TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Hsiao, Ching-Lien A1 - Hultman, Lars A1 - Birch, Jens A1 - Gueorguiev, Gueorgui Kostov T1 - Electronic and optical properties of core-shell InAlN nanorods: a comparative study via LDA, LDA-1/2, mBJ, HSE06, G0W0 and BSE methods JF - Physical Chemistry Chemical Physics Y1 - 2024 U6 - https://doi.org/10.1039/D3CP05295H VL - 26 SP - 7504 EP - 7514 PB - Royal Society of Chemistry ER - TY - CHAP A1 - Christgau, Steffen A1 - Everingham, Dylan A1 - Mikolajczak, Florian A1 - Schelten, Niklas A1 - Schnor, Bettina A1 - Schroetter, Max A1 - Stabernack, Benno A1 - Steinert, Fritjof T1 - Enabling Communication with FPGA-based Network-attached Accelerators for HPC Workloads T2 - Proceedings of the SC'23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, SC-W 2023, Denver, CO, USA, November 12-17, 2023 N2 - The use of stand-alone, network-coupled Field Programmable Gate Array (FPGA) accelerators is intended to significantly increase the energy efficiency of HPC applications and thus also of HPC data centers. A loose coupling between the nodes of the HPC data center and the FPGAs is established through the high-speed network of the data center. This allows greater flexibility in combining different nodes and accelerators. Both the resulting energy savings and the increased flexibility through the network connection, enable the economical use of FPGAs. This work presents a communication stack to integrate the so-called Network-attached Accelerator (NAA) into the HPC data center. A low-level Remote Direct Memory Access (RDMA) Application Programming Interface (API) and a high-level Remote Procedure Call (RPC) API is designed on top of the RDMA over Converged Ethernet v2 (RoCEv2) communication stack. The experimental results over 100 Gbps RoCEv2 show that our design and implementation deliver performance close to the theoretical maximum. Y1 - 2023 U6 - https://doi.org/10.1145/3624062.3624540 SP - 530 EP - 538 PB - ACM ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Structure of liquid–vapor interfaces: perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence X-ray diffraction JF - The Journal of Chemical Physics N2 - Grazing-incidence X-ray diffraction (GIXRD) is a scattering technique which allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of the surface tension and of the interface roughness. However, the corresponding standard data analysis at non-zero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here we overcome this ambiguity by proposing a physically consistent model of the bulk contribution which is based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the X-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid--vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid--vapor coexistence line. A sensitivity analysis demonstrates the robustness of our findings concerning the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments. Y1 - 2024 U6 - https://doi.org/10.1063/5.0186955 VL - 160 SP - 104107 ER - TY - CHAP A1 - Skoblin, Viktor A1 - Höfling, Felix A1 - Christgau, Steffen T1 - Gaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL T2 - 29. PARS-Workshop 2023 N2 - Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of HAL’s MD package that has been successfully migrated from CUDA to SYCL. We describe the different strategies that we followed in the process of porting the code. Following these strategies, we achieved code portability across major GPU vendors. Depending on the actual kernels, both significant performance improvements and regressions are observed. As a side effect of the migration process, we obtained impressing speedups also for execution on CPUs. Y1 - 2023 SN - 0177-0454 VL - 36 ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Vona, Cecilia A1 - Lubeck, Sven A1 - Alex, Ben A1 - Gonzalez Oliva, Ignacio A1 - Draxl, Claudia T1 - Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2 JF - npj Comput. Mater. Y1 - 2024 U6 - https://doi.org/10.1038/s41524-024-01253-2 VL - 10 SP - 77 ER - TY - JOUR A1 - Krishnadas, Anirudh A1 - Sinha, Nidhi A1 - Kirchner, Tom A1 - Antony, Bobby T1 - Calculation of electron-impact ionization of various benzene derivatives JF - IOP Publications- Physica Scripta N2 - Calculations of the electron-impact ionization cross-section of pyrene, anthracene, benzoyl