@inproceedings{ChristgauSteinke2020, author = {Christgau, Steffen and Steinke, Thomas}, title = {Leveraging a Heterogeneous Memory System for a Legacy Fortran Code: The Interplay of Storage Class Memory, DRAM and OS}, booktitle = {2020 IEEE/ACM Workshop on Memory Centric High Performance Computing (MCHPC)}, publisher = {IEEE}, isbn = {978-0-7381-1067-7}, doi = {10.1109/MCHPC51950.2020.00008}, pages = {17 -- 24}, year = {2020}, abstract = {Large capacity Storage Class Memory (SCM) opens new possibilities for workloads requiring a large memory footprint. We examine optimization strategies for a legacy Fortran application on systems with an heterogeneous memory configuration comprising SCM and DRAM. We present a performance study for the multigrid solver component of the large-eddy simulation framework PALM for different memory configurations with large capacity SCM. An important optimization approach is the explicit assignment of storage locations depending on the data access characteristic to take advantage of the heterogeneous memory configuration. We are able to demonstrate that an explicit control over memory locations provides better performance compared to transparent hardware settings. As on aforementioned systems the page management by the OS appears as critical performance factor, we study the impact of different huge page settings.}, language = {en} } @article{SchneckWeiserWende2021, author = {Schneck, Jakob and Weiser, Martin and Wende, Florian}, title = {Impact of mixed precision and storage layout on additive Schwarz smoothers}, volume = {28}, journal = {Numerical Linear Algebra with Applications}, number = {4}, doi = {10.1002/nla.2366}, year = {2021}, abstract = {The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth-bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage.}, language = {en} } @article{SchimunekSeidlElezetal.2024, author = {Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\´e}, Frank and Olsson, Simon and Raich, Llu{\´i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and Bousquet-Melou, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\´e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Itsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and Eghbal-Zadeh, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Goßen, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and Mu{\~n}iz-Chicharro, Abraham and Musiani, Francesco and Nunes-Alves, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\´i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and Garc{\´i}a-Sastre, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.}, title = {A community effort in SARS-CoV-2 drug discovery}, volume = {43}, journal = {Molecular Informatics}, number = {1}, doi = {https://doi.org/10.1002/minf.202300262}, pages = {e202300262}, year = {2024}, language = {en} } @article{GorgullaNigamKoopetal.2023, author = {Gorgulla, Christoph and Nigam, AkshatKumar and Koop, Matt and Selim {\c{C}}{\i}naroğlu, S{\"u}leyman and Secker, Christopher and Haddadnia, Mohammad and Kumar, Abhishek and Malets, Yehor and Hasson, Alexander and Li, Minkai and Tang, Ming and Levin-Konigsberg, Roni and Radchenko, Dmitry and Kumar, Aditya and Gehev, Minko and Aquilanti, Pierre-Yves and Gabb, Henry and Alhossary, Amr and Wagner, Gerhard and Aspuru-Guzik, Al{\´a}n and Moroz, Yurii S. and Fackeldey, Konstantin and Arthanari, Haribabu}, title = {VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules}, journal = {bioRxiv}, doi = {10.1101/2023.04.25.537981}, year = {2023}, language = {en} } @article{RodriguesPelaHsiaoHultmanetal.2024, author = {Rodrigues Pela, Ronaldo and Hsiao, Ching-Lien and Hultman, Lars and Birch, Jens and Gueorguiev, Gueorgui Kostov}, title = {Electronic and optical properties of core-shell InAlN nanorods: a comparative study via LDA, LDA-1/2, mBJ, HSE06, G0W0 and BSE methods}, volume = {26}, journal = {Physical Chemistry Chemical Physics}, publisher = {Royal Society of Chemistry}, arxiv = {http://arxiv.org/abs/https://arxiv.org/abs/2309.14889}, doi = {10.1039/D3CP05295H}, pages = {7504 -- 7514}, year = {2024}, language = {en} } @article{RodriguesPelaVonaLubecketal.2024, author = {Rodrigues Pela, Ronaldo and Vona, Cecilia and Lubeck, Sven and Alex, Ben and Gonzalez Oliva, Ignacio and Draxl, Claudia}, title = {Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2}, volume = {10}, journal = {npj Comput. Mater.}, arxiv = {http://arxiv.org/abs/https://arxiv.org/abs/2310.04198}, doi = {10.1038/s41524-024-01253-2}, pages = {77}, year = {2024}, 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} } @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} } @article{GroussinJordaAttreeetal.2025, author = {Groussin, Olivier and Jorda, L. and Attree, N. and Birch, S.P.D. and B{\"u}rger, Johanna and Guti{\´e}rrez, Pedro and Jindal, Abhinav S. and Keller, H.U. and Kramer, Tobias and Lasagni Manghi, Riccardo and L{\"a}uter, Matthias and Markkanen, J. and Marschall, R. and Schuckart, C.}, title = {Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko}, volume = {694}, journal = {Astronomy and Astrophysics}, doi = {10.1051/0004-6361/202452260}, pages = {A21}, year = {2025}, abstract = {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.