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

Mean free path and Mean free time01:22

Mean free path and Mean free time

5.1K
Consider the gas molecules in a cylinder. They move in a random motion as they collide with each other and change speed and direction. The average of all the path lengths between collisions is known as the "mean free path."
5.1K
Path Between Thermodynamics States01:21

Path Between Thermodynamics States

4.0K
Consider the two thermodynamic processes involving an ideal gas that are represented by paths AC and ABC in Figure 1:
4.0K
Interference: Path Lengths01:10

Interference: Path Lengths

2.2K
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...
2.2K
Energy Basics02:27

Energy Basics

47.6K
Chemical reactions, such as those that occur when you light a match, involve changes in energy as well as matter.
47.6K
Behavior of Gas Molecules: Molecular Diffusion, Mean Free Path, and Effusion03:48

Behavior of Gas Molecules: Molecular Diffusion, Mean Free Path, and Effusion

31.3K
Although gaseous molecules travel at tremendous speeds (hundreds of meters per second), they collide with other gaseous molecules and travel in many different directions before reaching the desired target. At room temperature, a gaseous molecule will experience billions of collisions per second. The mean free path is the average distance a molecule travels between collisions. The mean free path increases with decreasing pressure; in general, the mean free path for a gaseous molecule will be...
31.3K
Basicity of Aliphatic Amines01:21

Basicity of Aliphatic Amines

6.9K
Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates higher...
6.9K

You might also read

Related Articles

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

Sort by
Same author

Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors.

ACS pharmacology & translational science·2026
Same author

Scalable Boltzmann generators for equilibrium sampling of large-scale materials.

Nature communications·2026
Same author

MDNA : a software module for DNA structure generation and analysis.

Nucleic acids research·2026
Same author

Nucleation of NaCl crystals from solution: Rate prediction and influence of noisy order parameters on the committor.

The Journal of chemical physics·2026
Same author

Mapping the avoid-ome: a systematic open-science approach to predictive ADMET.

Nature communications·2026
Same author

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.

Journal of chemical information and modeling·2026

Related Experiment Video

Updated: Feb 3, 2026

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions
09:46

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions

Published on: May 10, 2012

13.1K

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.

David W H Swenson1,2, Jan-Hendrik Prinz2,3, Frank Noe3

  • 1van 't Hoff Institute for Molecular Sciences , University of Amsterdam , P.O. Box 94157, 1090 GD Amsterdam , The Netherlands.

Journal of Chemical Theory and Computation
|October 19, 2018
PubMed
Summary

OpenPathSampling (OPS) is a new Python framework simplifying rare event analysis in molecular dynamics simulations. It makes advanced transition path sampling methods accessible for studying complex biological and chemical systems.

More Related Videos

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
Development of a Gaze-Contingent Display Framework Designed for Perceptual and Oculomotor Research with Simulated Central Vision Loss
07:12

Development of a Gaze-Contingent Display Framework Designed for Perceptual and Oculomotor Research with Simulated Central Vision Loss

Published on: April 11, 2025

951

Related Experiment Videos

Last Updated: Feb 3, 2026

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions
09:46

MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions

Published on: May 10, 2012

13.1K
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
Development of a Gaze-Contingent Display Framework Designed for Perceptual and Oculomotor Research with Simulated Central Vision Loss
07:12

Development of a Gaze-Contingent Display Framework Designed for Perceptual and Oculomotor Research with Simulated Central Vision Loss

Published on: April 11, 2025

951

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biophysics

Background:

  • Transition path sampling (TPS) methods enhance molecular dynamics simulations by focusing on rare events.
  • Implementation complexity has limited the widespread adoption of TPS techniques.
  • Understanding rare dynamical events is crucial for mechanism elucidation and rate calculations.

Purpose of the Study:

  • Introduce OpenPathSampling (OPS), an accessible and extensible Python framework for path sampling.
  • Lower the barrier to entry for applying advanced path sampling methodologies.
  • Facilitate the development and application of novel path sampling schemes.

Main Methods:

  • Developed a user-friendly Python framework (OpenPathSampling).
  • Integrated interfaces for OpenMM and an internal dynamics engine.
  • Implemented standard TPS, TIS, RETIS, MSTIS, and MISTIS methodologies.
  • Provided tools for creating new path sampling algorithms.

Main Results:

  • Demonstrated the ease of use and extensibility of the OPS framework.
  • Successfully applied various path sampling algorithms to benchmark problems.
  • Showcased the framework's capability to handle complex (bio)molecular systems.

Conclusions:

  • OpenPathSampling significantly simplifies the application of advanced rare event simulation techniques.
  • The framework empowers researchers to investigate complex molecular dynamics with greater ease.
  • OPS is a valuable tool for advancing the study of reaction mechanisms and kinetics in chemistry and biology.