chloride, benzophenone, and phthalonitrile are reported over a wide energy range. A comparison of theoretical models, viz. spherical complex optical potential (SCOP), pixel counting method (PCM), and the binary encounter Bethe (BEB) model is carried out. SCOP calculations provide the inelastic cross-section, and the ionization cross-section is extracted from it. This result is modified with PCM, a model previously applied to ion collisions which takes geometric screening corrections into account. The BEB model is used as an independent approach to calculate the ionization cross-section. It is demonstrated that all model results are in reasonable agreement with each other. Comparison is also made with other theoretical data where available. Y1 - 2024 U6 - https://doi.org/10.1088/1402-4896/ad640a VL - 99 IS - 9 SP - 095403 ER - TY - JOUR A1 - Krishnadas, Anirudh A1 - Charron, Nicolas A1 - Fournier, Rene T1 - Melting Transitions in Small Aluminum Clusters Simulated with Energies Approaching DFT Accuracy. JF - ACS Publications- Journal of Chemical Theory and Computation N2 - We describe a computational framework for modelling melting-like transitions in atomic clusters that combines first-principles energy calculations, global optimization, and machine-learned interatomic potentials. A diverse set of configurations is generated by global optimization, and energies are calculated by Density Functional Theory. The energies are fitted to an accuracy of 10 meV/atom or better with an Allegro E(3)-equivariant neural network potential. The model allows efficient parallel tempering Monte Carlo simulations with near DFT-level accuracy. This methodology was validated by simulating Na_20 and comparing it to earlier experimental and computational results. We used it to study melting-like transitions in Al_n+ clusters (n=9 to 16), and Al_n and Al_n^- (n=12, 13,14). The simulated heat capacity of these clusters, in particular Al_16+, are in qualitative agreement with experiments. The melting point of Al_n+ clusters with n=11-16 are well above the bulk melting point (934 K). The closed-shell Al_13- species has an exceptionally high melting point, close to 2100 K. Y1 - 2025 ER - TY - JOUR A1 - Krishnadas, Anirudh A1 - Moshi, Maryam A1 - Quintana, Ramon Alain Miranda A1 - Fournier, Rene T1 - Geometric Features and a Neural Network Classifier for Detecting Melting-Like Transitions in Clusters. JF - AIP Publications - The Journal of Chemical Physics N2 - 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 ). Y1 - 2025 ER - TY - JOUR A1 - Hölter, Arne A1 - Lemke, Mathias A1 - Weinzierl, Stefan A1 - Stein, Lewin T1 - Non-Reflecting Characteristic Boundary Conditions for Adjoint Time-Domain Acoustic Simulations JF - Journal of Theoretical and Computational Acoustics N2 - 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. Y1 - 2025 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Memory effects in colloidal motion under confinement and driving JF - J. Phys. A: Math. Theor. N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1088/1751-8121/ad5b2d SN - 1751-8113 VL - 57 SP - 295003 PB - IOP Publishing ER - TY - GEN A1 - Secker, Christopher T1 - Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists (Dataset) N2 - 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) Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96220 ER - TY - THES A1 - Bena, Noor-Cella T1 - Finding Rules and Patterns in Egyptological Research Objects using Boolean Polynomial Rings Y1 - 2023 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Olivet, Julien A1 - Blavier, Jeremy A1 - Kostova, Simona A1 - Maseko, Sibusiso B 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 - Choi, Soon Gang 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 - Molecular Systems Biology N2 - 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. KW - Applied Mathematics KW - Computational Theory and Mathematics KW - General Agricultural and Biological Sciences KW - General Immunology and Microbiology KW - General Biochemistry, Genetics and Molecular Biology KW - Information Systems Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s44320-024-00019-8 SN - 1744-4292 VL - 20 IS - 4 SP - 428 EP - 457 PB - Springer Science and Business Media LLC ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Speeding up all-electron real-time TDDFT