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

Bootstrapping01:24

Bootstrapping

959
The term "bootstrap" originated in the 19th century as a metaphor for self-improvement or achieving something independently, without external assistance. This concept extends to statistical bootstrapping, a self-contained method for estimating population parameters through resampling, even though it can be computationally intensive. Developed by the American statistician Dr. Bradley Efron in 1979, bootstrapping provides a robust way to perform inference when the original sample size is...
959
Genetic Drift03:33

Genetic Drift

45.1K
Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
45.1K
Sampling Theorem01:15

Sampling Theorem

1.6K
In signal processing, the analysis of continuous-time signals, denoted as x(t), often involves sampling techniques to convert these signals into discrete-time signals. This process is essential for digital representation and manipulation. A critical component in sampling is the train of impulses, characterized by the sampling interval and the sampling frequency. The relationship between these parameters and the original signal's properties dictates the success of the sampling process.
1.6K
Censoring Survival Data01:09

Censoring Survival Data

647
Survival analysis is a statistical method used to analyze time-to-event data, often employed in fields such as medicine, engineering, and social sciences. One of the key challenges in survival analysis is dealing with incomplete data, a phenomenon known as "censoring." Censoring occurs when the event of interest (such as death, relapse, or system failure) has not occurred for some individuals by the end of the study period or is otherwise unobservable, and it might have many different...
647
Evolution of New Traits in Microbes01:24

Evolution of New Traits in Microbes

97
Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
97

You might also read

Related Articles

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

Sort by
Same author

Toward Quantitative Reaction Dynamics of O<sub>3</sub>.

The journal of physical chemistry letters·2026
Same author

Reaction Pathway Dynamics for Atmospheric Decomposition Reactions: Unimolecular Dissociation of H<sub>2</sub>COO.

The journal of physical chemistry letters·2026
Same author

Compact Kernel/Neural Network Representation for Accurate, Fast, and Global Reactive Molecular Potential Energy Surfaces.

Precision chemistry·2026
Same author

High-Accuracy Molecular Simulations with Machine-Learning Potentials and Semiclassical Approximations to Quantum Dynamics.

Chimia·2026
Same author

Tripeptide dynamics from empirical and machine-learned energy functions.

Biophysical journal·2026
Same author

Efficient and Equivariant Prediction of Distributed Charges for Accurate Molecular Electrostatics.

Journal of chemical theory and computation·2026
Same journal

Nuclear Gradients from Auxiliary-Field Quantum Monte Carlo and Their Applications in ML-Driven Geometry Optimization and Transition State Search.

Journal of chemical theory and computation·2026
Same journal

Correction to "Cluster-in-Molecule Local Correlation Method with an Accurate Distant Pair Correction for Large Systems".

Journal of chemical theory and computation·2026
Same journal

Machine-Learned Force Fields for Lattice Dynamics at Coupled-Cluster Level Accuracy.

Journal of chemical theory and computation·2026
Same journal

Systematic Molecularity-Dependent Entropy Errors in Continuum/RRHO Solution Thermochemistry: Origin and Correction.

Journal of chemical theory and computation·2026
Same journal

After 100 Years of Quantum Mechanics: Toward a Constructive Observation-Centered Perspective.

Journal of chemical theory and computation·2026
Same journal

Sample-Based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds.

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

Related Experiment Video

Updated: Mar 29, 2026

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan
11:58

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan

Published on: June 29, 2018

10.2K

Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping.

Nuria Plattner1, J D Doll2, Markus Meuwly3

  • 1Department of Mathematics and Computer Science, Free University Berlin , Arnimallee 6, 14195 Berlin, Germany.

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

Infinite swapping (INS) offers a more efficient computational sampling method than parallel tempering (PT). This enhanced technique, utilizing symmetrized configurations, significantly improves sampling for biological systems like proteins.

More Related Videos

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow
08:58

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

808
An Unbiased Approach of Sampling TEM Sections in Neuroscience
10:56

An Unbiased Approach of Sampling TEM Sections in Neuroscience

Published on: April 13, 2019

7.8K

Related Experiment Videos

Last Updated: Mar 29, 2026

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan
11:58

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan

Published on: June 29, 2018

10.2K
Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow
08:58

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

808
An Unbiased Approach of Sampling TEM Sections in Neuroscience
10:56

An Unbiased Approach of Sampling TEM Sections in Neuroscience

Published on: April 13, 2019

7.8K

Area of Science:

  • Computational biology
  • Biophysics
  • Molecular dynamics

Background:

  • Rare event sampling is crucial for understanding molecular processes.
  • Parallel tempering (PT) is a common method but can be limited.
  • Infinite swapping (INS) is a novel approach to enhance sampling efficiency.

Purpose of the Study:

  • To evaluate the efficiency of Infinite Swapping (INS) compared to Parallel Tempering (PT).
  • To assess INS performance across diverse biological systems with varying sampling challenges.
  • To investigate the impact of symmetrized distributions and enhanced replica exchange in INS.

Main Methods:

  • Implementation of Infinite Swapping (INS) using an expanded computational ensemble.
  • Application of INS to three distinct biological systems: blocked alanine dipeptide, Villin headpiece, and neuroglobin.
  • Quantitative comparison of sampling efficiency between INS and PT.

Main Results:

  • Infinite Swapping (INS) demonstrated substantially higher sampling efficiency across all tested biological systems.
  • Symmetrization of configurations in temperature space enhanced information exchange between replicas.
  • INS proved effective for small molecule dynamics, protein folding, and substate sampling in folded proteins.

Conclusions:

  • Infinite Swapping (INS) is a more efficient method for rare event sampling in computational biology.
  • The enhanced information exchange in INS significantly accelerates the exploration of conformational landscapes.
  • INS offers a powerful alternative to PT for complex biological simulations.