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 Concept Videos

Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

1.1K
The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
1.1K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.4K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.4K
2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

429
Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
429

You might also read

Related Articles

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

Sort by
Same author

Microsecond dynamics in proteins by two-dimensional ESR: Predictions.

The Journal of chemical physics·2020
See all related articles

Related Experiment Video

Updated: Nov 16, 2025

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.4K

Microsecond dynamics in proteins by two-dimensional ESR. II. Addressing computational challenges.

Pranav Gupta1, Kevin Chaudhari2, Jack H Freed1

  • 1National Biomedical Center for Advanced ESR Technology and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

The Journal of Chemical Physics
|February 28, 2021
PubMed
Summary
This summary is machine-generated.

High-frequency 2D-ELDOR experiments offer detailed molecular motion insights. A new rational Arnoldi algorithm significantly speeds up simulations of protein domain motions, improving computational efficiency.

More Related Videos

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.3K
High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
08:48

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

2.0K

Related Experiment Videos

Last Updated: Nov 16, 2025

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.4K
Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.3K
High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
08:48

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

2.0K

Area of Science:

  • Spectroscopy
  • Biophysics
  • Computational Chemistry

Background:

  • Two-dimensional electron-electron double resonance (2D-ELDOR) is a powerful technique for studying molecular dynamics.
  • Higher frequency (95 GHz) 2D-ELDOR experiments provide enhanced molecular orientational resolution.
  • Simulating domain motions in slowly tumbling proteins using standard methods is computationally intensive.

Purpose of the Study:

  • To investigate the efficiency of the rational Arnoldi algorithm for simulating molecular motions in complex systems.
  • To reduce the significant computation time associated with previous simulation methods.
  • To optimize the selection of frequency shifts and matrix dimension reduction for improved simulation accuracy and speed.

Main Methods:

  • Application of the rational Arnoldi algorithm to solve the stochastic Liouville equation.
  • Reduction of the large-dimension stochastic Liouville matrix (N) to a smaller dimension (m) using Krylov subspace projection.
  • Development and implementation of an adaptive shift choice method for optimizing frequency shift selection.
  • Optimization of matrix pruning techniques to reduce computational complexity.

Main Results:

  • The rational Arnoldi algorithm achieves a significant reduction in computation time for 2D-ELDOR simulations.
  • Matrix dimension is reduced from N ~ O(10^4) to m ~ 60, enabling faster spectral prediction.
  • The adaptive shift choice method effectively optimizes the selection of frequency shifts.
  • The described procedures enhance the pruning of the stochastic Liouville matrix, further improving computational efficiency.

Conclusions:

  • The rational Arnoldi algorithm offers a computationally efficient approach for 2D-ELDOR simulations of molecular motions.
  • This method provides a faster and optimized pathway for analyzing complex protein dynamics.
  • The developed techniques pave the way for more extensive investigations into molecular motions using high-frequency 2D-ELDOR.