}, language = {en} } @article{StraubeOliconMendezWinkelmannetal.2025, author = {Straube, Arthur and Olic{\´o}n M{\´e}ndez, Guillermo and Winkelmann, Stefanie and H{\"o}fling, Felix and Engel, Maximilian}, title = {Unfolding the geometric structure and multiple timescales of the urea-urease pH oscillator}, arxiv = {http://arxiv.org/abs/2508.07275}, year = {2025}, abstract = {We study a two-variable dynamical system modeling pH oscillations in the urea-urease reaction within giant lipid vesicles - a problem that intrinsically contains multiple, well-separated timescales. Building on an existing, deterministic formulation via ordinary differential equations, we resolve different orders of magnitude within a small parameter and analyze the system's limit cycle behavior using geometric singular perturbation theory (GSPT). By introducing two different coordinate scalings - each valid in a distinct region of the phase space - we resolve the local dynamics near critical fold points, using the extension of GSPT through such singular points due to Krupa and Szmolyan. This framework enables a geometric decomposition of the periodic orbits into slow and fast segments and yields closed-form estimates for the period of oscillation. In particular, we link the existence of such oscillations to an underlying biochemical asymmetry, namely, the differential transport across the vesicle membrane.}, language = {en} } @misc{OPUS4-10176, title = {Mathematical Optimization for Machine Learning}, editor = {Fackeldey, Konstantin and Kannan, Aswin and Pokutta, Sebastian and Sharma, Kartikey and Walter, Daniel and Walter, Andrea and Weiser, Martin}, publisher = {De Gruyter}, isbn = {9783111376776}, doi = {10.1515/9783111376776}, year = {2025}, abstract = {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.}, language = {en} } @article{SeckerFackeldeyWeberetal.2023, author = {Secker, Christopher and Fackeldey, Konstantin and Weber, Marcus and Ray, Sourav and Gorgulla, Christoph and Sch{\"u}tte, Christof}, title = {Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists}, volume = {15}, journal = {Journal of Cheminformatics}, doi = {10.1186/s13321-023-00746-4}, year = {2023}, abstract = {Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the μ-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported β-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale.}, language = {en} } @article{HoeflingDietrich2020, author = {H{\"o}fling, Felix and Dietrich, Siegfried}, title = {Finite-size corrections for the static structure factor of a liquid slab with open boundaries}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0017923}, pages = {054119}, year = {2020}, abstract = {The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures.}, language = {en} } @article{EbrahimiViandHoeflingKleinetal.2020, author = {Ebrahimi Viand, Roya and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Theory and simulation of open systems out of equilibrium}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0014065}, pages = {101102}, year = {2020}, abstract = {We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.}, language = {en} } @article{SteinStraubeWeinzierletal.2020, author = {Stein, Lewin and Straube, Florian and Weinzierl, Stefan and Lemke, Mathias}, title = {Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach}, volume = {148}, journal = {Acoustical Society of America}, number = {5}, publisher = {The Journal of the Acoustical Society of America}, doi = {https://doi.org/10.1121/10.0002425}, pages = {3075 -- 3085}, year = {2020}, abstract = {An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774-1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions.}, language = {en} } @article{RayFackeldeySteinetal.2023, author = {Ray, Sourav and Fackeldey, Konstantin and Stein, Christoph and Weber, Marcus}, title = {Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane}, volume = {3}, journal = {Biophysica}, number = {2}, doi = {10.3390/biophysica3020017}, pages = {263 -- 275}, year = {2023}, abstract = {In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the 𝜇-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the 𝜇-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe's parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane.}, language = {en} } @article{TrepteSeckerKostovaetal.2023, author = {Trepte, Philipp and Secker, Christopher and Kostova, Simona and Maseko, Sibusiso B. and Gang Choi, Soon and Blavier, Jeremy 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 Olivet, Julien 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}, journal = {bioRxiv}, doi = {10.1101/2023.06.14.544560}, year = {2023}, language = {en} } @inproceedings{BaumannNoackSteinke2021, author = {Baumann, Tobias and Noack, Matthias and Steinke, Thomas}, title = {Performance Evaluation and Improvements of the PoCL Open-Source OpenCL Implementation on Intel CPUs}, booktitle = {IWOCL'21: International Workshop on OpenCL}, doi = {10.1145/3456669.3456698}, year = {2021}, abstract = {The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs - which run 92 \% of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy.}, language = {en} }