demonstrated by the exciting package JF - Comput. Phys. Commun. Y1 - 2024 U6 - https://doi.org/10.1016/j.cpc.2024.109292 VL - 304 SP - 109292 ER - TY - JOUR A1 - Fritsch, Daniel A1 - Schorr, Susan T1 - Disorder induced band gap lowering in kesterite type Cu2ZnSnSe4 and Ag2ZnSnSe4: a first-principles and special quasirandom structures investigation JF - Journal of Physics: Condensed Matter N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1088/1361-648X/ad52de SN - 0953-8984 VL - 36 IS - 37 PB - IOP Publishing ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Benchmarking the rotating jet model of cometary activity with the trajectory of comet 67P/Churyumov-Gerasimenko T2 - EPSC Abstracts N2 - 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). Y1 - 2024 U6 - https://doi.org/10.5194/epsc2024-207 VL - 17 ER - TY - JOUR A1 - Attree, Nicholas A1 - Gutiérrez, Pedro A1 - Groussin, Olivier A1 - Bürger, Johanna A1 - Keller, Horst Uwe A1 - Kramer, Tobias A1 - LASAGNI MANGHI, RICCARDO A1 - Läuter, Matthias A1 - Lemos, Pablo A1 - Markkanen, Johannes A1 - Marschall, Raphael A1 - Schuckart, Christian T1 - Varying water activity and momentum transfer on comet 67P/Churyumov-Gerasimenko from its non-gravitational forces and torques JF - Astronomy and Astrophysics N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1051/0004-6361/202450728 VL - 690 SP - A82 ER - TY - CHAP A1 - Attree, Nicholas A1 - Gutiérrez, Pedro A1 - Groussin, Olivier A1 - Bürger, Johanna A1 - Keller, Horst Uwe A1 - Kramer, Tobias A1 - Lasagni Manghi, Riccardo A1 - Läuter, Matthias A1 - Lemos, Pablo A1 - Markkanen, Johannes A1 - Marschall, Raphael A1 - Schuckart, Christian T1 - The Results of ISSI Team #547: Understanding the Activity of Comets Through 67P's Dynamics T2 - EPSC Abstracts N2 - 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. Y1 - 2024 U6 - https://doi.org/10.5194/epsc2024-82 VL - 17 ER - TY - JOUR A1 - Roy, Sutapa A1 - Höfling, Felix T1 - Critical surface adsorption of confined binary liquids with locally conserved mass and composition JF - Molecular Physics N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1080/00268976.2024.2391998 VL - 122 IS - 21-22 SP - e2391998 ER - TY - JOUR A1 - Caruso, Fabio A1 - Sentef, Michael A1 - Attaccalite, Claudio A1 - Bonitz, Michael A1 - Draxl, Claudia A1 - De Giovannini, Umberto A1 - Eckstein, Martin A1 - Ernstorfer, Ralph A1 - Fechner, Michael A1 - Grüning, Myrta A1 - Hübener, Hannes A1 - Joost, Jan-Philip A1 - Juraschek, Dominik A1 - Karrasch, Christoph A1 - Marvin Kennes, Dante A1 - Latini, Simone A1 - Lu, I-Te A1 - Neufeld, Ofer A1 - Perfetto, Enrico A1 - Rettig, Laurenz A1 - Rodrigues Pelá, Ronaldo A1 - Rubio, Angel A1 - Rudzinski, Joseph A1 - Ruggenthaler, Michael A1 - Sangalli, Davide A1 - Schüler, Michael A1 - Shallcross, Samuel A1 - Sharma, Sangeeta A1 - Stefanucci, Gianluca A1 - Werner, Philipp T1 - The 2025 Roadmap to Ultrafast Dynamics: Frontiers of Theoretical and Computational Modelling JF - J. Phys. Mater. Y1 - 2026 U6 - https://doi.org/10.1088/2515-7639/ae1165 VL - 9 IS - 1 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Rotation dynamics and torque efficiency of cometary nuclei JF - Astronomy & Astrophysics N2 - The dynamics of a rigid cometary nucleus is described by the evolutions of its center-of-mass and of its rotation state. Solar irradiation that reaches the surface of a cometary nucleus causes the sublimation of volatiles that form the coma around the nucleus. The sublimation process transfers linear momentum and rotational angular momentum from the nucleus to the surrounding space, and thus affects the dynamics via nongravitational forces and nongravitational torques. With the exception of close approaches to planets, these torques exert the dominant influence on the rotation states of cometary nuclei. The Rosetta mission 2014-2016 accompanying comet 67P/Churyumov-Gerasimenko provides the longest continuous observational data to track its rotation state. In particular, the data set encompasses the direction of the angular velocity, denoted by ω, and the angular frequency |ω|over a time period of approximately 700 days. The observed change of the rotation state is not explained by a low heat conductivity thermophysical model in combination with a homogeneous surface ice coverage of comet 67P. Spatially and/or temporally varying weights