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

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

200
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
200
Molecular Models02:00

Molecular Models

43.0K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.0K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

43.3K
VSEPR Theory for Determination of Electron Pair Geometries
43.3K
Real Gases: Effects of Intermolecular Forces and Molecular Volume Deriving Van der Waals Equation04:01

Real Gases: Effects of Intermolecular Forces and Molecular Volume Deriving Van der Waals Equation

38.1K
Thus far, the ideal gas law, PV = nRT, has been applied to a variety of different types of problems, ranging from reaction stoichiometry and empirical and molecular formula problems to determining the density and molar mass of a gas. However, the behavior of a gas is often non-ideal, meaning that the observed relationships between its pressure, volume, and temperature are not accurately described by the gas laws.
38.1K
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models01:06

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

190
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
190
Van der Waals Equation01:10

Van der Waals Equation

5.9K
The ideal gas law is an approximation that works well at high temperatures and low pressures. The van der Waals equation of state (named after the Dutch physicist Johannes van der Waals, 1837−1923) improves it by considering two factors.
First, the attractive forces between molecules, which are stronger at higher densities and reduce the pressure, are considered by adding to the pressure a term equal to the square of the molar density multiplied by a positive coefficient a. Second, the volume...
5.9K

You might also read

Related Articles

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

Sort by
Same author

Generative-model-based null-space iterative reconstruction for atomic electron tomography with sparse data.

Nature communications·2026
Same author

Platelet-Collagen Interactions in Hemostatic Mechanisms.

Advanced healthcare materials·2026
Same author

Solid Pseudopapillary Neoplasms of the Pancreas with Delayed Ovarian Metastasis During Pregnancy: A Case Report and Literature Review.

International journal of women's health·2026
Same author

The relationship between high-sensitivity C-reactive protein levels and asthma in middle-aged and elderly Chinese population: a cross-sectional study based on China Health and Retirement Longitudinal Study (CHARLS).

The Journal of asthma : official journal of the Association for the Care of Asthma·2026
Same author

Association between serum vitamin D levels and cardiovascular disease risk in patients with hyperuricemia: A cross-sectional study.

PloS one·2026
Same author

Water kefir grain polysaccharides: Ultrasonic-assisted extraction optimization, structural characterization, bioactivities, and application in goat yogurt.

Ultrasonics sonochemistry·2026
Same journal

HeartSimSage: Attention-Enhanced Graph Neural Networks for Accelerating Cardiac Mechanics Modeling.

Journal of computational physics·2026
Same journal

Composite B-spline regularized delta functions for the immersed boundary method: Divergence-free interpolation and gradient-preserving force spreading.

Journal of computational physics·2026
Same journal

Improving the robustness of the immersed interface method through regularized velocity reconstruction.

Journal of computational physics·2025
Same journal

Laplacian Eigenfunction-Based Neural Operator for Learning Nonlinear Reaction-Diffusion Dynamics.

Journal of computational physics·2025
Same journal

An efficient adaptive algorithm for photon-electron coupled Boltzmann equation in radiation therapy.

Journal of computational physics·2025
Same journal

On generalizing the induced surface charge method to heterogeneous Poisson-Boltzmann models for electrostatic free energy calculation.

Journal of computational physics·2025
See all related articles

Related Experiment Video

Updated: Dec 8, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.9K

Data-driven molecular modeling with the generalized Langevin equation.

Francesca Grogan1, Huan Lei2,3, Xiantao Li4

  • 1Pacific Northwest National Laboratory, Richland, WA 99352, United States.

Journal of Computational Physics
|September 21, 2020
PubMed
Summary
This summary is machine-generated.

We developed a data-driven method to approximate the generalized Langevin equation (GLE) memory kernel. This approach makes complex molecular dynamics simulations more computationally tractable and accurate for studying molecular behavior.

Keywords:
coarse-grained modelsdata-driven parametrizationdimension reductiongeneralized Langevin equationmolecular dynamics

More Related Videos

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K
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

3.5K

Related Experiment Videos

Last Updated: Dec 8, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.9K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K
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

3.5K

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Statistical Mechanics

Background:

  • Molecular dynamics simulations are computationally intensive.
  • Coarse-graining and dimension reduction are essential for simplifying complex systems.
  • The generalized Langevin equation (GLE) models coarse-grained dynamics but its memory kernel is challenging to compute.

Purpose of the Study:

  • To develop a data-driven rational approximation for the GLE memory kernel.
  • To enable accurate and efficient simulation of complex molecular systems.
  • To overcome the computational challenges associated with characterizing the GLE memory kernel.

Main Methods:

  • Constructed a data-driven rational approximation for the GLE.
  • Extended previous GLE simulation methods to more complex molecules.
  • Validated the approximation against exact simulation methods.

Main Results:

  • Demonstrated the effectiveness of the rational approximation for the GLE memory kernel.
  • Successfully applied the method to complex molecules with many degrees of freedom.
  • Achieved accurate predictions of observables like autocorrelation and transition rates.

Conclusions:

  • The data-driven rational approximation significantly improves the tractability of GLE simulations.
  • This method provides a robust approach for studying non-equilibrium dynamics in complex molecular systems.
  • The developed technique offers a computationally efficient alternative to exact methods for molecular dynamics.