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

Molecular Models02:00

Molecular Models

37.5K
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.
37.5K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.1K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

1.0K
1.0K
Protein Complex Assembly02:41

Protein Complex Assembly

12.5K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
12.5K
Protein Complex Assembly02:41

Protein Complex Assembly

1.6K
1.6K
Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

4.3K
In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
4.3K

You might also read

Related Articles

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

Sort by
Same author

Filling the Gaps: Generating 4D Dense Cardiac Anatomy from Sparse CMR for Enhanced Tetralogy of Fallot Assessment.

Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance·2026
Same author

Neural implicit heart coordinates: 3D cardiac shape reconstruction from sparse segmentations.

Medical image analysis·2026
Same author

Statistical Atlas-Based Surrogate Model of Biventricular Wall Mechanics.

bioRxiv : the preprint server for biology·2026
Same author

Human Variant in the Cardiac Troponin I Switch Domain Causes Diastolic Dysfunction in a Novel Mouse Model.

Journal of the American Heart Association·2025
Same author

Excitation and mechanical contraction of a 3D cardiomyocyte model.

Biophysical journal·2025
Same author

Characteristics of left ventricular dysfunction in repaired tetralogy of Fallot: A multi-institutional deep learning analysis of regional strain and dyssynchrony.

Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance·2025
Same journal

An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map.

Molecular based mathematical biology·2021
Same journal

A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds.

Molecular based mathematical biology·2017
Same journal

Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators.

Molecular based mathematical biology·2015
Same journal

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding.

Molecular based mathematical biology·2014
Same journal

High-order fractional partial differential equation transform for molecular surface construction.

Molecular based mathematical biology·2013
Same journal

Progress in developing Poisson-Boltzmann equation solvers.

Molecular based mathematical biology·2013
See all related articles

Related Experiment Video

Updated: May 4, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

11.3K

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.

Tao Liao1, Yongjie Zhang1, Peter M Kekenes-Huskey2

  • 1Department of Mechanical Engineering, Carnegie Mellon University.

Molecular Based Mathematical Biology
|December 20, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient computational framework for multi-scale modeling of large biomolecular complexes using atomic data. The method accelerates model construction using Graphics Processing Units (GPUs) and multi-core CPUs.

Keywords:
GPUbiomolecular complex * mesh generationefficient computationmulti-core CPUmulti-scale modeling

More Related Videos

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

15.3K
Analysis of Multidimensional Microscopy Data Using Cell-ACDC
06:17

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

776

Related Experiment Videos

Last Updated: May 4, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

11.3K
Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

15.3K
Analysis of Multidimensional Microscopy Data Using Cell-ACDC
06:17

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

776

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Understanding large biomolecular complexes requires advanced modeling techniques.
  • Atomic resolution data from the Protein Data Bank (PDB) is crucial for structural insights.
  • Existing methods may lack efficiency in handling large-scale biomolecular data.

Purpose of the Study:

  • To present an efficient computational framework for constructing multi-scale models of biomolecular complexes.
  • To leverage atomic resolution data from the PDB for enhanced modeling.
  • To improve the speed and accuracy of biomolecular modeling through parallel processing.

Main Methods:

  • Developed an efficient computational framework for multi-scale modeling.
  • Utilized multi-level summation of Gaussian kernel functions for implicit biomolecular models.
  • Implemented neighboring search, KD-tree, and bounding volume hierarchy for optimized grid point analysis.
  • Compared CPU sequential, multi-core CPU parallel, and GPU parallel modes for mesh generation.

Main Results:

  • Successfully constructed multi-scale models from PDB atomic data.
  • Achieved acceleration through multi-core CPU and GPU parallel processing.
  • Demonstrated local resolution control on biomolecular surfaces.
  • Generated high-quality tetrahedral meshes using parallel processing modes.

Conclusions:

  • The presented framework offers an efficient approach to multi-scale biomolecular modeling.
  • Parallel computing (CPU and GPU) significantly enhances the speed of model construction and mesh generation.
  • The method provides accurate and locally controlled models for large biomolecular complexes.