for effective active fraction with respect to a prescribed set of surface regions provide a potential solution to this problem. Here, we present a methodology for classifying the surface based on vectorial efficiency of the torque. On any cometary surface without geometric symmetry, the methodology highlights the decomposition into eight characteristic regions that encode the signs of torque efficiency with respect to all vector components. This decomposition is divided into two subsets of four regions each of which is located in one of both hemispheric regions. We analyze in detail rotation states close to lowest energy and different thermophysical models, and we discuss how the uncertainties of observations affect the model parameters. We study the occurrence of these regions for an oblate ellipsoid, a nearprolate ellipsoid, a bilobed shape, and a shape model analogous to that of comet 67P. The sensitivity analysis for comet 67P indicates that the observations constrain only one of the eight weights uniquely. The other directions are poorly constrained and show the limitation of the rotational data to determine the regional activity on comet 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202553845 VL - 699 SP - A75 ER - TY - JOUR A1 - Rossi, Thomas A1 - Qiao, Lu A1 - Dykstra, Conner P. A1 - Rodrigues Pelá, Ronaldo A1 - Gnewkow, Richard A1 - Wallick, Rachel F. A1 - Burke, John H. A1 - Nicholas, Erin A1 - March, Anne-Marie A1 - Doumy, Gilles A1 - Buchholz, D. Bruce A1 - Deparis, Christiane A1 - Zuñiga-Pérez, Jesus A1 - Weise, Michael A1 - Ellmer, Klaus A1 - Fondell, Mattis A1 - Draxl, Claudia A1 - van der Veen, Renske T1 - Dynamic control of X-ray core-exciton resonances by Coulomb screening in photoexcited semiconductors JF - Communications Materials Y1 - 2025 U6 - https://doi.org/10.1038/s43246-025-00909-w VL - 6 SP - 191 ER - TY - JOUR A1 - Hawthorne, Felipe A1 - Raulino, Paulo R. E. A1 - Rodrigues Pelá, Ronaldo A1 - Woellner, Cristiano F. T1 - Efficient and Accurate Machine Learning Interatomic Potential for Graphene: Capturing Stress–Strain and Vibrational Properties JF - The Journal of Physical Chemistry C Y1 - 2025 U6 - https://doi.org/10.1021/acs.jpcc.5c03470 VL - 129 SP - 16319 EP - 16326 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Depinning transition of self-propelled particles JF - Physical Review E N2 - For self-propelled particles in a corrugated potential landscape, we describe a discontinuous change of the classical depinning transition and a host of unique behaviors sensitive to the persistence of the propulsion direction. Exact and semianalytic results for active Brownian particles corroborate a creep regime with a superexponentially suppressed drift velocity upon lowering the force towards the threshold value. This unusual nonlinear response emerges from the competition of two critical scaling laws with exponents of 1/2 for rapidly reorienting particles and 𝑑/2 for particles with a persistent orientation; the latter case depends on the dimensionality 𝑑 of rotational motion and also includes run-and-tumble particles. Additionally, different giant diffusion phenomena occur in the two regimes. Our findings extend to random dynamics with bounded noise near a saddle-node bifurcation and have potential applications in various nonequilibrium problems, including arrested active matter and cell migration. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevE.110.L062601 VL - 110 IS - 6 SP - L062601 ER - TY - JOUR A1 - Groussin, Olivier A1 - Jorda, L. A1 - Attree, N. A1 - Birch, S.P.D. A1 - Bürger, Johanna A1 - Gutiérrez, Pedro A1 - Jindal, Abhinav S. A1 - Keller, H.U. A1 - Kramer, Tobias A1 - Lasagni Manghi, Riccardo A1 - Läuter, Matthias A1 - Markkanen, J. A1 - Marschall, R. A1 - Schuckart, C. T1 - Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko JF - Astronomy and Astrophysics N2 - Aims. This paper focuses on how insolation affects the nucleus of comet 67P/Churyumov-Gerasimenko over its current orbit. We aim to better understand the thermal environment of the nucleus, in particular its surface temperature variations, erosion, relationship with topography, and how insolation affects the interior temperature for the location of volatile species (H2O and CO2). Methods. We have developed two thermal models to calculate the surface and subsurface