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

Diffusion in correlated random potentials, with applications to DNA.

Michael Slutsky1, Mehran Kardar, Leonid A Mirny

  • 1Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. mich@mit.edu

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|July 13, 2004
PubMed
Summary

Biological diffusion on complex energy landscapes shows significant fluctuations. These random walks, crucial for processes like DNA targeting, exhibit anomalous diffusion rules impacting transport times.

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

Genome-wide absolute quantification of chromatin looping.

Nature structural & molecular biology·2026
Same author

Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.

bioRxiv : the preprint server for biology·2026
Same author

Active RNA synthesis patterns nuclear condensates.

Cell systems·2026
Same author

Cohesin bridging as a physical principle of enhancer-promoter communication.

bioRxiv : the preprint server for biology·2026
Same author

Genetically homogeneous sector morphologies emerge from anisotropic colony growth.

Physical review. E·2026
Same author

Minimal model of self-organized clusters with phase transitions in ecological communities.

Physical review. E·2026

Area of Science:

  • Biophysics
  • Statistical Mechanics
  • Computational Biology

Background:

  • One-dimensional diffusion occurs over correlated, inhomogeneous energy landscapes.
  • Key biological processes like protein-DNA targeting, nucleosome repositioning, and DNA translocation involve this type of diffusion.
  • The correlation length (ξ(c)) in these biological systems is approximately 10 nm.

Purpose of the Study:

  • To investigate transport processes on correlated inhomogeneous energy landscapes using the mean first passage time (MFPT) formalism.
  • To analyze the impact of energy landscape fluctuations on diffusion times and biological process efficiency.

Main Methods:

  • Utilized the mean first passage time (MFPT) formalism to model diffusion.
  • Analyzed the average MFPT and its standard deviation over an ensemble of energy profiles.

Related Experiment Videos

  • Investigated the scaling behavior of diffusion times with displacement (N).

    • Main Results:

    • Diffusion times exhibit strong sample-to-sample fluctuations.
    • The average MFPT is diffusive, but its standard deviation scales as N(3/2).
    • Fluctuations dominate for displacements smaller than a characteristic N(c) >> ξ(c), leading to anomalous diffusion rules.

    Conclusions:

    • Random walks on these landscapes are characterized by rapid scans in favorable regions and occasional jumps.
    • Anomalous diffusion governs transport for smaller displacements, significantly differing from the mean behavior.
    • These findings have potential biological implications for understanding the efficiency and dynamics of molecular processes.