NUMERICAL MODELING OF THE HUMAN BRAIN:
FROM PHYSIOLOGY TO NEURODEGENERATIVE DISEASES

BRAINUM

The BraiNum project aims at developing advanced mathematical models for the physiological and pathological function of the brain and central nervous system. In this endeavor, we exploit the power and flexibility of mathematical modeling, numerical analysis, high-performance computing, and computational learning techniques.

BrainNum project is developed at the Laboratory for Modeling and Scientific Computing (MOX) of the Department of Mathematics, Politecnico di Milano.

We focus on:

  • Neurodegenerative diseases: high incidence (about 1/1000 subjects worldwide) and have a major clinical and societal impact on national systems. Their investigation and treatment are still the subject of open discussion in the medical community, and their study is ever more relevant, due to the overall aging of the world population.
  • Neurological disorders: broad spectrum of pathological conditions related to the impairment of neural firing rate or signal transmission. Epilepsy (the most common) affects 50 million people worldwide, and acute seizures entail possibly severe physical injuries.
  • Spine mechanics: patient-specific computational models of the spinal column, reconstructed from clinical imaging data, to investigate tissue mechanics, spinal disorders, and potential therapeutic or surgical interventions.
  • Glioma progression: patient-specific models of tumour proliferation, infiltration, and malignant transformation, aimed at reconstructing disease evolution and identifying regions at risk of recurrence or progression.

Research Team


Francesca Bonizzoni

Associate Professor


Stefano Pagani

Associate Professor


Nicola Parolini

Associate Professor


Ivan Fumagalli

Tenure-track Assistant Professor


Niteen Kumar

Assistant Professor


Mattia Corti

Research Fellowship Holder (art. 22-ter)

Mathematical modeling of the brain and CNS

The computational modelling of the Central Nervous System (CNS) involves several interconnected challenges:

  • Anatomical complexity: realistic representations of cerebral gyri and sulci, grey and white matter, the ventricular system, vascular networks, and cerebrospinal-fluid pathways.

  • Multiphysics coupling: the interaction between neuronal electrophysiology, cerebral blood supply and perfusion, cerebrospinal-fluid (CSF) and interstitial-fluid dynamics, tissue poromechanics, protein transport and clearance, and long-term tissue damage or atrophy.

  • Multiscale dynamics: processes ranging from cellular and local mechanisms—such as neuronal firing, ionic homeostasis, and protein aggregation—to organ-scale phenomena, including signal propagation, brain perfusion, CSF circulation, pathological protein spreading, and tissue deformation. These mechanisms evolve over time scales from milliseconds, for electrical activation, to years or decades, for neurodegeneration, atrophy, and disease progression.

Neurodegenerative diseases

We develop mathematical and computational models for the study of neurodegenerative diseases, with a particular focus on Alzheimer’s and Parkinson’s disease.

Our research investigates:

  • CSF and brain fluid dynamics, including coupled fluid–poroelastic models of CSF flow, intracranial pressure, tissue deformation, and mechanisms related to fluid and solute clearance.
  • Protein misfolding and spreading, through reaction–diffusion, heterodimer, and network-based models for amyloid-beta, tau, and alpha-synuclein propagation.
  • Long-term disease multiphysics progression, by coupling protein accumulation with tissue atrophy and cerebral hypoperfusion.
  • Patient-specific and data-driven modeling, using brain connectomes, neuroimaging data, uncertainty quantification, and machine-learning-based dynamical models.

These processes span different time scales: seconds to minutes for fluid dynamics, years for pathological protein propagation, and years to decades for atrophy and disease progression. Our computational framework combines anatomically informed brain models advanced numerical methods for complex multiphysics and multiscale problems.

    Neurological disorders

    We develop mathematical and computational models to investigate neuronal activity under physiological and pathological conditions, with particular attention to epilepsy and cerebral ischemia. Our research combines neuronal electrophysiology, ionic dynamics, cellular metabolism, and tissue-scale signal propagation within multiscale and multiphysics frameworks.

    Our research investigates:

    • Neuronal electrophysiology and seizure propagation: mathematical models of membrane potential, ionic currents, and neuronal excitability, coupled with tissue-scale descriptions of electrical signal propagation in grey and white matter.
    • Electro-metabolic coupling and cerebral ischemia: interactions between neuronal activity, oxygen availability, cellular metabolism, ionic-pump function, extracellular ionic concentrations, and cellular swelling under energy-deprived conditions.
    • Multiphysics and multiscale coupling: integration of fast electrophysiological dynamics with slower biochemical and metabolic processes, including the effects of amyloid-beta accumulation on calcium regulation, neuronal excitability, and seizure onset.
    • Advanced high-order numerical methods: discontinuous Galerkin methods on polygonal and polyhedral meshes, space- and time-adaptive strategies, and element-wise p-adaptivity for accurately resolving sharp electrical wavefronts while reducing computational cost.
    • Efficient solvers and high-performance computing: scalable non-overlapping Schwarz preconditioners, parallel assembly strategies, and computational tools for realistic and patient-specific brain geometries.

