We developped NextGenPB, software that efficiently calculates the electrostatic potential in the molecular systems' surroundings.

NextGenPB is a high-performance solver for the linearized Poisson–Boltzmann equation (PBE), built on an adaptive octree mesh. It efficiently computes electrostatic potentials in heterogeneous dielectric media using a flexible, hierarchical discretization scheme. Our adaptive-grid, FEM-based solution leverages analytical calculations to maximize the accuracy-to-computational-cost ratio.

Currenyly we are working on increasing the performance of the program implementing solutions based on Neural Networks.

Di Florio, V., Ansalone, P., Siryk, S. V., Decherchi, S., De Falco, C., & Rocchia, W.. NextGenPB: An analytically-enabled super resolution tool for solving the Poisson-Boltzmann Equation featuring local (de) refinement. Computer Physics  Communications, 2025

One of the goals of our research group is to develop methods for the computation of the Molecular Surface with particular attention on the consequences of its definition on the electrostatics component of the solvation free energy.

To this end, we developed NanoShaper, a tool aimed at computing the molecular surface and pockets of a biomolecular system.

NanoShaper is designed to measure molecular properties, construct a Finite Divergence grid for solving PDE, and compute protein pockets. The algorithm works by triangulating the molecular surface using ray-casting to inspect the surface's inner regions in a grid-based space. This process generates an in/out map, allowing for cavity identification, volume estimation, and optional cavity filling.

Currently we focus on implementing optimizations which support increased accuracy, improved speed, and a significantly reduced memory footprint.

We recently launched a web service that simplifies discovering protein pockets and cavities using advanced molecular surface analysis

Visit NanoShaper Web!

We propose a methodology to connect electrostatic calculations to the structural and functional features of protein-DNA systems and applied it on the nucleosome, to study the electrostatic effects of the histone tails, the intrinsically disordered terminal domains of the histone proteins.

Artemi Bendandi, Silvia Dante, Syeda Rehana Zia, Alberto Diaspro, and Walter Rocchia. Chromatin compaction multiscale modeling: A complex synergy between theory, simulation, and experiment. Frontiers in Molecular Biosciences, 7, February 2020. View

Artemi Bendandi, Alessandro S. Patelli, Alberto Diaspro, and Walter Rocchia. The role of histone tails in nucleosome stability: an electrostatic perspective. Computational and Structural Biotechnology,18:2799–2809, 2020. View