| Publication | Date of Publication | Type |
|---|
Riemannian denoising diffusion probabilistic models
Communications in Mathematical Sciences | 2026-06-11 | Paper |
On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics
Multiscale Modeling & Simulation | 2025-07-17 | Paper |
An efficient first-order conditional gradient algorithm in data-driven sparse identification of nonlinear dynamics to solve sparse recovery problems under noise
Journal of Computational and Applied Mathematics | 2025-06-11 | Paper |
Approximating particle-based clustering dynamics by stochastic PDEs
SIAM Journal on Applied Dynamical Systems | 2025-04-25 | Paper |
Chimeric U-net -- modifying the standard U-net towards explainability
Artificial Intelligence | 2025-01-17 | Paper |
Neural parameter calibration and uncertainty quantification for epidemic forecasting
PLOS ONE | 2024-10-17 | Paper |
| Implementation of the methods from the paper "A Mathematical perspective on Romanisation: Modelling the Roman road activation process in ancient Tunisia" | 2024-05-21 | Software |
Koopman-based surrogate models for multi-objective optimization of agent-based systems
Physica D | 2024-05-03 | Paper |
Approximating particle-based clustering dynamics by stochastic PDEs
(available as arXiv preprint) | 2024-01-01 | Paper |
Modelling opinion dynamics under the impact of influencer and media strategies
Scientific Reports | 2023-11-08 | Paper |
Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning
Acta Numerica | 2023-09-12 | Paper |
Rate-limiting recovery processes in neurotransmission under sustained stimulation
Mathematical Biosciences | 2023-09-04 | Paper |
| Partial mean-field model for neurotransmission dynamics | 2023-07-04 | Paper |
Optimal Reaction Coordinates: Variational Characterization and Sparse Computation
Multiscale Modeling & Simulation | 2023-06-30 | Paper |
A Route to the Hydrodynamic Limit of a Reaction-Diffusion Master Equation Using Gradient Structures
SIAM Journal on Applied Mathematics | 2023-05-26 | Paper |
Modelling altered signalling of G‑protein coupled receptors in inflamed environment to advance drug design
Nature | 2023-01-12 | Paper |
| Implementation of the model for the paper "Modelling opinion dynamics under the impact of influencer and media strategies" | 2023-01-01 | Software |
Objective priors in the empirical Bayes framework
Scandinavian Journal of Statistics | 2022-10-25 | Paper |
Understanding the romanization spreading on historical interregional networks in Northern Tunisia
Applied Network Science | 2022-08-02 | Paper |
Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks
Journal of Computational Physics | 2022-07-21 | Paper |
| Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics | 2022-06-14 | Paper |
A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations
Letters in Mathematical Physics | 2022-06-01 | Paper |
Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics
Mathematical Biosciences | 2022-03-22 | Paper |
A probabilistic algorithm for aggregating vastly undersampled large Markov chains
Physica D | 2022-03-21 | Paper |
Data-driven approximation of the Koopman generator: model reduction, system identification, and control
Physica D | 2022-03-17 | Paper |
Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs
Multiscale Modeling & Simulation | 2022-01-19 | Paper |
| Data-driven modelling of nonlinear dynamics by barycentric coordinates and memory | 2021-12-13 | Paper |
Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading
Mathematical Biosciences | 2021-11-09 | Paper |
Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks
(available as arXiv preprint) | 2021-10-27 | Paper |
Agent-based modeling: population limits and large timescales
Chaos: An Interdisciplinary Journal of Nonlinear Science | 2021-05-06 | Paper |
Dimensionality reduction of complex metastable systems via kernel embeddings of transition manifolds
Journal of Nonlinear Science | 2021-04-29 | Paper |
Extending transition path theory: periodically driven and finite-time dynamics
Journal of Nonlinear Science | 2021-04-29 | Paper |
Memory-based reduced modelling and data-based estimation of opinion spreading
Journal of Nonlinear Science | 2021-04-29 | Paper |
| Simulation results of the agent-based systems used for data-driven model reduction via the Koopman generator | 2021-04-21 | Dataset |
From interacting agents to density-based modeling with stochastic PDEs
Communications in Applied Mathematics and Computational Science | 2021-04-16 | Paper |
| CINDy: Conditional gradient-based Identification of Non-linear Dynamics -- Noise-robust recovery | 2021-01-07 | Paper |
Stochastic dynamics in computational biology
Frontiers in Applied Dynamical Systems: Reviews and Tutorials | 2021-01-07 | Paper |
| Data-driven model reduction of agent-based systems using the Koopman generator | 2020-12-14 | Paper |
A weak characterization of slow variables in stochastic dynamical systems
Advances in Dynamics, Optimization and Computation | 2020-11-09 | Paper |
Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces
Advances in Dynamics, Optimization and Computation | 2020-11-09 | Paper |
| The Augmented Jump Chain -- a sparse representation of time-dependent Markov jump processes | 2020-08-11 | Paper |
| Kernel Autocovariance Operators of Stationary Processes: Estimation and Convergence | 2020-04-02 | Paper |
Learning chemical reaction networks from trajectory data
SIAM Journal on Applied Dynamical Systems | 2020-01-03 | Paper |
Learning chemical reaction networks from trajectory data
SIAM Journal on Applied Dynamical Systems | 2020-01-03 | Paper |
Jarzynski's equality, fluctuation theorems, and variance reduction: mathematical analysis and numerical algorithms
Journal of Statistical Physics | 2019-08-01 | Paper |
A Multiscale Perturbation Expansion Approach for Markov State Modeling of Nonstationary Molecular Dynamics
Multiscale Modeling & Simulation | 2018-10-15 | Paper |
| Multidimensional approximation of nonlinear dynamical systems | 2018-09-07 | Paper |
Tensor-based dynamic mode decomposition
Nonlinearity | 2018-07-23 | Paper |
Data-driven model reduction and transfer operator approximation
Journal of Nonlinear Science | 2018-07-20 | Paper |
Statistical analysis of the first passage path ensemble of jump processes
Journal of Statistical Physics | 2018-05-28 | Paper |
Transition manifolds of complex metastable systems. Theory and data-driven computation of effective dynamics
Journal of Nonlinear Science | 2018-04-16 | Paper |
Importance sampling in path space for diffusion processes with slow-fast variables
Zeitschrift für Wahrscheinlichkeitstheorie und Verwandte Gebiete | 2018-02-12 | Paper |
| Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics | 2018-01-12 | Paper |
Nearest-neighbor interaction systems in the tensor-train format
Journal of Computational Physics | 2017-12-15 | Paper |
Sparse Non-Gaussian Component Analysis
IEEE Transactions on Information Theory | 2017-07-27 | Paper |
Graph algorithms for dynamical systems
Analysis, Modeling and Simulation of Multiscale Problems | 2017-07-19 | Paper |
Conditional averaging for diffusive fast-slow systems: a sketch for derivation
Analysis, Modeling and Simulation of Multiscale Problems | 2017-07-19 | Paper |
Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics
(available as arXiv preprint) | 2017-04-28 | Paper |
Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator
Journal of Computational Dynamics | 2017-04-25 | Paper |
| Random walks on complex modular networks | 2017-02-17 | Paper |
Finding dominant structures of nonreversible Markov processes
Multiscale Modeling & Simulation | 2016-12-13 | Paper |
Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model
Journal of Computational Physics | 2016-12-05 | Paper |
On the numerical approximation of the Perron-Frobenius and Koopman operator
Journal of Computational Dynamics | 2016-10-31 | Paper |
Model reduction algorithms for optimal control and importance sampling of diffusions
Nonlinearity | 2016-08-23 | Paper |
Markov state models for rare events in molecular dynamics
Entropy | 2016-06-15 | Paper |
Modularity of directed networks: cycle decomposition approach
Journal of Computational Dynamics | 2015-08-31 | Paper |
Markov model theory
Advances in Experimental Medicine and Biology | 2015-07-20 | Paper |
Applications of the cross-entropy method to importance sampling and optimal control of diffusions
SIAM Journal on Scientific Computing | 2015-03-02 | Paper |
| ``Markov control with rate state observation'': sensitivity analysis with respect to optimal treatment strategies against HIV-1 | 2015-02-16 | Paper |
Modularity revisited: a novel dynamics-based concept for decomposing complex networks
Journal of Computational Dynamics | 2015-01-06 | Paper |
Markov control processes with rare state observation: theory and application to treatment scheduling in HIV-1
Communications in Mathematical Sciences | 2014-12-22 | Paper |
| Metastability and Markov state models in molecular dynamics. Modeling, analysis, algorithmic approaches | 2014-01-31 | Paper |
A structure-preserving numerical discretization of reversible diffusions
Communications in Mathematical Sciences | 2014-01-21 | Paper |
Hybrid stochastic-deterministic solution of the chemical master equation
Multiscale Modeling & Simulation | 2013-05-02 | Paper |
Sequential change point detection in molecular dynamics trajectories
Multiscale Modeling & Simulation | 2013-05-02 | Paper |
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Proceedings of the National Academy of Sciences | 2013-01-07 | Paper |
Approximating selected non-dominant timescales by Markov state models
Communications in Mathematical Sciences | 2012-12-29 | Paper |
Optimal control of molecular dynamics using Markov state models
Mathematical Programming. Series A. Series B | 2012-11-02 | Paper |
Estimating the eigenvalue error of Markov state models
Multiscale Modeling & Simulation | 2012-08-30 | Paper |