    These models and numerical methods aim to clarify the mechanisms underlying pathological neuronal activity and provide reliable computational tools for studying disease progression and, in the longer term, supporting patient-specific prediction and treatment planning.

    Spine mechanics

    Computational mechanical modeling of the spinal column.
    Spinal disorders, such as low back pain, degenerative disc disease, spondylosis, disc herniation, have a huge impact on a patient’s quality of life and are one of the leading causes of disability worldwide. In severe cases, surgical intervention (e.g., spinal fusion, microdiscectomy, or osteotomy) is the only clinical treatment, and both its planning and the post-intervention rehabilitation strongly rely on imaging data (MRI and/or X-ray). Based on such patient-specific data, computational modeling can complement it by anticipating the mechanical response to treatment, thus providing a virtual testing platform to identify the optimal treatment among several surgical procedures. We model the complex anatomical system of the spine accounting for the rheology of the different components (vertebrae, intervertebral discs, and ligaments), and we employ state-of-the-art numerical methods for its computational simulation

    Publications

    A whole-brain model of amyloid beta accumulation and cerebral hypoperfusion in Alzheimer's disease

    Authors: M. Corti, A. Ahern, A. Goriely, E. Kuhl, P. F. Antonietti

    Journal Reference: Computer Methods in Applied Mechanics and Engineering, 461. 119196 (2026)

    A high-order discontinuous Galerkin method for the numerical modeling of epileptic seizures

    Authors: C.B. Leimer Saglio, S. Pagani, M. Corti, P.F. Antonietti

    Journal Reference: Computers & Mathematics with Applications, 205. 112-131 (2026)

    Polytopal mesh agglomeration via geometrical deep learning for three-dimensional heterogeneous domains

    Authors: P. F. Antonietti, M. Corti, G. Martinelli

    Journal Reference: Mathematics and Computers in Simulation, 241(part B). 335-353 (2026)

    A structure-preserving LDG discretization of Fisher-Kolmogorov equation for modeling neurodegenerative diseases

    Authors: P.F. Antonietti, M. Corti, S. Gómez, I. Perugia

    Journal reference: Mathematics and Computers in Simulation. 241(part A). 351-366 (2026)

    A p-adaptive polytopal discontinuous Galerkin method for high-order approximation of brain electrophysiology

    Authors: Caterina B. Leimer Saglio, Stefano Pagani, P.F. Antonietti

    Journal reference: Computer Methods in Applied Mechanics and Engineering. 446(part A). 118249 (2025)

    A high-order discontinuous Galerkin method for the numerical modeling of epileptic seizures

    Authors: C. B. Leimer Saglio, S. Pagani, M. Corti, P. F. Antonietti

    Journal Reference: Computers & Mathematics with Applications, 205. 112-131 (2026)

    Numerical modelling of protein misfolding in neurodegenerative diseases: a computational study

    Authors: P.F. Antonietti, M. Corti

    Chapter reference: Numerical Mathematics and Advanced Applications ENUMATH 2023, Volume 1. Springer (2025)

    Discontinuous Galerkin method for a three-dimensional coupled fluid-poroelastic model with applications to brain fluid mechanics

    Authors: I. Fumagalli

    Journal reference: Mathematics in Engineering. 7 (2). 130-161 (2025)

    A posteriori error analysis for a coupled Stokes-poroelastic system with multiple compartments

    Authors: I. Fumagalli, N. Parolini, M. Verani

    Journal reference: Journal of Scientific Computing. 103. 22 (2025)

    lymph: discontinuous poLYtopal methods for Multi-PHysics differential problems

    Authors: P.F. Antonietti, S. Bonetti, M. Botti, M. Corti, I. Fumagalli, I. Mazzieri

    Journal reference: ACM Transactions on Mathematical Software. 51 (1). 3:1-3:22 (2025)

    A coupled mathematical and numerical model for protein spreading and tissue atrophy applied to Alzheimer's disease

    Authors: V. Pederzoli, M. Corti, D. Riccobelli, P. F. Antonietti

    Journal reference: Computer Methods in Applied Mechanics and Engineering, 444. 118118 (2025)

    Discontinuous Galerkin approximations of the heterodimer model for protein-protein interaction

