@article{CharronMusilGuljasetal.2025, author = {Charron, Nicholas and Musil, F{\´e}lix and Guljas, Andrea and Chen, Yaoyi and Bonneau, Klara and Pasos-Trejo, Aldo and Jacopo, Venturin and Daria, Gusew and Zaporozhets, Iryna and Kr{\"a}mer, Andreas and Templeton, Clark and Atharva, Kelkar and Durumeric, Aleksander and Olsson, Simon and P{\´e}rez, Adri{\`a} and Majewski, Maciej and Husic, Brooke and Patel, Ankit and De Fabritiis, Gianni and No{\´e}, Frank and Clementi, Cecilia}, title = {Navigating protein landscapes with a machine-learned transferable coarse-grained model}, volume = {17}, journal = {Nature Chemistry}, arxiv = {http://arxiv.org/abs/2310.18278}, doi = {10.1038/s41557-025-01874-0}, pages = {1284 -- 1292}, year = {2025}, abstract = {The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins.}, language = {en} } @masterthesis{Simon2011, type = {Bachelor Thesis}, author = {Simon, Felix}, title = {Postoptimierung bei der Planung von FTTx-Netzen}, year = {2011}, language = {de} } @misc{BetkerGamrathKosiankowskietal.2014, author = {Betker, Andreas and Gamrath, Inken and Kosiankowski, Dirk and Lange, Christoph and Lehmann, Heiko and Pfeuffer, Frank and Simon, Felix and Werner, Axel}, title = {Comprehensive Topology and Traffic Model of a Nation-wide Telecommunication Network}, issn = {1438-0064}, doi = {10.1364/JOCN.6.001038}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52670}, year = {2014}, abstract = {As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies, but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load-adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered.}, language = {en} } @article{BetkerGamrathKosiankowskietal.2014, author = {Betker, Andreas and Gamrath, Inken and Kosiankowski, Dirk and Lange, Christoph and Lehmann, Heiko and Pfeuffer, Frank and Simon, Felix and Werner, Axel}, title = {Comprehensive Topology and Traffic Model of a Nationwide Telecommunication Network}, volume = {6}, journal = {Journal of Optical Communications and Networking}, number = {11}, doi = {10.1364/JOCN.6.001038}, pages = {1038 -- 1047}, year = {2014}, abstract = {As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered.}, language = {en} }