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

Diffusive dynamics on multidimensional rough free energy surfaces.

Polina Banushkina1, Markus Meuwly

  • 1Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.

The Journal of Chemical Physics
|October 9, 2007
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

Toward Quantitative Reaction Dynamics of O<sub>3</sub>.

The journal of physical chemistry letters·2026
Same author

Reaction Pathway Dynamics for Atmospheric Decomposition Reactions: Unimolecular Dissociation of H<sub>2</sub>COO.

The journal of physical chemistry letters·2026
Same author

Compact Kernel/Neural Network Representation for Accurate, Fast, and Global Reactive Molecular Potential Energy Surfaces.

Precision chemistry·2026
Same author

High-Accuracy Molecular Simulations with Machine-Learning Potentials and Semiclassical Approximations to Quantum Dynamics.

Chimia·2026
Same author

Tripeptide dynamics from empirical and machine-learned energy functions.

Biophysical journal·2026
Same author

Efficient and Equivariant Prediction of Distributed Charges for Accurate Molecular Electrostatics.

Journal of chemical theory and computation·2026
Same journal

Anharmonic phonons via quantum thermal bath simulations.

The Journal of chemical physics·2026
Same journal

Quantum simulation of alignment dependent differential cross sections in co-propagating molecular beams at cold collision energies.

The Journal of chemical physics·2026
Same journal

Non-additive ion effects on the coil-globule equilibrium of a generic polymer in aqueous salt solutions.

The Journal of chemical physics·2026
Same journal

Insights into the unexpected small reduction of the temperature of maximum density of water by lithium chloride addition.

The Journal of chemical physics·2026
Same journal

Optical frequency comb double-resonance spectroscopy of the 9030-9175 cm-1 states of ethylene.

The Journal of chemical physics·2026
Same journal

Time reversal breaking of colloidal particles in cells.

The Journal of chemical physics·2026
See all related articles

Investigating chemical and biophysical dynamics on complex free energy landscapes, this study uses a novel algorithm to solve the Smoluchowski equation for ligand rebinding and protein folding.

Area of Science:

  • Chemistry
  • Biophysics
  • Computational Biology

Background:

  • Free energy landscapes govern molecular dynamics.
  • Understanding ligand rebinding and protein folding is crucial in biophysics.
  • Previous methods struggled to accurately model dynamics on rough landscapes.

Purpose of the Study:

  • To investigate chemical and biophysical process dynamics on rough free energy landscapes.
  • To apply a new algorithm for solving the Smoluchowski equation.
  • To calculate experimentally accessible quantities like rebinding and folding times.

Main Methods:

  • Developed a novel algorithm to solve the Smoluchowski equation.
  • Constructed a 2D free energy surface (FES) for MbCO rebinding using molecular dynamics.

Related Experiment Videos

  • Utilized a previously determined 2D FES for protein G folding.
  • Employed a hierarchical discrete approximation method to solve the Smoluchowski equation.

    • Main Results:

    • Calculated free energy barriers for CO rebinding in myoglobin (Mb) (approx. 6 kcal/mol).
    • Identified a significantly larger barrier for CO in the Xe4 pocket and distal pocket compared to the inner barrier.
    • Determined a folding barrier of approx. 10 kcal/mol for protein G.
    • Obtained folding times for protein G on the order of milliseconds.

    Conclusions:

    • The new algorithm accurately models diffusive dynamics on rough free energy landscapes.
    • The calculated barriers and folding times for MbCO rebinding and protein G folding are consistent with experimental observations.
    • This approach provides a powerful tool for studying complex molecular processes.