    Authors: P.F. Antonietti, F. Bonizzoni, M. Corti, A. Dall’Olio

    Journal reference: Computer Methods in Applied Mechanics and Engineering. 431. 117282 (2024)

    Exploring tau protein and amyloid-beta propagation: A sensitivity analysis of mathematical models based on biological data

    Authors: M. Corti

    Journal reference: Brain Multiphysics 7:100098 (2024)

    Structure preserving polytopal discontinuous Galerkin methods for the numerical modeling of neurodegenerative diseases

    Authors: M. Corti, F. Bonizzoni, P.F. Antonietti

    Journal reference: Journal of Scientific Computing. 100. 39 (2024)

    Uncertainty quantification for Fisher-Kolmogorov equation on graphs with application to patient-specific Alzheimer's disease

    Authors: M. Corti, F. Bonizzoni, P.F. Antonietti, A.M. Quarteroni

    Journal reference: ESAIM: Mathematical Modelling and Numerical Analysis. 58 (6). 2135-2154 (2024)

    Discontinuous Galerkin methods for Fisher–Kolmogorov equation with application to α-synuclein spreading in Parkinson’s disease

    Authors: M. Corti, F. Bonizzoni, L. Dede’, A.M. Quarteroni, P.F. Antonietti

    Journal reference: Computer Methods in Applied Mechanics and Engineering. 417. 116450 (2023)   

    Numerical modeling of the brain poromechanics by high-order discontinuous Galerkin methods

    Authors: M. Corti, P.F. Antonietti, L. Dede’, A.M. Quarteroni

    Journal reference: Mathematical Models and Methods in Applied Sciences. 33(08). 1577-1609 (2023)

    Polytopal discontinuous Galerkin discretization of brain multiphysics flow dynamics

    Authors: I. Fumagalli, M. Corti, N. Parolini, P.F. Antonietti

    Journal reference: Journal of Computational Physics. 513. 113115 (2024)

    Preprints

    Patient-specific computational mechanics of functional lumbar spine units

    Authors:  I. Fumagalli; M. Campioni; A. Sirtori; S. Pagani; R. Levi; L.S. Politi; G. Capo; P.F. Antonietti.

    Preprint Reference: bioRxiv preprint https://doi.org/10.64898/2026.06.03.729850 (2026)

    High-fidelity and Network-based Spatio-temporal Mathematical Models of Alzheimer's Disease Progression and their Validation Against PET-SUVR Imaging Data

    Authors:  B. Caon; M. Corti; F. Bonizzoni; P. F. Antonietti. 

    Preprint Reference: ArXiv preprint 2604.18470 (2026)

    A massively parallel non-overlapping Schwarz preconditioner for PolyDG methods in brain electrophysiology

    Authors:  C. B. Leimer Saglio, S. Pagani, P. F. Antonietti

    Preprint Reference: ArXiv preprint 2512.19536 (2025)

    Mathematical and numerical modeling of coupled oxygen dynamics and neuronal electrophysiology

    Authors: F. Daniele, C. B. Leimer Saglio, S. Pagani, P. F. Antonietti

    Preprint Reference: Arxiv preprint 2509.22863 (2025)

    Structure-preserving local discontinuous Galerkin discretization of conformational conversion systems

    Authors: P. F. Antonietti, M. Corti, S. Gómez, I. Perugia

    Preprint Reference: Arxiv preprint 2511.04830 (2025)

    A novel mathematical and computational framework of amyloid-beta triggered seizure dynamics in Alzheimer's disease

    Authors: C. B. Leimer Saglio, M. Corti, S. Pagani, P. F. Antonietti
    Preprint Reference: ArXiv preprint 2511.10369 (2025)

    Predicting Alzheimer's disease progression from sparse multimodal data by NeuralODE models

    Authors: A. Zanin, S. Pagani, M. Corti, V. Crepaldi, G. Di Fede, P.F. Antonietti, and for the Alzheimer’s Disease Neuroimaging Initiative (ADNI)

    Preprint Reference: Biorxiv preprint 2025.08.26.672412 (2025)

    A discontinuous Galerkin method for the three-dimensional heterodimer model with application to prion-like proteins’ dynamics

    Authors: P.F. Antonietti, M. Corti, G. Lorenzon

    Preprint reference: ArXiv preprint 2407.16065 (2024)

    PhD Theses

    Mathematical Models and Numerical Methods for Neurodegenerative Diseases

    Author: M. Corti

    Advisor: P. F. Antonietti

    PhD in Mathematical Models and Methods in Engineering, Politecnico di Milano

    Year: 2025

     

    Advanced computational methods for the numerical modeling of epileptic seizures

    Author: C. B. Leimer Saglio

    Advisors: P. F. Antonietti, S. Pagani

    PhD in Mathematical Models and Methods in Engineering, Politecnico di Milano

    Year: in progress

     

