@article{KrishnadasMoshiQuintanaetal.2025, author = {Krishnadas, Anirudh and Moshi, Maryam and Quintana, Ramon Alain Miranda and Fournier, Rene}, title = {Geometric Features and a Neural Network Classifier for Detecting Melting-Like Transitions in Clusters.}, journal = {AIP Publications - The Journal of Chemical Physics}, year = {2025}, abstract = {Melting-like transitions in clusters are normally identified by a peak in the heat capacity curve C(T ) at T = Tc. Computing C(T ) requires costly simulations with millions of steps. We discuss four easily calculated functions of temperature that help detect and characterize melting-like transitions. The first, f1 (or WU ), is the width of the potential energy distribution which shows an abrupt increase near Tc. The other three are statistics of the ordered set of N(N - 1)/2 interatomic distances rij: (i) f2 is a measure of dissimilarity to the lowest energy configuration, or global minimum; (ii) f3 is the effective number of rij's found in a small interval centered around (r1 + r2)/2 where r1, r2 are the positions of the first two peaks in the pair distribution function; and (iii) f4 is a measure of non-uniformity in the distribution of the ri j's. Numerical tests with empirical potentials that model three types of bonding (van der Waals, covalent, and metallic) show that f1, f2, f3, and f4 produce estimates for the middle of the melting region in general agreement with Tc. An Artificial Neural Network (ANN) classifier that takes, as inputs, f2, f3, and many variants of f4, is used to calculate the solid fraction FS(T) and find the solid-liquid coexistence region between freezing and melting temperatures, [Tf , Tm]. Inflection points in f3(T ) and FS(T ) are very sensitive indicators of phase transitions. Estimates of Tc obtained from them converge one to three orders of magnitude faster, in simulation time, than those obtained with C(T ).}, language = {en} } @article{HoelterLemkeWeinzierletal.2025, author = {H{\"o}lter, Arne and Lemke, Mathias and Weinzierl, Stefan and Stein, Lewin}, title = {Non-Reflecting Characteristic Boundary Conditions for Adjoint Time-Domain Acoustic Simulations}, journal = {Journal of Theoretical and Computational Acoustics}, year = {2025}, abstract = {Accurate acoustic simulations in the free field require non-reflective boundary conditions to suppress spurious reflections at the computational domain boundaries. Although several characteristic-based formulations for direct (forward) simulations have been proposed in recent decades, the adjoint formulations of such characteristic-based boundary conditions (CBCs) have received limited atten- tion in the literature and lack a comprehensive analysis. This paper presents the derivation and evaluation of adjoint CBCs complementing the existing direct CBCs. Both the forward and adjoint CBCs are applied to the (nonlinear) Euler equations and linear acoustic equations in time-domain simulations. In this manner, the CBCs are investigated and subsequently compared to assess their respective accuracy and consistency. The CBCs were implemented using both a single-point and a zonal approach, with the former optionally combined with a sponge layer. Both approaches yielded comparable results in direct and adjoint simulations, while the zonal CBC exhibited improved ac- curacy at lower frequencies. Across the evaluated frequency range of approximately 350 - 5600 Hz, spurious reflections were attenuated by up to -70dB in both forward and adjoint cases, demon- strating the effectiveness and consistency of the proposed boundary treatment.}, language = {en} } @article{StraubeHoefling2024, author = {Straube, Arthur and H{\"o}fling, Felix}, title = {Memory effects in colloidal motion under confinement and driving}, volume = {57}, journal = {J. Phys. A: Math. Theor.