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Related Concept Videos

Molecular Models02:00

Molecular Models

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.
Surface Tension01:24

Surface Tension

Surface tension is defined as the force per unit length (γ) acting along the surface of a liquid. It arises due to strong intermolecular forces of attraction. A molecule located inside the bulk of the liquid is surrounded by other molecules and experiences equal forces in all directions. However, a molecule at the surface experiences unbalanced forces because there are more neighboring molecules below than above. This creates a net inward force that pulls surface molecules toward the interior,...
Surface Tension of Fluid01:22

Surface Tension of Fluid

Surface tension is a fundamental property of fluids, occurring at the boundary between a liquid and a gas or between two immiscible liquids. This phenomenon arises from the cohesive forces between molecules at the fluid's surface, creating an effect similar to a stretched elastic membrane. Inside each fluid, molecules are equally attracted in all directions by neighboring molecules, but surface molecules experience a net inward force, resulting in surface tension.
Surface tension varies with...
Surface Tension and Surface Energy01:16

Surface Tension and Surface Energy

When a paint brush is immersed in water, the bristles wave freely inside the water. When it is taken out, the bristles stick together. The reason behind this effect is surface tension.
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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...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

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Related Experiment Video

Updated: Jun 19, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Interactive visualization of molecular surface dynamics.

Michael Krone1, Katrin Bidmon, Thomas Ertl

  • 1Visualization Research Center VISUS, Universität Stuttgart, Germany. michael.krone@vis.uni-stuttgart.de

IEEE Transactions on Visualization and Computer Graphics
|October 17, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel GPU ray casting method for visualizing protein Solvent Excluded Surfaces (SES) interactively. This technique enhances the analysis of molecular dynamics simulations by offering high-quality rendering at interactive speeds.

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

Published on: October 2, 2016

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Visualization

Background:

  • Molecular dynamics (MD) simulations are crucial in pharmaceutical, biochemical, and medical research.
  • High-quality, interactive visualization of protein systems, especially time-dependent data, is essential for analysis.
  • Current methods often involve a trade-off between rendering quality and performance for protein surface visualization.

Purpose of the Study:

  • To develop an efficient and high-quality visualization technique for protein Solvent Excluded Surfaces (SES).
  • To enable interactive analysis of long, time-dependent protein simulation trajectories.
  • To address the limitations of conventional precomputation-based methods.

Main Methods:

  • Implementation of a GPU ray casting technique for SES rendering.
  • Development of a semantic simplification method for protein data to reduce visual complexity.
  • Application of the SES method for visualizing spatial probability density of protein atoms.

Main Results:

  • Achieved interactive frame rates for visualizing protein trajectories, overcoming previous performance bottlenecks.
  • Demonstrated that semantic simplification accelerates rendering without compromising the perception of protein shape.
  • Enabled qualitative analysis of protein flexibility by visualizing atomic spatial probability density in a single frame.

Conclusions:

  • The proposed GPU ray casting approach offers a significant advancement in interactive protein visualization.
  • Semantic simplification effectively balances visual complexity and rendering speed.
  • The method provides novel insights into protein dynamics and flexibility from simulation data.