    Projects and Collaborations

    SACMS: Stability Analysis and Control Mechanisms of Seizures

    The goal of the SACMS project is to advance the understanding of seizure dynamics and potential therapeutic strategies through mathematical modelling, simulation and optimal control. Specifically, we will develop differential models to study epilepsy and analyze the influence of changes in neurotransmitter/ionic species concentrations on pathophysiological brain function, which is still poorly understood. The SACMS project’s primary objective includes conducting a bifurcation analysis to study the effect of High-Frequency Oscillations (HFOs) on brain stability and quantifying the influence of ionic instability on seizures. Bridging neuroscience with nonlinear dynamics is expected to significantly benefit brain function research and modelling.

    AHEAD: Advanced AI Techniques for Early Detection and Personalized Monitoring in Alzheimer’s Disease

    This technology is a software platform developed in collaboration with the Fondazione IRCCS Istituto Neurologico Carlo Besta in Milan. It integrates longitudinal, multimodal clinical data with deep-learning models to support personalised early diagnosis and to predict disease progression. Unlike many current AI tools, which rely on a single examination type or on isolated measurements, the platform jointly analyses heterogeneous data collected over time. This enables the reconstruction of each patient’s individual disease trajectory, improving predictive accuracy and extending the applicability of the approach across complex clinical settings. The technology has already been tested in the context of Alzheimer’s disease, demonstrating its potential to support personalised clinical assessment and longitudinal disease monitoring.

    Patient-Specific Computational Modelling of the Spine

    This project, developed in collaboration with Humanitas Research Hospital in Milan (Neuochirugia I – Neurochirurgia Cranica e Spinale), focuses on patient-specific computational modelling of the spinal column to support the assessment and treatment planning of spinal disorders. Spinal conditions—including low back pain, degenerative disc disease, spondylosis, disc herniation, and spinal deformities—can severely affect quality of life and are a major cause of disability. Using MRI and X-ray data, we build subject-specific mechanical models of the spine that account for the different material and rheological properties of vertebrae, intervertebral discs, and ligaments. Advanced numerical methods are then used to simulate the biomechanical response of the spinal system and to provide a virtual testing environment for comparing therapeutic and surgical options, such as spinal fusion, microdiscectomy, and osteotomy. The long-term objective is to support more informed, personalised treatment planning and post-operative rehabilitation.

    Patient-Specific Modelling of Glioma Progression

    Developed in collaboration with Humanitas Research Hospital in Milan (Neurochirurgia I – Neurochirurgia Cranica e Spinale), this project aims to support the clinical management of diffuse gliomas through patient-specific mathematical and computational modelling.

    Low-grade gliomas are infiltrative brain tumours that may progressively transform into more aggressive high-grade lesions, often leading to a marked worsening of prognosis. Starting from clinical and neuroimaging data, we develop physics-based models of tumour proliferation, invasion, and malignant transformation to reconstruct the spatiotemporal evolution of the disease. The platform is designed to estimate the risk and timing of malignant progression and to identify brain regions that may be more prone to future tumour recurrence or aggressive transformation.

    roADmap: Tracking Disease Progression Across the Alzheimer’s Continuum Through Multimodal Integration of MRI Biomarkers and Neurotransmitter Distributions

    The roADmap project has been selected for funding by the Italian Ministry of Health under the “Ricerca Finalizzata 2024” call, within the Young Researchers – Theory-Enhancing category. The project is led by a multidisciplinary research team comprising Anna Nigri (PI), Davide Fedeli (Co-PI), researchers at the Neuroradiology Unit ofFondazione IRCCS Istituto Neurologico C. Besta, and Stefano Pagani (Unit Coordinator). Through the development of innovative multimodal brain models, the roADmap project aims to investigate the interplay between macroscopic neurobiological alterations and abnormal neurotransmitter activity across the Alzheimer’s disease continuum.

    This project is partially supported by

    Italian Research Center on High Performance Computing, Big Data and Quantum Computing (ICSC), under the NextGenerationEU project. National Recovery and Resilience Plan (NRRP), Mission 4, Component 1 – Investment 3.4 and Investment 4.1 funded by the European Union.

    – PRIN 2020, research grant n. 20204LN5N5 “Advanced polyhedral discretisations of heterogeneous PDEs for multiphysics problems” funded by MUR (National Coordinator).

    – ERC Sinergy Grant NEMESIS “NEw generation MEthods for Numerical SimulationS”, project number 101115663, funded by European Research Council

    – SACMS – Stability Analysis and Control Mechanisms of Seizures MUR