}, publisher = {IOP Publishing}, issn = {1751-8113}, doi = {10.1088/1751-8121/ad5b2d}, pages = {295003}, year = {2024}, abstract = {The transport of individual particles in inhomogeneous environments is complex and exhibits non-Markovian responses. The latter may be quantified by a memory function within the framework of the linear generalised Langevin equation (GLE). Here, we exemplify the implications of steady driving on the memory function of a colloidal model system for Brownian motion in a corrugated potential landscape, specifically, for one-dimensional motion in a sinusoidal potential. To this end, we consider the overdamped limit of the GLE, which is facilitated by separating the memory function into a singular (Markovian) and a regular (non-Markovian) part. Relying on exact solutions for the investigated model, we show that the random force entering the GLE must display a bias far from equilibrium, which corroborates a recent general prediction. Based on data for the mean-square displacement (MSD) obtained from Brownian dynamics simulations, we estimate the memory function for different driving strengths and show that already moderate driving accelerates the decay of the memory function by several orders of magnitude in time. We find that the memory may persist on much longer timescales than expected from the convergence of the MSD to its long-time asymptote. Furthermore, the functional form of the memory function changes from a monotonic decay to a non-monotonic, damped oscillatory behaviour, which can be understood from a competition of confined motion and depinning. Our analysis of the simulation data further reveals a pronounced non-Gaussianity, which questions the Gaussian approximation of the random force entering the GLE.}, language = {en} } @misc{Secker2023, author = {Secker, Christopher}, title = {Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists (Dataset)}, doi = {10.12752/9622}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-96220}, year = {2023}, abstract = {Virtual Screening Dataset for the paper "Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists" by Secker et al. (https://doi.org/10.1186/s13321-023-00746-4)}, language = {en} } @masterthesis{Bena2023, type = {Bachelor Thesis}, author = {Bena, Noor-Cella}, title = {Finding Rules and Patterns in Egyptological Research Objects using Boolean Polynomial Rings}, pages = {35}, year = {2023}, language = {en} } @article{TrepteSeckerOlivetetal.2024, author = {Trepte, Philipp and Secker, Christopher and Olivet, Julien and Blavier, Jeremy and Kostova, Simona and Maseko, Sibusiso B and Minia, Igor and Silva Ramos, Eduardo and Cassonnet, Patricia and Golusik, Sabrina and Zenkner, Martina and Beetz, Stephanie and Liebich, Mara J and Scharek, Nadine and Sch{\"u}tz, Anja and Sperling, Marcel and Lisurek, Michael and Wang, Yang and Spirohn, Kerstin and Hao, Tong and Calderwood, Michael A and Hill, David E and Landthaler, Markus and Choi, Soon Gang and Twizere, Jean-Claude and Vidal, Marc and Wanker, Erich E}, title = {AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor}, volume = {20}, journal = {Molecular Systems Biology}, number = {4}, publisher = {Springer Science and Business Media LLC}, issn = {1744-4292}, doi = {https://doi.org/10.1038/s44320-024-00019-8}, pages = {428 -- 457}, year = {2024}, abstract = {Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.}, language = {en} } @article{RodriguesPelaDraxl2024, author = {Rodrigues Pel{\´a}, Ronaldo and Draxl, Claudia}, title = {Speeding up all-electron real-time TDDFT demonstrated by the exciting package}, volume = {304}, journal = {Comput. Phys. Commun.}, arxiv = {http://arxiv.org/abs/https://arxiv.org/abs/2403.04351}, doi = {10.1016/j.cpc.2024.109292}, pages = {109292}, year = {2024}, language = {en} } @article{FritschSchorr2024, author = {Fritsch, Daniel and Schorr, Susan}, title = {Disorder induced band gap lowering in kesterite type Cu2ZnSnSe4 and Ag2ZnSnSe4: a first-principles and special quasirandom structures investigation}, volume = {36}, journal = {Journal of Physics: Condensed Matter}, number = {37}, publisher = {IOP Publishing}, issn = {0953-8984}, doi = {10.1088/1361-648X/ad52de}, year = {2024}, abstract = {Abstract Quaternary chalcogenides, i.e. Cu2ZnSnS4, crystallising in the kesterite crystal structure have already been demonstrated as potential building blocks of thin film solar cells, containing only abundant elements and exhibiting power conversion efficiencies of about 14.9\% so far. However, due to the potential presence of several structurally similar polymorphs, the unequivocal identification of their ground state crystal structures required the application of more elaborate