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Related Concept Videos

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.
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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.
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Molecular Models02:00

Molecular Models

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Fluid Mosaic Model01:19

Fluid Mosaic Model

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Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...

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Related Experiment Video

Updated: May 7, 2026

Automated System for Single Molecule Fluorescence Measurements of Surface-immobilized Biomolecules
10:57

Automated System for Single Molecule Fluorescence Measurements of Surface-immobilized Biomolecules

Published on: November 2, 2009

Fast blending scheme for molecular surface representation.

Julius Parulek1, Andrea Brambilla

  • 1University of Bergen.

IEEE Transactions on Visualization and Computer Graphics
|September 21, 2013
PubMed
Summary
This summary is machine-generated.

We developed a novel molecular surface representation that balances detailed visualization with fast rendering performance. This new method offers a computationally efficient alternative to existing models for molecular interaction studies.

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Single Molecule Fluorescence Microscopy on Planar Supported Bilayers
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Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

Published on: October 31, 2015

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Last Updated: May 7, 2026

Automated System for Single Molecule Fluorescence Measurements of Surface-immobilized Biomolecules
10:57

Automated System for Single Molecule Fluorescence Measurements of Surface-immobilized Biomolecules

Published on: November 2, 2009

Single Molecule Fluorescence Microscopy on Planar Supported Bilayers
20:00

Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

Published on: October 31, 2015

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Computer graphics

Background:

  • Molecular surface representation is crucial for studying molecular interactions.
  • The Solvent Excluded Surface (SES) model offers detailed visualization but is computationally expensive.
  • The Gaussian model is faster but less accurate, often preferred for performance reasons.

Purpose of the Study:

  • Introduce a novel molecular surface representation.
  • Achieve visualization quality similar to SES with rendering performance close to the Gaussian model.
  • Provide a computationally efficient alternative for molecular interaction studies.

Main Methods:

  • Iterative blending of implicit functions for surface generation.
  • Avoidance of pre-computation steps.
  • A GPU-based ray-casting algorithm for efficient visualization.

Main Results:

  • The novel representation achieves rendering performance comparable to the Gaussian model.
  • Qualitative and quantitative comparisons demonstrate its validity against SES and Gaussian models.
  • The technique offers a viable alternative where SES is computationally prohibitive.

Conclusions:

  • The proposed molecular surface representation is an appealing and efficient alternative.
  • It bridges the gap between detailed SES models and faster Gaussian models.
  • This method is particularly valuable for large-scale molecular interaction analyses.