temperatures of 67P over its 6.45-year orbit. The first model, with high resolution (300 000 facets), calculates surface temperatures, taking shadows and self-heating into account but ignoring thermal conductivity. The second model, with lower resolution (10 000 facets), includes thermal conductivity to estimate temperatures down to ∼3 m below the surface. Results. The thermal environment of 67P is strongly influenced by its large obliquity (52◦), which causes significant seasonal effects and polar nights. The northern hemisphere is the coldest region, with temperatures of 210–300 K. H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) except during polar night around perihelion, when CO2 accumulates near the surface. Cliffs erode 3–5 times faster than plains, forming terraces. The equatorial region receives maximum solar energy (8.5×109 J m−2 per orbit), with maximum surface temperatures of 300–350 K. On the plains, H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) and never accumulates near the surface. In the southern hemisphere, a brief intense perihelion heating raises temperatures to 350–400 K, which is followed by a 5-year polar night when surface temperatures drop to 55 K. Here H2O remains in the first few centimetres, while CO2 accumulates shallowly during polar night, enriching the region. Erosion is maximal in the southern hemisphere and concentrated on the plains, which explains the observed overall flatness of this hemisphere compared to the northern one. Over one orbit, the total energy from self-heating is 17% of the total energy budget, and 34% for thermal conduction. Our study contributes to a better understanding of the surface changes observed on 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202452260 VL - 694 SP - A21 ER - TY - JOUR A1 - Coomber, Celvic A1 - Chewle, Surahit A1 - Secker, Christopher A1 - Fackeldey, Konstantin A1 - Weber, Marcus A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Investigating Endogenous Opioids Unravels the Mechanisms Behind Opioid-Induced Constipation, a Mathematical Modeling Approach JF - International Journal of Molecular Sciences N2 - Endogenous opioids, such as Endomorphin-2, are not typically associated with severe constipation, unlike pharmaceutical opioids, which induce opioid-induced constipation (OIC) by activating μ-opioid receptors in the gastrointestinal tract. In this study, we present a mathematical model, which integrates the serotonergic and opioid pathways, simulating the interaction between serotonin and opioid signaling within the enteric nervous system (ENS). The model explores the mechanisms underlying OIC, with a focus on the change in adenylyl cyclase (AC) activity, cAMP accumulation, and the distinct functionalities of Endomorphin-2 compared to commonly used pharmaceutical opioids. We study the effects of Morphine, Fentanyl, and Methadone and contrast them with Endomorphin-2. Our findings reveal that opioids do not perturb the signaling of serotonin, but only the activity of AC, suggesting that serotonin levels have no influence on improving opioid-induced constipation. Furthermore, this study reveals that the primary difference between endogenous and pharmaceutical opioids is their degradation rates. This finding shows that modulating opioid degradation rates significantly improves cAMP recovery. In conclusion, our insights steer towards exploring opioid degrading enzymes, localized to the gut, as a strategy for mitigating OIC. Y1 - 2025 U6 - https://doi.org/10.3390/ijms26136207 VL - 26 IS - 13 ER - TY - GEN ED - Fackeldey, Konstantin ED - Kannan, Aswin ED - Pokutta, Sebastian ED - Sharma, Kartikey ED - Walter, Daniel ED - Walter, Andrea ED - Weiser, Martin T1 - Mathematical Optimization for Machine Learning N2 - Mathematical optimization and machine learning are closely related. This proceedings volume of the Thematic Einstein Semester 2023 of the Berlin Mathematics Research Center MATH+ collects recent progress on their interplay in topics such as discrete optimization, nonlinear programming, optimal control, first-order methods, multilevel optimization, machine learning in optimization, physics-informed learning, and fairness in machine learning. Y1 - 2025 SN - 9783111376776 U6 - https://doi.org/10.1515/9783111376776 PB - De Gruyter ER - TY - JOUR A1 - Wolf, Sarah A1 - Fürst, Steffen