neutron diffraction experiments. One particular complication arose from the later identified Cu-Zn disorder, present in virtually all thin film samples. Subsequently, it has been shown experimentally that this unavoidable Cu-Zn disorder leads to a band gap lowering in the respective samples. Additional theoretical investigations, mostly based on Monte-Carlo methods, tried to understand the atomistic origin of this disorder induced band gap lowering. Here, we present theoretical results from first-principles calculations based on density functional theory for the disorder induced band gap lowering in kesterite Cu2ZnSnSe4 and Ag2ZnSnSe4, where the Cu-Zn and Ag-Zn disorder is modelled via a supercell approach and special quasirandom structures. Results of subsequent analyses of structural, electronic, and optical properties are discussed with respect to available experimental results, and will provide additional insight and knowledge towards the atomistic origin of the observed disorder induced band gap lowering in kesterite type materials.}, language = {en} } @inproceedings{KramerLaeuter2024, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {Benchmarking the rotating jet model of cometary activity with the trajectory of comet 67P/Churyumov-Gerasimenko}, volume = {17}, booktitle = {EPSC Abstracts}, doi = {10.5194/epsc2024-207}, year = {2024}, abstract = {An important tool to assess the composition and the spatial origin of cometary material is the analysis of its trajectory reflecting gravitational acceleration due to solar system bodies complemented by non-gravitational accelerations (NGA).}, language = {en} } @article{AttreeGutierrezGroussinetal.2024, author = {Attree, Nicholas and Guti{\´e}rrez, Pedro and Groussin, Olivier and B{\"u}rger, Johanna and Keller, Horst Uwe and Kramer, Tobias and LASAGNI MANGHI, RICCARDO and L{\"a}uter, Matthias and Lemos, Pablo and Markkanen, Johannes and Marschall, Raphael and Schuckart, Christian}, title = {Varying water activity and momentum transfer on comet 67P/Churyumov-Gerasimenko from its non-gravitational forces and torques}, volume = {690}, journal = {Astronomy and Astrophysics}, arxiv = {http://arxiv.org/abs/2408.10877}, doi = {10.1051/0004-6361/202450728}, pages = {A82}, year = {2024}, abstract = {Aims. We investigate the ability of a simultaneous fitting of comet 67P/Churyumov-Gerasimenko's non-gravitational forces, torques, and total water-outgassing rate, as observed by Rosetta, to constrain complex thermophysical models of cometary material. Methods. We extend the previous work of fitting geographically defined surface outgassing models to the Rosetta observations by testing the effects of a more detailed geomorphological mapping, the resolution of the shape-model used, self-heating by neighbouring facets on the shape-model, thermal inertia in the outgassing solution, and the variation in the momentum coupling between the gas and the nucleus. We also directly compare the non-gravitational acceleration curves available in the literature. Results. We correct an error in the calculation of pole-orientation in the previous paper. We find that, under the assumptions of the model, non-gravitational forces and torques are driven by water sublimation from the nucleus, thermal inertia and self-heating have only minor effects, spatially uniform activity cannot explain 67P's non-gravitational dynamics, spatially uniform momentum transfer cannot explain 67P's non-gravitational dynamics, and different terrain types have different instantaneous responses to insolation. Conclusions. Consolidated terrain facing south on 67P/Churyumov-Gerasimenko has a high outgassing flux, a steep response to insolation, and a large gas momentum transfer coefficient. Instead, that facing north behaves differently, producing little to no water outgassing, and with a lower momentum transfer efficiency. Dusty terrain also has a lower outgassing rate and momentum transfer efficiency, and either depletes its volatile component or is buried in fall-back as the comet approaches the Sun. Momentum transfer appears correlated with insolation, likely due to an increased enhancement in the gas temperature as the dust it flows through is heated.