharmacological sciences·2023
Same author

Burden and distribution of dengue infection in Pakistan (2000-19): a review.

Brazilian journal of biology = Revista brasleira de biologia·2023
Same author

Topological phases and curvature-driven pattern formation in cholesteric shells.

Soft matter·2023
Same journal

Revisiting crossed-correlated baths in open quantum systems simulated by HEOM or T-TEDOPA.

The Journal of chemical physics·2026
Same journal

Vesicle size and membrane composition control monomer transfer pathways in multicomponent lipid vesicles.

The Journal of chemical physics·2026
Same journal

Polaron-mediated exciton dynamics of P(NDI2OD-T2) unveiled by transient absorption spectroscopy under electrochemical conditions.

The Journal of chemical physics·2026
Same journal

Green-Kubo relation in a mesoscale odd fluid model.

The Journal of chemical physics·2026
Same journal

Nitrogenation of microscopic MoS2 surfaces by oxidation scanning probe lithography.

The Journal of chemical physics·2026
Same journal

Molecular structure, binding, and disorder in TDBC-Ag plexcitonic assemblies.

The Journal of chemical physics·2026
See all related articles

We simulated polymer chain packaging into a permeable capsid, finding flexible chains pack randomly and semiflexible chains spool-like. Including fluid flow (hydrodynamics) significantly speeds up this polymer packaging process.

Area of Science:

  • Biophysics
  • Computational Biology
  • Polymer Physics

Background:

  • Understanding how polymers pack into confined spaces like viral capsids is crucial for molecular biology and nanotechnology.
  • Previous models often simplified polymer behavior or neglected hydrodynamic interactions, limiting their predictive power.

Purpose of the Study:

  • To investigate the dynamics of flexible and semiflexible polymer packaging into a permeable capsid using advanced simulation methods.
  • To elucidate the role of polymer flexibility and hydrodynamic interactions on the packaging process and rate.

Main Methods:

  • Stochastic Rotation Dynamics (SRD) algorithm was employed to simulate polymer chains (flexible and semiflexible) being packaged into a capsid.
  • Hydrodynamic interactions due to local solvent flow were incorporated into the model.

Related Experiment Videos

  • Packing rates and chain configurations were analyzed at varying degrees of chain packing.

    • Main Results:

    • Flexible polymer chains adopted random configurations during packaging, while semiflexible chains initially formed spool-like structures that became more random at higher packing densities.
    • The polymer packaging rate decreased as more of the chain was packed, with distinct behaviors observed for flexible versus semiflexible chains.
    • Simulations reproduced experimental observations of pauses during packaging due to motor slippage on fluctuating beads.
    • Inclusion of hydrodynamic interactions significantly increased the polymer packaging rate.

    Conclusions:

    • Hydrodynamic interactions play a critical role in accelerating polymer packaging into capsids.
    • The flexibility of polymer chains dictates their configuration and packing dynamics within confined environments.
    • The SRD model provides a valuable framework for studying complex biophysical processes like viral capsid filling.