Related Experiment Video
Updated: Jul 18, 2026

Analysis of SEC-SAXS data via EFA deconvolution and Scatter
Published on: January 28, 2021
Harmonic Fourier beads method for studying rare events on rugged energy surfaces
Ilja V Khavrutskii1, Karunesh Arora, Charles L Brooks
1Department of Molecular Biology, The Scripps Research Institute, TPC6, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. ikhavru@scripps.edu
Abstract:
We present a robust, distributable method for computing minimum free energy paths of large molecular systems with rugged energy landscapes. The method, which we call harmonic Fourier beads (HFB), exploits the Fourier representation of a path in an appropriate coordinate space and proceeds iteratively by evolving a discrete set of harmonically restrained path points-beads-to generate positions for the next path. The HFB method does not require explicit knowledge of the free energy to locate the path. To compute the free energy profile along the final path we employ an umbrella sampling method in two generalized dimensions. The proposed HFB method is anticipated to aid the study of rare events in biomolecular systems. Its utility is demonstrated with an application to conformational isomerization of the alanine dipeptide in gas phase.
Related Concept Videos
Convergence of Fourier Series
The Gibbs phenomenon refers to the persistent oscillations and overshoots that occur near discontinuities...
Energy Bands in Solids
Band Formation:
When atoms are brought close together, as in a solid, these discrete energy levels begin to split due to the overlap of electron orbitals from adjacent atoms. This split occurs because of the Pauli exclusion principle, which states that no two...
Discrete Fourier Transform
¹H NMR: Interpreting Distorted and Overlapping Signals
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations
Trigonometric Fourier series
The trigonometric Fourier series specifically expresses a periodic function with a defined period T using sine...

