Publications
2025
Vignolo A., Baird T.J., Spiga F., Canevari C., Coretti A., Vuilleumier R., Cavalli A., Bonella S., Decherchi S.
A tale of two codes: CUDA vs OpenACC for mass-zero constrained dynamics
International Journal of High Performance Computing Applications
2025
Ciccotti G., Decherchi S., Meloni S.
Foundations of molecular dynamics simulations: how and what
Rivista del Nuovo Cimento della Societa Italiana di Fisica
2025
Abate C., Serra E., Rocchia W., Cavalli A., Decherchi S.
NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual
Journal of Chemical Information and Modeling
2025
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, vol. 317
2025
Serra E., Ghidini A., Decherchi S., Cavalli A.
Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation
Journal of Chemical Theory and Computation
2025
Serra E., Ghidini A., Aguti R., Bernetti M., Decherchi S., Cavalli A.
Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding
Journal of Chemical Information and Modeling, vol. 65, (no. 12), pp. 6057-6072
2024
Damiani C., Rodina Y., Decherchi S.
A hybrid federated kernel regularized least squares algorithm
Knowledge-Based Systems, vol. 305
2024
Abate C., Decherchi S., Cavalli A.
AMCG: a graph dual atomic-molecular conditional molecular generator
Machine Learning: Science and Technology, vol. 5, (no. 3)
2024
Ghidini A., Serra E., Decherchi S., Cavalli A.
Bidirectional path-based non-equilibrium simulations for binding free energy
Molecular Physics
2024
Balasubramanian K.K., Di Salvo M., Rocchia W., Decherchi S., Crepaldi M.
Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective
IEEE Access
2024
Bassi P.R.A.S., Decherchi S., Cavalli A.
Faster ISNet for Background Bias Mitigation on Deep Neural Networks
IEEE Access
2024
Martire S., Decherchi S., Cavalli A.
OBIWAN: An Element-Wise Scalable Feed-Forward Neural Network Potential
Journal of Chemical Theory and Computation
2024
Castagnola V., Tomati V., Boselli L., Braccia C., Decherchi S., Pompa P.P., Pedemonte N., Benfenati F., Armirotti A.
Sources of biases in the in vitro testing of nanomaterials: the role of the biomolecular corona
Nanoscale Horizons, vol. 9, (no. 5), pp. 799-816
2023
Rocutto L., Maronese M., Traversa F.L., Decherchi S., Cavalli A.
Assessing the Effectiveness of Non-Turing Computing Paradigms
IEEE Access, vol. 11, pp. 98751-98763
2023
Abate C., Decherchi S., Cavalli A.
Graph neural networks for conditional de novo drug design
Wiley Interdisciplinary Reviews: Computational Molecular Science, vol. 13, (no. 4)