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

Woodward–Hoffmann Selection Rules and Microscopic Reversibility01:34

Woodward–Hoffmann Selection Rules and Microscopic Reversibility

4.2K
Electrocyclic reactions, cycloadditions, and sigmatropic rearrangements are concerted pericyclic reactions that proceed via a cyclic transition state. These reactions are stereospecific and regioselective. The stereochemistry of the products depends on the symmetry characteristics of the interacting orbitals and the reaction conditions. Accordingly, pericyclic reactions are classified as either symmetry-allowed or symmetry-forbidden. Woodward and Hoffmann presented the selection criteria for...
4.2K
Exponential Equations for Modeling Growth01:26

Exponential Equations for Modeling Growth

427
Exponential models are essential for describing rapid, multiplicative changes in natural systems, such as population growth. When a population doubles at regular intervals, the process can be modeled using a suitable base. For instance, a bacterial culture that doubles every three hours follows the model n(t)=n0⋅2t/3, where n(t) is the population at the time t.A more general model uses the natural base e, especially for continuous growth. This takes the form n(t)=n0⋅ert, where r is...
427
Rationalizing Substitutions01:29

Rationalizing Substitutions

138
Integrals involving non-rational functions are often difficult to evaluate using standard techniques, especially when radicals appear in the integrand. Rationalizing substitution provides a systematic method for simplifying such integrals by converting them into rational forms that are easier to handle.Consider a rod whose linear mass density depends on a constant linear density, a characteristic length, and the distance from the left end of the rod. Determining the total mass requires...
138
Collisions in Multiple Dimensions: Problem Solving01:06

Collisions in Multiple Dimensions: Problem Solving

5.7K
In multiple dimensions, the conservation of momentum applies in each direction independently. Hence, to solve collisions in multiple dimensions, we should write down the momentum conservation in each direction separately. To help understand collisions in multiple dimensions, consider an example.
A small car of mass 1,200 kg traveling east at 60 km/h collides at an intersection with a truck of mass 3,000 kg traveling due north at 40 km/h. The two vehicles are locked together. What is the...
5.7K
Modeling and Similitude01:12

Modeling and Similitude

720
Scaled modeling is a fundamental technique in engineering, enabling the study of large and complex systems by creating smaller, manageable replicas that recreate critical characteristics of the original. In hydrology and civil infrastructure, for example, scaled models of dams help analyze water flow, turbulence, and pressure. This method allows for accurate predictions of real-world behavior within a controlled environment, significantly reducing the cost and time involved in full-scale...
720
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

You might also read

Related Articles

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

Sort by
Same author

Ether linkages in phospholipids provide modular control of membrane mechanics.

bioRxiv : the preprint server for biology·2026
Same author

Walking the Tightrope: Balancing Opposing Cooperativities as an Operating Principle in Dynein Assembly.

bioRxiv : the preprint server for biology·2026
Same author

Randomized iterative trajectory reweighting for steady-state distributions without discretization error.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.

bioRxiv : the preprint server for biology·2026
Same author

Investigator-blind discovery of structural elements controlling GPCR function.

bioRxiv : the preprint server for biology·2026
Same author

Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.

Cell systems·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
Same journal

Statistical Mechanics of Density- and Temperature-Dependent Potentials: Application to Condensed Phases within GenDPDE.

Journal of chemical theory and computation·2026
Same journal

BFEE-Docking: A User-Friendly and Customizable End-to-End Tool from High-Throughput Virtual Screening to Binding Free-Energy Calculations.

Journal of chemical theory and computation·2026
Same journal

On-the-Fly Trajectory Simulation of Two-Pulse, Three-Pulse, and Higher-Order Pump-Probe Signals.

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

Related Experiment Video

Updated: Mar 29, 2026

Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression
13:07

Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

Published on: January 15, 2022

4.7K

Resolution Exchange Simulation with Incremental Coarsening.

Edward Lyman1, Daniel M Zuckerman1

  • 1Department of Computational Biology, School of Medicine, and Department of Environmental and Occupational Health, Graduate School of Public Health, BST W1041, 200 Lothrop Street, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.

Journal of Chemical Theory and Computation
|December 3, 2015
PubMed
Summary
This summary is machine-generated.

We developed an improved "resolution exchange" algorithm for enhanced molecular sampling. This method efficiently refines atomic models by exchanging conformations between simulations at different resolutions and temperatures.

More Related Videos

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography
10:18

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography

Published on: February 21, 2017

8.9K
Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation
11:41

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Published on: February 1, 2020

21.1K

Related Experiment Videos

Last Updated: Mar 29, 2026

Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression
13:07

Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

Published on: January 15, 2022

4.7K
Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography
10:18

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography

Published on: February 21, 2017

8.9K
Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation
11:41

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Published on: February 1, 2020

21.1K

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biophysics

Background:

  • Accurate molecular modeling requires extensive conformational sampling.
  • Traditional simulations struggle with large systems and long timescales.
  • The 'resolution exchange' algorithm was previously developed to address these limitations.

Purpose of the Study:

  • To demonstrate a general incremental coarsening procedure for the resolution exchange algorithm.
  • To apply the enhanced algorithm to a larger peptide system, met-enkephalin.
  • To explore the combination of resolution and temperature exchange for improved simulation efficiency.

Main Methods:

  • Implementation of a generally applicable incremental coarsening procedure.
  • Application of the 'resolution exchange' algorithm to met-enkephalin simulations.
  • Integration of elevated temperatures in coarser simulation replicas.
  • Utilizing a 'top-down' simulation approach for efficient CPU allocation.

Main Results:

  • Successful application of the incremental coarsening procedure to a larger peptide.
  • Demonstration of combined resolution and temperature exchange.
  • Efficient allocation of computational resources across simulation replicas.

Conclusions:

  • The enhanced resolution exchange algorithm provides a robust method for improving canonical sampling.
  • The combined resolution and temperature exchange offers a powerful strategy for accelerating molecular simulations.
  • This approach facilitates more efficient exploration of conformational landscapes for larger biomolecules.