TY - JOUR A1 - Steudle, Gesine A1 - Winkelmann, Stefanie A1 - Fürst, Steffen A1 - Wolf, Sarah T1 - Understanding Memory Mechanisms in Socio-Technical Systems: the Case of an Agent-based Mobility Model JF - Advances in Complex Systems N2 - This paper explores memory mechanisms in complex socio-technical systems, using a mobility demand model as an example case. We simplified a large-scale agent-based mobility model into a Markov process and discover that the mobility decision process is non-Markovian. This is due to its dependence on the system’s history, including social structure and local infrastructure, which evolve based on prior mobility decisions. To make the process Markovian, we extend the state space by incorporating two history-dependent components. Although our model is a very much reduced version of the original one, it remains too complex for the application of usual analytic methods. Instead, we employ simulations to examine the functionalities of the two history-dependent components. We think that the structure of the analyzed stochastic process is exemplary for many socio-technical, -economic, -ecological systems. Additionally, it exhibits analogies with the framework of extended evolution, which has previously been used to study cultural evolution. Y1 - 2024 U6 - https://doi.org/10.1142/S0219525924400034 VL - 27 ER - TY - THES A1 - Chewle, Surahit T1 - Probing effects of organic solvents on paracetamol crystallization using in silico and orthogonal in situ methods N2 - Polymorphism is the property exhibited by many inorganic and organic molecules to crystallize in more than one crystal structure. There is a strong need for understanding the influencing factors on polymorphism, as it is responsible for differences in many physicochemical properties such as stability and solubility. Nearly 80 % of marketed drugs exhibit polymorphism. In this work, we took the model system of paracetamol to investigate the influence of solvent choice on its polymorphism. Different methods were developed and employed to understand the influence of small organic solvents on the crystallization of paracetamol. Non-equilibrium molecular dynamics simulations with periodic simulated annealing were used as a tool to probe the nature of precursors of the metastable intermediates occurring in the crystallization process. Using this method, it was found that the structures of the building blocks of crystals of paracetamol is governed by solvent-solute interactions. In situ Raman spectroscopy was used with a custom-made acoustic levitator to follow crystallization. This set-up is a reliable method for investigating solvent influence, attenuating heterogeneous nucleation and stabilizing other environmental factors. It was established that as a solvent, ethanol is much stronger than methanol in its effect of driving paracetamol solutions to their crystal form. The time-resolved Raman spectroscopy crystallization data was processed using a newly developed objective function based non-negative matrix factorization method (NMF). An orthogonal time-lapse photography was used in conjunction with NMF to get unique and accurate factors that pertain to the spectra and concentrations of different moieties of paracetamol crystallization existing as latent components in the untreated data. Y1 - 2023 UR - https://edoc.hu-berlin.de/handle/18452/27957 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Kostova, Simona A1 - Maseko, Sibusiso B. A1 - Gang Choi, Soon A1 - Blavier, Jeremy A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J. A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A. A1 - Hill, David E. A1 - Landthaler, Markus A1 - Olivet, Julien A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E. T1 - AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - bioRxiv Y1 - 2023 U6 - https://doi.org/10.1101/2023.06.14.544560 ER - TY - JOUR A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Computing eigenfrequency sensitivities near exceptional points JF - Phys. Rev. Research Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.023148 VL - 6 SP - 023148 ER - TY - GEN A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Source code and simulation results: Computing eigenfrequency sensitivities near exceptional points T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10715639 SP - doi: 10.5281/zenodo.10715639 ER - TY - CHAP A1 - Weiser, Martin A1 - Chegini, Fatemeh T1 - Adaptive multirate integration of cardiac electrophysiology with spectral deferred correction methods T2 - CMBE22 - 7th International Conference on Computational & Mathematical Biomedical Engineering N2 - The highly localized dynamics of cardiac electrophysiology models call for adaptive simulation methods. Unfortunately, the overhead incurred by classical mesh adaptivity turns out to outweigh the performance improvements achieved by reducing the problem size. Here, we explore a different approach to adaptivity based on algebraic degree of freedom subset selection during spectral deferred correction sweeps, which realizes a kind of multirate higher order integration. Numerical experience indicates a significant performance increase compared to uniform simulations. Y1 - 2022 SP - 528 EP - 531 ER - TY - JOUR A1 - Kostré, Margarita A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia JF - Applied Network Science N2 - Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process. However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural change in ancient times. KW - mesoscale spreading process KW - network inference KW - time-evolving network KW - romanization spreading KW - scarce data Y1 - 2022 U6 - https://doi.org/10.1007/s41109-022-00492-w VL - 7 PB - Springer Nature ER - TY - JOUR A1 - Schweigart, Fleur T1 - KARTHAGO, TUNESIEN Datengesteuerte Modellierung des Romanisierungsprozesses in Nordafrika JF - e-Forschungsberichte des Deutschen Archäologischen Instituts. Berlin: Deutsches Archäologisches Institut, Zentrale. