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

Indirect Motor Pathways01:22

Indirect Motor Pathways

3.8K
The indirect motor or extrapyramidal pathways originate in the brainstem, the lower portion of the brain that connects it to the spinal cord. They consist of several distinct tracts, each with specialized functions. The four main tracts of the indirect motor pathways are the vestibulospinal tract, the reticulospinal tract, the tectospinal tract, and the rubrospinal tract.
The vestibulospinal tract originates in the vestibular nuclei of the brainstem. The vestibular system detects changes in...
3.8K
Interference: Path Lengths01:10

Interference: Path Lengths

2.4K
Consider two sources of sound, that may or may not be in phase, emitting waves at a single frequency, and consider the frequencies to be the same.
Two special sources may be considered when they are in phase. This can be easily achieved by feeding the two sources from the same source. An example would be synchronizing the two speakers by feeding them with the same source, such as the sound waves produced by a tuning fork. This setup ensures that the two sources have the same frequency and are...
2.4K
Reconstruction of Signal using Interpolation01:10

Reconstruction of Signal using Interpolation

839
Signal processing techniques are essential for accurately converting continuous signals to digital formats and vice versa. When a continuous signal is sampled with a period T, the resulting sampled signal exhibits replicas of the original spectrum in the frequency domain, spaced at intervals equal to the sampling frequency. To handle this sampled signal, a zero-order hold method can be applied, which creates a piecewise constant signal by retaining each sample's value until the next...
839
Path Between Thermodynamics States01:21

Path Between Thermodynamics States

5.0K
Consider the two thermodynamic processes involving an ideal gas that are represented by paths AC and ABC in Figure 1:
5.0K
Direct Motor Pathways01:11

Direct Motor Pathways

5.2K
The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
The corticospinal tract is responsible for the voluntary movement of the limbs and trunk. It originates in the cerebral cortex of the brain and descends through the cerebrum's internal capsule and...
5.2K
Propagation of Action Potentials01:23

Propagation of Action Potentials

13.9K
The propagation of an action potential refers to the process by which a nerve impulse, or "action potential," travels along a neuron.
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
13.9K

You might also read

Related Articles

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

Sort by
Same author

Accelerated Reaction Exploration across Scales: A Hybrid Operando and Modeling Study of Oxidation Kinetics in Monolayer Tungsten Disulfide.

Journal of the American Chemical Society·2026
Same author

Comparison of predictive approaches to the dynamics of activated catalytic processes.

Physical chemistry chemical physics : PCCP·2026
Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026
Same author

Energy Landscape Analysis of Membrane Proteins Using NMR-Based Hybrid Restraint Potentials.

Journal of chemical theory and computation·2026
Same author

Energy landscapes of the water hexamer and octamer for the MB-pol and TIP4P/2005 potentials.

The Journal of chemical physics·2026
Same author

Visualizing the energy landscape for a molecular dynamics trajectory.

The Journal of chemical physics·2026
Same journal

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame.

Journal of chemical theory and computation·2026
Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·2026
Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026
Same journal

Efficient Coupled-Cluster Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture.

Journal of chemical theory and computation·2026
Same journal

Extending the MARTINI 3 Coarse-Grained Force Field to Polypeptoids.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Mar 29, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

18.7K

Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations.

David J Wales1, Joanne M Carr1

  • 1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Journal of Chemical Theory and Computation
|November 24, 2015
PubMed
Summary
This summary is machine-generated.

A new quasi-continuous interpolation (QCI) method generates realistic pathways for molecular systems. This approach aids in transition state searches and kinetic network construction for peptides, proteins, and atomic clusters.

More Related Videos

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.7K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K

Related Experiment Videos

Last Updated: Mar 29, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

18.7K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.7K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Materials Science

Background:

  • Characterizing reaction pathways is crucial for understanding molecular transformations.
  • Accurate initial pathways are needed for efficient transition state searches.
  • Existing methods may struggle with complex molecular rearrangements.

Purpose of the Study:

  • Introduce a quasi-continuous interpolation (QCI) scheme.
  • Enable the generation of physically realistic initial pathways.
  • Facilitate transition state searches and kinetic network construction.

Main Methods:

  • End point alignment using a shortest augmenting path algorithm for isomer optimization.
  • An interpolating potential that preserves covalent bonds and includes repulsive terms.
  • Minimizing contributions from connected images to identify paths and detect unphysical geometries.
  • Atom-by-atom growth for complex rearrangements with chain crossings.

Main Results:

  • Demonstrated QCI for peptides, proteins, and atomic cluster transformations.
  • Successfully generated initial pathways for transition state searches.
  • Benchmark calculations coupled QCI with transition state searches for complete pathway construction.

Conclusions:

  • QCI provides a robust method for generating realistic initial pathways.
  • The scheme is applicable to diverse systems, including biomolecules and atomic clusters.
  • QCI enhances the efficiency and accuracy of molecular dynamics simulations and kinetic modeling.