Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

The Quantum-Mechanical Model of an Atom02:45

The Quantum-Mechanical Model of an Atom

58.4K
Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra.
58.4K
Atomic Orbitals02:44

Atomic Orbitals

44.2K
An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.
44.2K
The Atomic Theory of Matter02:59

The Atomic Theory of Matter

128.6K
The earliest recorded discussion of the basic structure of matter comes from ancient Greek philosophers. Leucippus and Democritus argued that all matter was composed of small, finite particles that they called atomos, meaning “indivisible.” Later, Aristotle and others came to the conclusion that matter consisted of various combinations of the four “elements” — fire, earth, air, and water — and could be infinitely divided. Interestingly, these philosophers...
128.6K
Atomic Structure01:33

Atomic Structure

210.3K
Overview
210.3K
Atomic Mass01:52

Atomic Mass

70.3K
Atoms — and the protons, neutrons, and electrons that compose them — are extremely small. For example, a carbon atom weighs less than 2 × 10−23 g. When describing the properties of tiny objects such as atoms, we use appropriately small units of measure, such as the atomic mass unit (amu). The amu was originally defined based on hydrogen, the lightest element, then later in terms of oxygen. Since 1961, it has been defined with regard to the most abundant isotope of carbon, atoms of which...
70.3K
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

67.6K
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...
67.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Implementation of hydroponic teaching and research platforms at primarily undergraduate institutions.

Frontiers in education·2026
Same author

Automated L3 Skeletal Muscle Segmentation for the Evaluation of Sarcopenia: Development and Independent Validation of an Ensemble-Based 2D nnU-Net Pipeline in a Complex Liver Disease Cohort.

Muscles (Basel, Switzerland)·2026
Same author

Treatment of Coagulopathy.

Techniques in vascular and interventional radiology·2026
Same author

Barriers to Sunscreen Use in a Diverse Patient Population: A Survey-Based Study.

Cureus·2026
Same author

Improving ALS Clinic Care Through Experience-Based Co-Design: A Participatory Action Research Study.

Muscle & nerve·2026
Same author

Cross-resistance patterns in SARS-CoV-2 against 3CL protease inhibitors.

Nature communications·2026

Related Experiment Video

Updated: Feb 6, 2026

gP2S, an Information Management System for CryoEM Experiments
13:01

gP2S, an Information Management System for CryoEM Experiments

Published on: June 10, 2021

5.9K

Building atomic models based on near atomic resolution cryoEM maps with existing tools.

Iris Yu1, Lisa Nguyen1, Jaycob Avaylon2

  • 1Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.

Journal of Structural Biology
|August 17, 2018
PubMed
Summary

Students improved atomic models of biological structures using cryo-electron microscopy (cryoEM) and molecular modeling. This challenge provided hands-on experience with atomic modeling and refinement techniques for new researchers.

Keywords:
Cryo-electron microscopyIon channelMolecular modelingProteasomeRibosome

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

2.1K
Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.6K

Related Experiment Videos

Last Updated: Feb 6, 2026

gP2S, an Information Management System for CryoEM Experiments
13:01

gP2S, an Information Management System for CryoEM Experiments

Published on: June 10, 2021

5.9K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

2.1K
Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.6K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • The EMDataBank Validation Challenge offered a practical learning environment for students new to cryo-electron microscopy (cryoEM) and molecular modeling.
  • Students practiced atomic modeling and refinement on published structures, gaining experience with advanced techniques.

Purpose of the Study:

  • To regularize and improve atomic models of three biological targets using manual molecular modeling.
  • To explore the capabilities of atomic modeling and refinement in cryoEM.
  • To develop a cohesive methodology for de novo modeling applicable to new researchers.

Main Methods:

  • Utilized manual molecular modeling software including Coot, Phenix, and Chimera.
  • Applied modeling techniques to T20S proteasome, TRPV1 ion channel, and 70S ribosome structures.
  • Developed de novo modeling strategies with and without homology models.

Main Results:

  • Successfully regularized and improved the atomic models for all three targets.
  • Gained broader understanding of modeling techniques through proteasome and ion channel targets.
  • Tested and refined abilities using the complex 70S ribosome structure.

Conclusions:

  • The validation challenge effectively enhanced student understanding and skills in cryoEM and molecular modeling.
  • A reproducible methodology for de novo modeling was established, benefiting future cryoEM researchers.
  • Constructive feedback was provided to ease the entry of new students into the cryoEM field.