Future Projects

This page outlines several research and development directions planned for the NextGenPB software. These projects aim to extend its physical accuracy, usability, and applicability.

NextGenPB Web Server

Goal: Develop a web-based interface for submitting jobs and visualizing results directly in the browser.

  • Designed for users without local installation or HPC access.
  • Simplifies workflows for non-expert users in biology, chemistry, and nanotechnology.
  • Inspired by the NanoShaper Web Server for surface generation, which will be integrated as a backend service for SES computation.

MM-PBSA Integration

Goal: Compute the full solvation free energy, including both electrostatic and non-polar components.

  • Enables direct integration with molecular dynamics pipelines (e.g., GROMACS or AMBER).
  • Facilitates binding free energy estimation for biomolecular complexes.

Electrostatic Force Calculations

Goal: Derive electrostatic forces acting on atoms directly from the NGPB solution.

  • Useful for system relaxation and force-based refinement.
  • Opens the path for hybrid MD–continuum simulations.

Zeta Potential Estimation

Goal: Estimate zeta potential from surface electrostatics in ionic environments.

  • Important for colloidal stability analysis.
  • Relevant for nanoparticle functionalization and biosensing applications.

Nonlinear Poisson–Boltzmann Solver

Goal: Accurately solve the nonlinear PBE, going beyond the classical low-potential approximation.

  • Linearization neglects essential physical effects:
    • High surface charge density
    • Multivalent ions
    • Moderately concentrated electrolytes
  • Nonlinear models allow:
    • More realistic ionic density distributions
    • Better agreement with experiments in strong coupling regimes