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.34780/d469-84h2 VL - Fasc. 1 ER - TY - CHAP A1 - Kostre, Margarita A1 - Sunkara, Vikram A1 - Djurdjevac Conrad, Natasa T1 - Inference of historical influence networks T2 - International Conference on Complex Networks & Their Applications Proceedings N2 - We study the romanization process of northern Africa from 50 BC till 300 AD. Our goal is to infer the communication strength between different subregions, based on the evolution of the status of cities. Herefore, we use the general inverse infection model, that infers the weights of a known underlying network, given observations of the spreading on this network. As infection process we choose the SI metapopulation model, where I stands for a city with a Roman status. To solve the minimization problem we use the particle swarm optimization algorithm with a specific choice of parameters. Y1 - 2021 U6 - https://doi.org/10.12752/8558 SP - 110 EP - 113 ET - International Conference on Complex Networks & Their Applications ER - TY - THES A1 - Chemnitz, Robin T1 - Spectral Coarse-Graining of SIS Dynamics on Networks Y1 - 2021 ER - TY - THES A1 - Helfmann, Luzie T1 - Non-stationary Transition Path Theory with applications to tipping and agent-based models N2 - The interesting dynamical regimes in agent-based models (ABMs) of social dynamics are the transient dynamics leading to metastable or absorbing states, and the transition paths between metastable states possibly caused by external influences. In this thesis, we are particularly interested in the pathways of rare and critical transitions such as the tipping of the public opinion in a population or the forming of social movements. For a detailed quantitative analysis of these transition paths, we consider the agent-based models as Markov chains and employ Transition Path Theory. Since ABMs are usually not considered in stationarity and possibly even forced, we generalize Transition Path Theory to time-dependent dynamics, for example on finite-time intervals or with periodically varying transition probabilities. We also specifically consider the case of dynamics with absorbing states and show how the transitions prior to absorption can be studied. These generalizations can also be useful in other application domains such as for studying tipping in climate models or transitions in molecular models with external stimuli. Another obstacle when analysing the dynamics of agent-based models is the large number of agents resulting in a high-dimensional state space for the model. However, the emergent dynamics of the ABM usually has significantly fewer degrees of freedom and many symmetries enabling a model reduction. On the example of two stationary ABMs we demonstrate how a long model simulation can be employed to find a lower-dimensional parametrization of the state space using a manifold learning algorithm called Diffusion Maps. In the considered models, agents adapt their binary behaviour to the local neighbourhood. When the interaction network consists of several densely connected communities, the dynamics result in a largely coherent behaviour in each community. The low-dimensional structure of the state space is therefore a hypercube. The corners represent metastable states with coherent agent behaviour in each group and the edges correspond to transition paths where agents in a community change their behaviour through a chain reaction. Finally, we can apply Transition Path Theory to the effective dynamics in the reduced space to reveal, for example, the dominant transition paths or the agents that are most indicative of an impending tipping event. Y1 - 2022 UR - https://refubium.fu-berlin.de/handle/fub188/35660 U6 - https://doi.org/http://dx.doi.org/10.17169/refubium-35374 ER - TY - CHAP A1 - Rickert, Lucas A1 - Gao, Timm A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Heindel, Tobias T1 - A Plug&Play Telecom-Wavelength Single-Photon Source for Quantum Key Distribution T2 - Quantum 2.0 Y1 - 2022 U6 - https://doi.org/10.1364/QUANTUM.2022.QTu4C.6 SP - QTu4C.6 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Zumbansen, Maximilian A1 - Weber, Marcus T1 - Parameter estimation on multivalent ITC data sets JF - Scientific Reports N2 - The Wiseman fitting can be used to extract binding parameters from ITC data sets, such as heat of binding, number of binding sites, and the overall dissociation rate. The classical Wiseman fitting assumes a direct binding process and neglects the possibility of intermediate binding steps. In principle, it only provides thermodynamic information and not the kinetics of the process. In this article we show that a concentration dependent dissociation constant could possibly stem from intermediate binding steps. The mathematical form of this dependency can be exploited with the aid of the Robust Perron Cluster Cluster Analysis method. Our proposed extension of the Wiseman fitting rationalizes the concentration dependency, and can probably also be used to determine the kinetic parameters of intermediate binding steps of a multivalent binding process. The novelty of this paper is to assume that the binding rate varies per titration step due to the change of the ligand concentration and to use this information in the Wiseman fitting. We do not claim to produce the most accurate values of the binding parameters, we rather present a novel method of how to approach multivalent bindings from a different angle. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17188-x VL - 12 SP - 13402 ER -