| Efficient Rare Event Simulation by Optimal Nonequilibrium Forcing | 2012-08-15 | Paper |
| On Markov state models for metastable processes | 2011-11-11 | Paper |
Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems
The Journal of Chemical Physics | 2011-07-07 | Paper |
On the approximation quality of Markov state models
Multiscale Modeling & Simulation | 2011-01-21 | Paper |
Balanced truncation of linear second-order systems: a Hamiltonian approach
Multiscale Modeling & Simulation | 2011-01-21 | Paper |
Optimal Fuzzy Aggregation of Networks
Multiscale Modeling & Simulation | 2011-01-21 | Paper |
On metastable conformational analysis of nonequilibrium biomolecular time series
Multiscale Modeling & Simulation | 2010-06-10 | Paper |
Likelihood-Based Estimation of Multidimensional Langevin Models and Its Application to Biomolecular Dynamics
Multiscale Modeling & Simulation | 2009-10-19 | Paper |
Transition Path Theory for Markov Jump Processes
Multiscale Modeling & Simulation | 2009-10-16 | Paper |
Towards effective dynamics in complex systems by Markov kernel approximation
ESAIM: Mathematical Modelling and Numerical Analysis | 2009-08-06 | Paper |
| scientific article; zbMATH DE number 5587342 (Why is no real title available?) | 2009-07-27 | Paper |
Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA
SIAM Journal on Applied Dynamical Systems | 2009-04-30 | Paper |
Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis
Multiscale Modeling & Simulation | 2008-12-11 | Paper |
| Molecular conformation dynamics and computational drug design | 2008-04-14 | Paper |
| Hierarchical uncoupling-coupling of metastable conformations | 2008-04-14 | Paper |
Generator estimation of Markov jump processes
Journal of Computational Physics | 2007-11-30 | Paper |
Automated Model Reduction for Complex Systems Exhibiting Metastability
Multiscale Modeling & Simulation | 2007-09-07 | Paper |
Comment on two distinct notions of free energy
Physica D | 2007-05-23 | Paper |
Reduced Stochastic Models for Complex Molecular Systems
Computing and Visualization in Science | 2006-11-22 | Paper |
A geometric approach to constrained molecular dynamics and free energy
Communications in Mathematical Sciences | 2005-10-11 | Paper |
A constrained hybrid Monte‐Carlo algorithm and the problem of calculating the free energy in several variables
ZAMM - Journal of Applied Mathematics and Mechanics / Zeitschrift für Angewandte Mathematik und Mechanik | 2005-10-10 | Paper |
Eigenvalue bounds on restrictions of reversible nearly uncoupled Markov chains
Linear Algebra and its Applications | 2005-05-04 | Paper |
| scientific article; zbMATH DE number 2152902 (Why is no real title available?) | 2005-04-05 | Paper |
Uncoupling-Coupling Techniques for Metastable Dynamical Systems
Lecture Notes in Computational Science and Engineering | 2005-03-10 | Paper |
An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations
Multiscale Modeling & Simulation | 2005-03-01 | Paper |
Metastability of Diffusion Processes
Solid Mechanics and Its Applications | 2005-02-11 | Paper |
Phase transitions and metastability in Markovian and molecular systems
The Annals of Applied Probability | 2004-06-10 | Paper |
Extracting macroscopic stochastic dynamics: Model problems
Communications on Pure and Applied Mathematics | 2003-01-28 | Paper |
| scientific article; zbMATH DE number 1779195 (Why is no real title available?) | 2002-08-12 | Paper |
| scientific article; zbMATH DE number 1552589 (Why is no real title available?) | 2002-01-19 | Paper |
| scientific article; zbMATH DE number 1595164 (Why is no real title available?) | 2001-08-21 | Paper |
| scientific article; zbMATH DE number 1595180 (Why is no real title available?) | 2001-08-21 | Paper |
Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains
Linear Algebra and its Applications | 2001-06-19 | Paper |
| scientific article; zbMATH DE number 1595181 (Why is no real title available?) | 2001-05-06 | Paper |
Adaptive accuracy control for Car-Parrinello simulations
Numerische Mathematik | 2000-04-04 | Paper |
A direct approach to conformational dynamics based on hybrid Monte Carlo
Journal of Computational Physics | 2000-03-30 | Paper |
On the Singular Limit of the Quantum-Classical Molecular Dynamics Model
SIAM Journal on Applied Mathematics | 1999-09-13 | Paper |
Homogenization approach to smoothed molecular dynamics
Nonlinear Analysis: Theory, Methods & Applications | 1999-09-02 | Paper |
A mathematical investigation of the Car-Parrinello method
Numerische Mathematik | 1998-02-01 | Paper |
Homogenization of Hamiltonian systems with a strong constraining potential
Physica D | 1997-03-12 | Paper |
Quantum-classical molecular dynamics as an approximation to full quantum dynamics
The Journal of Chemical Physics | 1996-07-15 | Paper |
A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation
IMPACT of Computing in Science and Engineering | 1994-06-13 | Paper |
On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics
(available as arXiv preprint) | N/A | Paper |