}, language = {en} } @inproceedings{AttreeGutierrezGroussinetal.2024, author = {Attree, Nicholas and Guti{\´e}rrez, Pedro and Groussin, Olivier and B{\"u}rger, Johanna and Keller, Horst Uwe and Kramer, Tobias and Lasagni Manghi, Riccardo and L{\"a}uter, Matthias and Lemos, Pablo and Markkanen, Johannes and Marschall, Raphael and Schuckart, Christian}, title = {The Results of ISSI Team \#547: Understanding the Activity of Comets Through 67P's Dynamics}, volume = {17}, booktitle = {EPSC Abstracts}, doi = {10.5194/epsc2024-82}, year = {2024}, abstract = {Understanding cometary activity gives us an insight into the materials properties, and therefore formation and evolution processes of these relatively pristine protoplanetary objects. We will present the results of an International Space Science Institute project to investigate the phenomenon through the effects of the outgassing activity on the orbit and spin-state of comet 67P/Churymov-Gerasimenko, e.g. its non-gravitational dynamics. This International Team gathered experts in orbital dynamics and trajectory reconstruction together with thermophysical modellers and comet observationalists, in order to compare the available extractions of 67P's non-gravitational acceleration (NGA) from its trajectory. The team then fitted a combination of the NGA, the non-gravitational torque (NGT), and the total water-outgassing rate with a thermophysical activity model. The results of this model will be presented. In particular, it was found that: non-gravitational forces and torques are driven by water sublimation from the nucleus; thermal inertia and self-heating have only minor effects; spatially uniform activity cannot explain 67P's non-gravitational dynamics; spatially uniform momentum transfer cannot explain 67P's non-gravitational dynamics; and different terrain types have different instantaneous responses to insolation. The implications of these findings for the modelling of cometary material and the variety of surface types seen on 67P will be discussed.}, language = {en} } @article{RoyHoefling2024, author = {Roy, Sutapa and H{\"o}fling, Felix}, title = {Critical surface adsorption of confined binary liquids with locally conserved mass and composition}, volume = {122}, journal = {Molecular Physics}, number = {21-22}, doi = {10.1080/00268976.2024.2391998}, pages = {e2391998}, year = {2024}, abstract = {Close to a solid surface, the properties of a fluid deviate significantly from their bulk values. In this context, we study the surface adsorption profiles of a symmetric binary liquid confined to a slit pore by means of molecular dynamics simulations; the latter naturally entails that mass and concentration are locally conserved. Near a bulk consolute point, where the liquid exhibits a demixing transition with the local concentration as the order parameter, we determine the order parameter profiles and characterise the relevant critical scaling behaviour, in the regime of strong surface attraction, for a range of pore widths and temperatures. The obtained order parameter profiles decay monotonically near the surfaces, also in the presence of a pronounced layering in the number density. Overall, our results agree qualitatively with recent theoretical predictions from a mesoscopic field-theoretical approach for the canonical ensemble.}, language = {en} } @article{CarusoSentefAttaccaliteetal.2026, author = {Caruso, Fabio and Sentef, Michael and Attaccalite, Claudio and Bonitz, Michael and Draxl, Claudia and De Giovannini, Umberto and Eckstein, Martin and Ernstorfer, Ralph and Fechner, Michael and Gr{\"u}ning, Myrta and H{\"u}bener, Hannes and Joost, Jan-Philip and Juraschek, Dominik and Karrasch, Christoph and Marvin Kennes, Dante and Latini, Simone and Lu, I-Te and Neufeld, Ofer and Perfetto, Enrico and Rettig, Laurenz and Rodrigues Pel{\´a}, Ronaldo and Rubio, Angel and Rudzinski, Joseph and Ruggenthaler, Michael and Sangalli, Davide and Sch{\"u}ler, Michael and Shallcross, Samuel and Sharma, Sangeeta and Stefanucci, Gianluca and Werner, Philipp}, title = {The 2025 Roadmap to Ultrafast Dynamics: Frontiers of Theoretical and Computational Modelling}, volume = {9}, journal = {J. Phys. Mater.}, number = {1}, arxiv = {http://arxiv.org/abs/2501.06752}, doi = {10.1088/2515-7639/ae1165}, year = {2026}, language = {en} }