A1 - Geiges, Andreas A1 - Laublichler, Manfred A1 - Mielke, Jahel A1 - Steudle, Gesine A1 - Winter, Konstantin A1 - Jaeger, Carlo T1 - The Decision Theatre Triangle for societal challenges – an example case and research needs JF - Journal of Cleaner Production N2 - Tackling societal challenges relating to sustainability requires both an understanding of the underlying complex socio-ecological systems and participation of scientists as well as relevant stakeholders, such as practice experts, decision makers, and citizens. This paper introduces the Decision Theatre Triangle, a method which combines empirical information, mathematical modelling and simulation, and a format for dialogue between scientists and stakeholders. While it builds on previous Decision Theatre work, the new structuring into these three elements emphasizes what is needed for setting up a Decision Theatre for a given challenge. Based on experience with a specific example – sustainable mobility in Germany – it is argued that agent-based models are particularly suitable for Decision Theatres and that the method is useful not only for decision support but also for science communication and co-creation of a deeper knowledge of the system under discussion. As a step towards facilitating a broader use of the Decision Theatre Triangle method, the paper then sketches research needs for each of its three elements, with a focus on mathematical modelling and simulation. Y1 - 2023 U6 - https://doi.org/10.1016/j.jclepro.2023.136299 VL - 394 SP - 136299 ER - TY - CHAP A1 - Chegini, Fatemeh A1 - Steinke, Thomas A1 - Weiser, Martin T1 - Efficient adaptivity for simulating cardiac electrophysiology with spectral deferred correction methods N2 - The locality of solution features in cardiac electrophysiology simulations calls for adaptive methods. Due to the overhead incurred by established mesh refinement and coarsening, however, such approaches failed in accelerating the computations. Here we investigate a different route to spatial adaptivity that is based on nested subset selection for algebraic degrees of freedom in spectral deferred correction methods. This combination of algebraic adaptivity and iterative solvers for higher order collocation time stepping realizes a multirate integration with minimal overhead. This leads to moderate but significant speedups in both monodomain and cell-by-cell models of cardiac excitation, as demonstrated at four numerical examples. Y1 - 2022 ER - TY - JOUR A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties JF - Journal of Geophysical Research: Planets N2 - The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes. Y1 - 2024 U6 - https://doi.org/10.1029/2023JE008152 VL - 129 IS - 3 ER - TY - CHAP A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - Investigating the Latitudinal Dependence of Lunar Regolith Properties Using LRO/Diviner Data and a Microphysical Thermal Model T2 - Bulletin of the AAS N2 - Regolith is formed through weathering of the local rock by meteorite bombardment, space weathering (Pieters & Noble, 2016) and thermal erosion (Delbo et al., 2014). In the case of the Moon, the space weathering effects and diurnal temperature variations are reduced towards the poles. The aim of this study is to investigate whether the lunar regolith properties derived from the comparison of regolith temperatures measured by the Diviner radiometer (Paige et al., 2010) on board the Lunar Reconnaissance Orbiter (LRO) with simulated temperatures derived from a microphysical thermal model show a latitudinal dependence. The developed microphysical thermal model expands upon previous models by more directly simulating regolith properties, such as grain radius and volume filling factor. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i207p02 VL - 55 IS - 8 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Non-gravitational acceleration and torque on comet 67P/Churyumov-Gerasimenko T2 - Bulletin of the AAS N2 - From August 2014 to September 2016, the ESA operated the Rosetta spacecraft mission alongside with comet 67P/Churyumov-Gerasimenko (67P). The mission provided valuable long-term data on the comet’s nucleus, including its volume, mass, tensor of inertia, spatial position of the orbital trajectory, and rotational state. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i218p02 VL - 55 IS - 8 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Garza, Alejandro J. A1 - Kapil, Venkat A1 - Fackeldey, Konstantin T1 - QUASAR: A Flexible QM-MM Method for Biomolecular Systems based on Restraining Spheres JF - Computer Physics Communications N2 - Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as nuclear quantum effects. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system. KW - QM-MM Methods KW - Path Integral KW - biomolecular systems KW - CADD KW - Free Energy KW - Binding Y1 - 2025 U6 - https://doi.org/10.1016/j.cpc.2025.109949 SN - 0010-4655 VL - 320 ER - TY - JOUR A1 - Gonnermann-Müller, Jana A1 - Haase, Jennifer A1 - Leins, Nicolas A1 - Igel, Moritz A1 - Fackeldey, Konstantin A1 - Pokutta, Sebastian T1 - FACET: Multi-Agent AI Supporting Teachers in Scaling Differentiated Learning for Diverse Students JF - arXiv N2 - Classrooms are becoming increasingly heterogeneous, comprising learners with diverse performance and motivation levels, language proficiencies, and learning differences such as dyslexia and ADHD. While teachers recognize the need for differentiated instruction, growing workloads create substantial barriers, making differentiated instruction an ideal that is often unrealized in practice. Current AI educational tools, which promise differentiated materials, are predominantly student-facing and performance-centric, ignoring other aspects that shape learning outcomes. We introduce FACET, a teacher-facing multi-agent framework designed to address these gaps by supporting differentiation that accounts for motivation, performance, and learning differences. Developed with educational stakeholders from the outset, the framework coordinates four specialized agents, including learner simulation, diagnostic assessment, material generation, and evaluation within a teacher-in-the-loop design. School principals (N = 30) shaped system requirements through participatory workshops, while in-service K-12 teachers (N = 70) evaluated material quality. Mixed-methods evaluation demonstrates strong perceived value for inclusive differentiation. Practitioners emphasized both the urgent need arising from classroom heterogeneity and the importance of maintaining pedagogical autonomy as a prerequisite for adoption. We discuss implications for future school deployment and outline partnerships for longitudinal classroom implementation. Y1 - 2026 U6 - https://doi.org/https://arxiv.org/abs/2601.22788 ER - TY - JOUR A1 - Gonnermann-Müller, Jana A1 - Haase, Jennifer A1 - Fackeldey, Konstantin A1 - Pokutta, Sebastian T1 - FACET: Teacher-Centred LLM-Based Multi-Agent Systems-Towards Personalized Educational Worksheets N2 - The increasing heterogeneity of student populations poses significant challenges for teachers, particularly in mathematics education, where cognitive, motivational, and emotional differences strongly influence learning outcomes. While AI-driven personalization tools have emerged, most remain performance-focused, offering limited support for teachers and neglecting broader pedagogical needs. This paper presents the FACET framework, a teacher-facing, large language model (LLM)-based multi-agent system designed to generate individualized classroom materials that integrate both cognitive and motivational dimensions of learner profiles. The framework comprises three specialized agents: (1) learner agents that simulate diverse profiles incorporating topic proficiency and intrinsic motivation, (2) a teacher agent that adapts instructional content according to didactical principles, and (3) an evaluator agent that provides automated quality assurance. We tested the system using authentic grade 8 mathematics curriculum content and evaluated its feasibility through a) automated agent-based assessment of output quality and b) exploratory feedback from K-12 in-service teachers. Results from ten internal evaluations highlighted high stability and alignment between generated materials and learner profiles, and teacher feedback particularly highlighted structure and suitability of tasks. The findings demonstrate the potential of multi-agent LLM architectures to provide scalable, context-aware personalization in heterogeneous classroom settings, and outline directions for extending the framework to richer learner profiles and real-world classroom trials. Y1 - 2025 ER -