Donati, Luca, Dr.

Contact

Position

Guest

Room

4033

Phone

+49 30 84185-403

Website

https://www.zib.de/userpage/donati/

Publications

2025

Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN 23rd International Conference on Computational Methods in Systems Biology, CMSB 2025, 2025 (accepted for publication) Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber, Susanna Röblitz BibTeX

2024

Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal Journal of Computational Chemistry, 46(1), p. e27529, 2024 (epub ahead of print) Simon Ghysbrecht, Luca Donati, Bettina G. Keller BibTeX
arXiv
DOI

Augmented ant colony algorithm for virtual drug discovery Journal of Mathematical Chemistry, Vol.62, pp. 367-385, 2024 Luca Donati, Konstantin Fackeldey, Marcus Weber BibTeX
DOI

Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies Journal of Chemical Physics, Vol.160, p. 104112, 2024 Alexander Sikorski, Amir Niknejad, Marcus Weber, Luca Donati BibTeX
arXiv
DOI

The Kramers turnover in terms of a macro-state projection on phase space Molecular Physics, p. e2356748, 2024 (epub ahead of print) Luca Donati, Christof Schütte, Marcus Weber BibTeX
DOI

Topological analysis reveals multiple pathways in molecular dynamics 2024 (under review) Luca Donati, Surahit Chewle, Dominik St. Pierre, Vijay Natarajan, Marcus Weber BibTeX
arXiv

2023

Efficient Estimation of Transition Rates as Functions of pH Proceedings in Applied Mathematics & Mechanics, Vol.23, 2023 (epub ahead of print) Luca Donati, Marcus Weber BibTeX
arXiv
DOI

2022

A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models Journal of Mathematical Physics, 63(12), pp. 123306-1-123306-21, 2022 Luca Donati, Marcus Weber, Bettina G. Keller BibTeX
DOI

Assessing transition rates as functions of environmental variables The Journal of Chemical Physics, 157(22), pp. 224103-1-224103-14, 2022 Luca Donati, Marcus Weber BibTeX
DOI

2021

Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux Journal of Physics: Condensed Matter, 33(11), p. 115902, 2021 Luca Donati, Marcus Weber, Bettina G. Keller BibTeX
DOI

2020

Dynamical reweighting methods for Markov models Current Opinion in Structural Biology, Vol.61, pp. 124-131, 2020 Stefanie Kieninger, Luca Donati, Bettina G. Keller BibTeX
DOI

2019

Reweighting methods for Molecular Dynamics Doctoral thesis, Freie Universität Berlin, Bettina G Keller, Marcus Weber (Advisors), 2019 Luca Donati BibTeX
DOI
URN

2018

An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates SIAM Journal on Scientific Computing, 40(2), pp. A653-A670, 2018 (preprint available as ) Jannes Quer, Luca Donati, Bettina Keller, Marcus Weber BibTeX
DOI

Estimation of the infinitesimal generator by square-root approximation J. Phys.: Condens. Matter, 30(42), pp. 425201-425201, 2018 Luca Donati, Martin Heida, Bettina G. Keller, Marcus Weber BibTeX
DOI

Girsanov reweighting for metadynamics simulations The Journal of Chemical Physics, 149(7), p. 072335, 2018 (in press) Luca Donati, Bettina G. Keller BibTeX
DOI

Markov State Models in Drug Design Biomolecular Simulations in Structure‐Based Drug Discovery, Wiley-Interscience, Weinheim, pp. 67-86, 2018, ISBN: 1865-0562 (in press) Bettina G. Keller, Stevan Aleksić, Luca Donati BibTeX
DOI

The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations Chemical Physics Letters, Vol.698, pp. 227-233, 2018 (in press) Irtaza Hassan, Luca Donati, Till Stensitzki, Bettina G Keller, Karsten Heyne, Petra Imhof BibTeX
DOI

2017

Girsanov reweighting for path ensembles and Markov state models The Journal of Chemical Physics, 146(24), p. 244112, 2017 (in press) Luca Donati, Carsten Hartmann, Bettina G. Keller BibTeX
DOI