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 Experiment Videos

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann

Amirhossein Molavi Tabrizi1, Spencer Goossens1, Ali Mehdizadeh Rahimi1

  • 1Department of Mechanical and Industrial Engineering, Northeastern University , Boston, Massachusetts 02115, United States.

Journal of Chemical Theory and Computation
|April 6, 2017
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

An Investigation of Physics Informed Neural Networks to Solve the Poisson-Boltzmann Equation in Molecular Electrostatics.

Journal of chemical theory and computation·2025
Same author

Some Challenges of Diffused Interfaces in Implicit-Solvent Models.

Journal of computational chemistry·2025
Same author

Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation.

Journal of computational chemistry·2023
Same author

Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model.

Journal of chemical theory and computation·2023
Same author

Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode.

The journal of physical chemistry. B·2022
Same author

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model.

Journal of chemical theory and computation·2022
Same journal

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame.

Journal of chemical theory and computation·2026
Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·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
See all related articles
This summary is machine-generated.

We developed a new solvation model (SLIC/LPB) that significantly improves electrostatic calculations for molecules. This enhanced model uses fewer parameters and is more accurate than traditional methods, even for hydrophobic groups.

Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Continuum electrostatic models like linearized Poisson-Boltzmann (LPB) are crucial for molecular solvation studies.
  • Traditional LPB models face limitations in accurately describing charge-hydration asymmetry and first-shell water response.
  • Existing models often require numerous, empirically fitted parameters, reducing their predictive power.

Purpose of the Study:

  • To develop an improved continuum electrostatic model that accurately captures charge-hydration asymmetry and first-shell solvation effects.
  • To reduce the number of fitting parameters in solvation models while maintaining or enhancing accuracy.
  • To provide a computationally efficient and accurate tool for simulating large biomolecules.

Main Methods:

Related Experiment Videos

  • Extension of the linearized Poisson-Boltzmann (LPB) model with a new solvation-layer interface condition (SLIC).
  • Development of a GPU-accelerated treecode implementation for efficient simulation of large systems.
  • Parametrization of the model using physical insights into first-shell water behavior and Lennard-Jones radii.

Main Results:

  • The SLIC/LPB model demonstrates significant accuracy improvements over traditional LPB models, with a 6-fold reduction in RMS error for atomic solvation free energies (0.55 vs. 3.05 kcal/mol).
  • The number of fitting parameters is reduced from dozens to five physically meaningful parameters.
  • The model accurately predicts octanol/water transfer free energies (RMS error 1.07 kcal/mol) and reproduces positive charging free energies for hydrophobic groups, a feat unattainable by standard PB models.
  • A GPU-accelerated solver is developed for simulating large proteins.

Conclusions:

  • The SLIC/LPB model offers a more accurate and parsimonious approach to continuum electrostatic solvation.
  • The findings provide insights into improving other coarse-grained models like Generalized-Born theories.
  • The developed computational tools are publicly available, facilitating broader adoption and research.