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

Simulation of biomolecular diffusion and complex formation.

S A Allison, S H Northrup, J A McCammon

    Biophysical Journal
    |January 1, 1986
    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

    Dynamic light-scattering studies of internal motions in DNA. III. Evidence for titratable joints associated with bound polycations.

    Biopolymers·2020
    Same author

    RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations.

    Computer physics communications·2018
    Same author

    Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems.

    Journal of chemical theory and computation·2015
    Same author

    Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions.

    Journal of chemical theory and computation·2015
    Same author

    Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.

    The Journal of chemical physics·2015
    Same author

    Erratum: "Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation" [J. Chem. Phys. 140, 174106 (2014)].

    The Journal of chemical physics·2015
    Same journal

    Tau protein differentially affects Piezo1 and Kir2.1 channels in brain capillary endothelial cells.

    Biophysical journal·2026
    Same journal

    Emergent Intercellular Junction Stability during Cyclic Tissue Loading.

    Biophysical journal·2026
    Same journal

    Enhanced-Sampling Simulations Reveal Distinct Intermediates in SARS-CoV-2 FSE Pseudoknot Interconversion.

    Biophysical journal·2026
    Same journal

    Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of an infection-critical peptide externalization event.

    Biophysical journal·2026
    Same journal

    Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

    Biophysical journal·2026
    Same journal

    Anisotropic unbinding and location-dependent hovering of a kinesin motor head over microtubule.

    Biophysical journal·2026
    See all related articles

    Computer simulations offer detailed insights into molecular diffusion, crucial for understanding biomolecular processes like protein assembly and ligand binding. These advanced techniques enhance our ability to model and analyze complex molecular interactions.

    Area of Science:

    • Molecular Biophysics
    • Computational Biology
    • Biochemistry

    Background:

    • Diffusion is fundamental to molecular biophysics, influencing molecular assembly, ligand binding, and internal molecular dynamics.
    • Realistic modeling of diffusion requires detailed descriptions of molecular structures, interactions, and solvent effects.

    Purpose of the Study:

    • To review the theory and techniques of diffusional simulations in molecular biophysics.
    • To highlight recent applications and discuss future directions in the field.

    Main Methods:

    • Utilizing advanced computer simulation techniques to model diffusional processes at the submolecular level.
    • Incorporating detailed electrostatic interactions, solvent screening, and hydrodynamic effects into simulations.
    • Analyzing simulation trajectories to extract biomolecular function and interpret experimental data.

    Related Experiment Videos

    Main Results:

    • Current simulation techniques provide unprecedented detail in describing diffusional processes.
    • Applications include studying large-scale DNA motion and enzyme-substrate interactions.
    • Simulations can yield direct functional information, such as bimolecular rate constants.

    Conclusions:

    • Diffusional simulations are powerful tools for understanding complex biomolecular systems.
    • Future work will likely focus on areas such as protein complex formation and further refinement of simulation methodologies.