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

Maxwell-Boltzmann Distribution: Problem Solving01:20

Maxwell-Boltzmann Distribution: Problem Solving

2.3K
Individual molecules in a gas move in random directions, but a gas containing numerous molecules has a predictable distribution of molecular speeds, which is known as the Maxwell-Boltzmann distribution, f(v).
This distribution function f(v) is defined by saying that the expected number N (v1,v2) of particles with speeds between v1 and v2 is given by
2.3K
Poisson's And Laplace's Equation01:25

Poisson's And Laplace's Equation

4.3K
The electric potential of the system can be calculated by relating it to the electric charge densities that give rise to the electric potential. The differential form of Gauss's law expresses the electric field's divergence in terms of the electric charge density.
4.3K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

438
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...
438
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

4.0K
The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
4.0K

You might also read

Related Articles

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

Sort by
Same author

A study on a high efficiency phase organization segmentation model for SEM images based on deep learning.

Nanoscale·2026
Same author

Poisoning-Resistant Complete Hydrogenation of Liquid Organic Hydrogen Carriers Over Ni-Based Inverse Catalysts.

Angewandte Chemie (International ed. in English)·2026
Same author

Constructing Face-Shared Configuration at the Hetero-Interface in Li-Rich Layered Oxide Cathodes.

Angewandte Chemie (International ed. in English)·2026
Same author

Co-Confinement of Enzymes and Cofactors Within Pickering Droplet Derived Microreactors for Continuous Flow Catalysis.

Angewandte Chemie (International ed. in English)·2026
Same author

The study of hydrogen adsorption-induced topological surface state in-out hop in MgB<sub>2</sub> nodal-line semimetals <i>via</i> physics-informed Bayesian optimization.

Physical chemistry chemical physics : PCCP·2026
Same author

Investigation into the mechanism of damage removal in the compaction zone using dynamic negative pressure perforation.

Scientific reports·2026

Related Experiment Video

Updated: May 3, 2026

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

3.3K

Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

Changhao Wang1, Jun Wang2, Qin Cai3

  • 1Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA ; Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA.

Computational & Theoretical Chemistry
|January 21, 2014
PubMed
Summary

A new numerical method improves electrostatic calculations for biomolecules by solving the Poisson-Boltzmann equation more accurately near molecular surfaces. This enhances computational analyses of molecular structures and dynamics.

Keywords:
Continuum solvent modelsFinite difference methodImmersed interface methodPoisson-Boltzmann equation

More Related Videos

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.5K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

9.2K

Related Experiment Videos

Last Updated: May 3, 2026

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

3.3K
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.5K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

9.2K

Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Accurate electrostatic calculations are vital for understanding biomolecular structures and dynamics.
  • The Poisson-Boltzmann equation is a standard model for these calculations.
  • Existing numerical methods face challenges with accuracy, especially near molecular boundaries.

Purpose of the Study:

  • To explore a second-order finite-difference numerical method, the immersed interface method, for solving the Poisson-Boltzmann equation.
  • To assess the accuracy and convergence of this new method compared to classical approaches.
  • To identify areas for improvement in electrostatic analysis of biomolecules.

Main Methods:

  • Implementation and validation of the immersed interface method for biomolecular electrostatics.
  • Comparison with the weighted harmonic averaging method using various test biomolecules.
  • Analysis of numerical reaction field grid potentials, energies, and atomic solvation forces.

Main Results:

  • The immersed interface method was validated and showed consistency with the classical method.
  • Similar convergence behaviors were observed for both methods.
  • The immersed interface method provided more accurate and better-converged grid potentials near molecular surfaces.

Conclusions:

  • The immersed interface method offers improved accuracy for electrostatic potentials on or near biomolecular surfaces.
  • Further enhancements in interpolation/extrapolation schemes are needed alongside higher-order numerical methods.
  • This study highlights potential advancements in computational biomolecular electrostatics.