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

Relative Motion Analysis using Rotating Axes01:25

Relative Motion Analysis using Rotating Axes

1.0K
Consider a component AB undergoing a linear motion. Along with a linear motion, point B also rotates around point A. To comprehend this complex movement, position vectors for both points A and B are established using a stationary reference frame.
However, to express the relative position of point B relative to point A, an additional frame of reference, denoted as x'y', is necessary. This additional frame not only translates but also rotates relative to the fixed frame, making it...
1.0K
Relative Motion Analysis using Rotating Axes-Problem Solving01:29

Relative Motion Analysis using Rotating Axes-Problem Solving

800
Consider a crane whose telescopic boom rotates with an angular velocity of 0.04 rad/s and angular acceleration of 0.02 rad/s2. Along with the rotation, the boom also extends linearly with a uniform speed of 5 m/s. The extension of the boom is measured at point D, which is measured with respect to the fixed point C on the other end of the boom. For the given instant, the distance between points C and D is 60 meters.
Here, in order to determine the magnitude of velocity and acceleration for point...
800
Relative Motion Analysis - Velocity01:24

Relative Motion Analysis - Velocity

835
A stroke engine has a slider-crank mechanism that converts rotational motion from the crank into linear motion of the slider or vice versa. This mechanism consists of three main parts: the crank, the connecting rod, and the slider.
When an external force is exerted, it sets the crank into a rotational movement. This, in turn, instigates the motion of the connecting rod, leading to what is referred to as a general plane motion. This process involves two key points - point A on the connecting rod...
835
Absolute Motion Analysis- General Plane Motion01:24

Absolute Motion Analysis- General Plane Motion

623
Visualize a drone, with its propellers spinning rapidly, hovering mid-air. The fascinating movements and operations of this drone can be comprehended by applying the principle of general plane motion.
As the drone's propellers rotate, an upward force is generated that counteracts the force of gravity, enabling the drone to lift off from the ground. This initial movement of the drone is along a straight path, representing a form of translational motion. In this phase, every point on the...
623
Curvilinear Motion: Rectangular Components01:23

Curvilinear Motion: Rectangular Components

1.4K
Curvilinear motion characterizes the movement of a particle or object along a curved path, notably evident when envisioning a car navigating a winding road. If the car starts at point A, its position vector is established within a fixed frame of reference, where the ratio of the position vector to its magnitude signifies the unit vector pointing in the position vector's direction.
As the car advances, its position evolves over time. Quantifying the car's velocity involves computing the...
1.4K
Relative Motion Analysis - Acceleration01:10

Relative Motion Analysis - Acceleration

966
A slider-crank mechanism converts rotational motion from the crank into linear motion of the slider or vice versa. This mechanism consists of three main parts: the crank, the connecting rod, and the slider. The movement of the slider-crank is an example of general plane motion as the fluctuating angle between the crank and the connecting rod. Consider a segment AB where point A is at the end of the slider and point B is on the diametrically opposite end to point A, on a crack. The variance in...
966

You might also read

Related Articles

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

Sort by
Same author

Transitional Pain Services and Clinics: A Scoping Review of Recent Literature.

Journal of pain research·2026
Same author

National Institutes of Health funding for venous thromboembolism research.

Journal of thrombosis and haemostasis : JTH·2026
Same author

K294E change in the rotavirus factory forming protein NSP2 stabilizes a rare C-terminal conformation.

Journal of biomolecular structure & dynamics·2025
Same author

Use of machine learning models to identify National Institutes of Health-funded cardiac arrest research.

Resuscitation·2025
Same author

Impact of Amidation on Aβ<sub>25-35</sub> Aggregation.

The journal of physical chemistry. B·2025
Same author

Transforming Physiology and Healthcare through Foundation Models.

Physiology (Bethesda, Md.)·2025
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Feb 24, 2026

Profiling Maternal Behavior Responses During Whole-Brain Imaging
07:12

Profiling Maternal Behavior Responses During Whole-Brain Imaging

Published on: January 24, 2025

1.5K

Visualizing correlated motion with HDBSCAN clustering.

Ryan L Melvin1,2, Jiajie Xiao1,3, Ryan C Godwin1

  • 1Department of Physics, Wake Forest University, Winston Salem, North Carolina.

Protein Science : a Publication of the Protein Society
|August 12, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to visualize protein dynamics, identifying "Dynamic Domains" based on residue motion similarity. This approach complements traditional methods by revealing subtle correlations for better biopolymer analysis.

Keywords:
HDBSCANclusteringcorrelationmolecular dynamics

More Related Videos

Trajectory Data Analyses for Pedestrian Space-time Activity Study
16:14

Trajectory Data Analyses for Pedestrian Space-time Activity Study

Published on: February 25, 2013

14.3K
Author Spotlight: Assessment of Visual Acuity in Central Vision Loss Through Motion-Based Peripheral Vision Testing
06:25

Author Spotlight: Assessment of Visual Acuity in Central Vision Loss Through Motion-Based Peripheral Vision Testing

Published on: February 23, 2024

1.2K

Related Experiment Videos

Last Updated: Feb 24, 2026

Profiling Maternal Behavior Responses During Whole-Brain Imaging
07:12

Profiling Maternal Behavior Responses During Whole-Brain Imaging

Published on: January 24, 2025

1.5K
Trajectory Data Analyses for Pedestrian Space-time Activity Study
16:14

Trajectory Data Analyses for Pedestrian Space-time Activity Study

Published on: February 25, 2013

14.3K
Author Spotlight: Assessment of Visual Acuity in Central Vision Loss Through Motion-Based Peripheral Vision Testing
06:25

Author Spotlight: Assessment of Visual Acuity in Central Vision Loss Through Motion-Based Peripheral Vision Testing

Published on: February 23, 2024

1.2K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Correlated motion analysis is key to understanding biopolymer dynamics and inter-residue communication.
  • Traditional correlation matrices (e.g., heat maps) excel at showing large-scale correlated motions but obscure finer details.
  • Identifying subtle dynamic similarities is crucial for a comprehensive understanding of protein function.

Purpose of the Study:

  • To develop a novel visualization method for protein correlations that highlights subtle dynamic similarities.
  • To introduce the concept of "Dynamic Domains"—groups of residues with similar dynamic behavior, independent of spatial proximity.
  • To provide a complementary approach to existing correlation analysis techniques for biopolymers.

Main Methods:

  • Utilized the HDBSCAN non-parametric clustering algorithm to group residues based on dynamic properties.
  • Developed a visualization technique focusing on the column space of correlation matrices.
  • Applied the method to all-atom molecular dynamics simulations of three human proteins: Nf-Kappa-Beta essential modulator, Thrombin, and MutS-alpha.

Main Results:

  • The proposed method effectively visualizes residue groupings with similar dynamic behaviors, termed "Dynamic Domains".
  • Demonstrated the technique's applicability across proteins of varying sizes and functions.
  • Showcased the ability to identify nuanced dynamic similarities missed by conventional methods.

Conclusions:

  • The new visualization method offers an intuitive way to understand residue dynamics and communication within proteins.
  • "Dynamic Domains" provide a powerful new perspective on protein structure-function relationships.
  • This technique is versatile and applicable to correlation matrices derived from various computational and experimental data sources.