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Related Concept Videos

Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

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.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Atomic Nuclei: Magnetic Resonance01:05

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The number of nuclear spins aligned in the lower energy state is slightly greater than those in the higher energy state. In the presence of an external magnetic field, as the spins precess at the Larmor frequency, the excess population results in a net magnetization oriented along the z axis. When a pulse or a short burst of radio waves at the Larmor frequency is applied along the x axis, the coupling of frequencies causes resonance and flips the nuclear spins of the excess population from the...
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Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
10:57

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Published on: November 11, 2025

Encoding molecular motions in voxel maps.

Juan Cortés1, Sophie Barbe, Monique Erard

  • 1LAAS-CNRS, 7 avenue du Colonel Roche, F-31077 Toulouse, France. jcortes@laas.fr

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|April 28, 2010
PubMed
Summary

This study introduces voxel maps to represent large-amplitude molecular motions, combining robotic path planning and molecular modeling for enhanced computational analysis.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Robotics

Background:

  • Accurately computing large-amplitude molecular motions is crucial for understanding molecular behavior.
  • Existing methods may face challenges in efficiently representing complex molecular dynamics.

Purpose of the Study:

  • To introduce voxel maps as a novel computational tool for encoding and representing large-amplitude molecular motions.
  • To demonstrate the utility of this representation through various applications.

Main Methods:

  • Integration of robotic path planning algorithms with molecular modeling techniques.
  • Development and application of voxel maps for motion representation.

Main Results:

  • Voxel maps effectively encode complex molecular motions.
  • Demonstrated applicability across several computational scenarios.
  • Illustrative results highlight the value of the voxel map representation.

Conclusions:

  • Voxel maps offer a promising computational approach for analyzing large-amplitude molecular motions.
  • This representation facilitates a deeper understanding of molecular dynamics.