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.

Research Team

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.

Arterial pressure, CSF pressure, and tissue displacement resulting from a multiple network poroelasticity simulation in physiological conditions [Corti, Antonietti, Dede’, Quarteroni. M3AS, accepted (2023)]

Brain poroelasticity: blood and ISF pressures

Arterial pressure, CSF pressure, and tissue displacement resulting from a multiple network poroelasticity simulation in physiological conditions.

M. Corti, P.F. Antonietti, L. Dede’, and A.M. Quarteroni – Mathematical Models and Methods in Applied Sciences (2023)

Interstitial and Cerebrospinal Fluids

Intracranial pressure and parenchymal displacement: simulation of CSF in the brain ventricles coupled with brain poroelastic tissue.

I. Fumagalli, M. Corti, N. Parolini, and P.F. Antonietti – Journal of Computational Physics (2026)

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.

    Parkinson's disease: α-synuclein spreading

    Patterns of α-synuclein concentration in Parkinson’s disease at different stages of the pathology and activation time of the pathology.

    M. Corti, F. Bonizzoni, L. Dede’, A.M. Quarteroni, and P.F. Antonietti – Computer Methods in Applied Mechanics and Engineering (2023)

    Alzheimer's disease: Amyloid-beta accumulation induced by hypoperfusion

    Amyloid-beta concentration at different times for three different dimensions of the hypoperfusion region: severe (first row), moderate (second row), and mild (third row).

    M. Corti, A. Ahern, A. Goriely, E. Kuhl, and P.F. Antonietti – Computer Methods in Applied Mechanics and Engineering (2026)

    Alzheimer's disease: Patient-specific model calibration on brain connectome

    Histogram and Gaussian distribution associated with the reaction parameters of amyloid-β, in each lobe of the brain and comparison between the medical data and the numerical results for the concentration on a connectome.

    M. Corti, F. Bonizzoni, P.F. Antonietti, and A.M. Quarteroni – ESAIM: Mathematical Modelling and Numerical Analysis (2024)

    Alzheimer's disease: Predictions from sparse multimodal data

    Schematic representation of the NeuralODE-based DPM and an example of a prediction of several features for three patient.

    A. Zanin, S. Pagani, M. Corti, V. Crepaldi, G. Di Fede, P.F. Antonietti, and for the ADNI – BiorXiv (2025)

    Neurological disorders

    Numerical modelling of epileptic seizures.
    Epilepsy is a clinical neurological disorder characterized by recurrent and spontaneous seizures generating an abnormal high-frequency electrical activity of the brain. Despite several clinical studies that have permitted the development of specific pharmacological and surgical treatments to control the onset of seizures there is still an open debate on the mechanisms and optimal patient-specific treatment. We consider the bidomain model to mathematically describe seizure evolution in the grey and white matter, coupled with specific ionic models for neuronal modelling in which the different dynamics of the potential and ionic currents are considered. The mathematical model is discretized by means of discontinuous Galerkin methods. Suitable (space-time) adaptive schemes are proposed to exploit the flexibility of the numerical approach to better describe the sharp propagating fronts that characterize seizure propagation. The numerical results provide insights into the mechanisms underlying seizures and might, in the future, support precision medicine, thanks to methods capable of predicting patient-specific behaviour and suggesting optimal treatment.

    Numerical modeling of epileptic seizures

    Temporal evolution of the transmembrane potential in a saggital section of the brainstem with two pathological initial conditions and auto-induced bursting behaviour and recostructed axonal direction for the white matter tissue (from DWI).

    C. B. Leimer Saglio,  S. Pagani, M. Corti, and P.F. Antonietti – Computer and Mathematics with Applications (2026)

    INCOLLA QUI L’ABSTRACT COMPLETO

    Efficient adaptive strategies for neuronal electrophysiology

    Computed transmembrane potential in a section of grey matter tissue, element-wise polynomial approximation degree, and suitable local error indicator.

    C. B. Leimer Saglio, S. Pagani, and P.F. Antonietti – Computer Methods in Applied Mechanics and Engineering (2025)

    Amyloid-beta triggered seizure dynamics in Alzheimer's disease.

    Pathological transmembrane potential evolution in presence of different abeta-myloid concentrations in a subregion of a coronal section. Real axonal directions are reconstructed for white matter tissue exploiting DWI.

    C. B. Leimer Saglio, M. Corti, S. Pagani, and P.F. Antonietti – Arxiv 2511.10369 (2025)

    Coupled oxygen dynamics and neuronal electrophysiology

    Ionic potassium and calcium concentrations evolution in a horizontal subsection triggered by pathological ischemic regions characterized by low oxygen levels.

    F. Daniele, C. B. Leimer Saglio, S. Pagani, and P.F. Antonietti – Arxiv 2509.22863 (2026)

    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

    MRI scan with semi-automatic segmentation of a lumbar vertebra.

    Deformation field of a lumbar spinal unit under a combined orthostatic and lateral bending load.

    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

    Abstract: 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

    Abstract: 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

    Abstract: This project, developed in collaboration with Humanitas Research Hospital in Milan, 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

    Abstract: Developed in collaboration with Humanitas Research Hospital in Milan, 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.

    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