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Related Concept Videos

Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...
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Comparing Intermolecular Forces: Melting Point, Boiling Point, and Miscibility

Intermolecular forces are attractive forces that exist between molecules. They dictate several bulk properties, such as melting points, boiling points, and solubilities (miscibilities) of substances. Molar mass, molecular shape, and polarity affect the strength of different intermolecular forces, which influence the magnitude of physical properties across a family of molecules.
Temporary attractive forces like dispersion are present in all molecules, whether they are polar or nonpolar. They...
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
Molecular Geometry and Dipole Moments02:36

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Behavior of Gas Molecules: Molecular Diffusion, Mean Free Path, and Effusion03:48

Behavior of Gas Molecules: Molecular Diffusion, Mean Free Path, and Effusion

Although gaseous molecules travel at tremendous speeds (hundreds of meters per second), they collide with other gaseous molecules and travel in many different directions before reaching the desired target. At room temperature, a gaseous molecule will experience billions of collisions per second. The mean free path is the average distance a molecule travels between collisions. The mean free path increases with decreasing pressure; in general, the mean free path for a gaseous molecule will be...
Diffusion01:12

Diffusion

Diffusion is the passive movement of substances down their concentration gradients—requiring no expenditure of cellular energy. Substances, such as molecules or ions, diffuse from an area of high concentration to an area of low concentration in the cytosol or across membranes. Eventually, the concentration will even out, with the substance moving randomly but causing no net change in concentration. Such a state is called dynamic equilibrium, which is essential for maintaining overall...

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Related Experiment Video

Updated: Jun 8, 2026

Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level
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Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

Published on: September 26, 2016

Using diffusion distances for flexible molecular shape comparison.

Yu-Shen Liu1, Qi Li, Guo-Qin Zheng

  • 1School of Software, Tsinghua University, Beijing 100084, China. liuyushen00@gmail.com

BMC Bioinformatics
|September 28, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces the Diffusion Distance Shape Descriptor (DDSD) for flexible molecular shape comparison. DDSD accurately captures molecular structures and deformations, outperforming rigid-body methods.

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Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level
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Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

Area of Science:

  • Computational chemistry
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Most molecular shape comparison (MSC) methods assume rigidity, potentially causing errors in recognizing flexible molecules.
  • Molecular flexibility is crucial for function, yet inadequately addressed by current MSC techniques.

Purpose of the Study:

  • To develop a novel shape descriptor for comparing 3D shapes of flexible molecules.
  • To address the limitations of rigid-body assumptions in molecular shape analysis.

Main Methods:

  • Introduced the Diffusion Distance Shape Descriptor (DDSD) based on inner distances between landmark points on molecular surfaces.
  • Represented molecular shape as a histogram of diffusion distances between all point pairs.
  • Reduced flexible MSC to comparing DDSD histograms.

Main Results:

  • The Diffusion Distance (DD) metric is robust to flexible shape deformation and topological changes.
  • DDSD effectively reflects molecular structure and deformation without explicit decomposition.
  • DDSD histograms provide a reliable representation for flexible molecular shape comparison.

Conclusions:

  • DDSD is insensitive to molecular shape deformation, offering superior performance over traditional descriptors.
  • The DDSD algorithm is robust and does not require prior knowledge of flexible molecular regions.
  • This method enhances the accuracy of molecular shape recognition for flexible molecules.