Publications

Publications in Journals

2024

S. Godbole, H. Voß, A. Gocke, S. Schlumbohm, Y. Schumann, B. Peng, M. Mynarek, S. Rutkowski, M. Dottermusch, M. M. Dorostkar, A. Korshunov, T. Mair, S. M. Pfister, M. Kwiatkowski, M. Hotze, P. Neumann, C. Hartmann, J. Weis, F. Liesche-Starnecker, Y. Guan, M. Moritz, B. Siebels, N. Struve, H. Schlüter, U. Schüller, C. Krisp, J. E. Neumann. Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level. Nature Communications, 15, 6237, 2024

S. K. Peravali, V. Jafari, A. K. Samanta, J. Küpper, M. Amin, P. Neumann, M. Breuer. Accuracy and performance evaluation of low density internal and external flow predictions using CFD and DSMC. Computers & Fluids, 106346, 2024

Y. Schumann, M. Dottermusch, L. Schweizer, M. Krech, T. Lempertz, U. Schüller, P. Neumann, J.E. Neumann. Morphology-Based Molecular Classification of Spinal Cord Ependymomas Using Deep Neural Networks. Brain Pathology, e13239, 2024

Koch, M., Le Borne, S. & Leinen, W. Smaller stencil preconditioners for linear systems in RBF-FD discretizations. Numerical Algorithms, 2024

2023

M. Dottermusch, A. Biabani, T. Lempertz, Y. Schumann, J. Navolic, S. Godbole, D. Obrecht, S. Frank, M.M. Dorostkar, H. Voß, H. Schlüter, S. Rutkowski, U. Schüller, J.E. Neumann. Integrated proteomics spotlight the proteasome as a therapeutic vulnerability in Embryonal Tumors with Multilayered Rosettes. Neuro-Oncology, noad265, 2023

J. Navolić, M. Moritz, H. Voß, S. Schlumbohm, Y. Schumann, H. Schlüter, J.E. Neumann, J. Hahn. Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics. Analytical Chemistry 95, pp. 17220-17227, 2023

S.J. Newcome, F.A. Gratl, P. Neumann, H.-J. Bungartz. Towards Auto-tuning Multi-Site Molecular Dynamics Simulations with AutoPas. Journal of Computational and Applied Mathematics 433, 115278, 2023

Y. Schumann, J.E. Neumann, P. Neumann. Robust Classification Using Average Correlations as Features (ACF). BMC Bioinformatics 24, 101, 2023

S. Le Borne, W. Leinen. Guidelines for RBF-FD Discretization: Numerical Experiments on the Interplay of a Multitude of Parameter Choices. Journal of Scientific Computing 95, 8, 2023

Y. Schumann, P. Neumann. On Linear Models for Discrete Operator Inference in Time Dependent Problems. Journal of Computational and Applied Mathematics, 425, 115022, 2023

2022

P. Jarmatz, H. Wittenberg, V. Jafari, A. Das Sharma, F. Maurer, N. Wittmer, P. Neumann. MaMiCo 2.0: An enhanced open-source framework for high-performance molecular-continuum flow simulation. SoftwareX 20, 101251, 2022

H. Voß, S. Schlumbohm, P. Barwikowski, M. Wurlitzer, M. Dottermusch, P. Neumann, H. Schlüter, J.E. Neumann, C. Krisp. HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values. Nature Communications 13:3523, 2022

P. Jarmatz, F. Maurer, H. Wittenberg, P. Neumann. MaMiCo: Non-local means and POD filtering with flexible data-flow for two-way coupled molecular-continuum HPC flow simulation. Journal of Computational Science, 61, 101617, 2022

F.A. Gratl, S. Seckler, H.-J. Bungartz, P. Neumann. N Ways to Simulate Short-Range Particle Systems: Automated Algorithm Selection with the Node-Level Library AutoPas. Computer Physics Communications 273, 108262, 2022

2021

H. Wittenberg, P. Neumann. Transient Two-way Molecular-Continuum Coupling with OpenFOAM and MaMiCo: A sensitivity study. Computation 9(12):128, 2021

M. Dottermusch, Y. Schumann, U. Kordes, M. Hasselblatt, J.E. Neumann. Spatial molecular profiling of a central nervous system low-grade diffusely infiltrative tumour with INI1 deficiency featuring a high-grade atypical teratoid/rhabdoid tumour component. Neuropathology and Applied Neurobiology, pp. 1-6, 2021

S. Seckler, F. Gratl, M. Heinen, J. Vrabec, H.-J. Bungartz, P. Neumann. AutoPas in ls1 mardyn: Massively Parallel Particle Simulations with Node-Level Auto-Tuning. Journal of Computational Science 50, 101296, 2021

F. Judt, D. Klocke, R. Rios-Berrios, B. Vanniere, F. Ziemen, L. Auger, J. Biercamp, C. Bretherton, X. Chen, P. Düben, C. Hohenegger, M. Khairoutdinov, C. Kodama, L. Kornblueh, S.-J. Lin, M. Nakano, P. Neumann, W. Putman, N. Röber, M. Roberts, M. Satoh, R. Shibuya, B. Stevens, P.L. Vidale, N. Wedi, L. Zhou. Tropical Cyclones in Global Storm-Resolving Models. Journal of the Meteorological Society of Japan. Ser. II, Article-ID 2021-029, 2021

2020

M. Horsch, C. Niethammer, G. Boccardo, P. Carbone, S. Chiacchiera, M. Chiricotto, J. Elliott, V. Lobaskin, P. Neumann, P. Schiffels, M. Seaton, I. Todorov, J. Vrabec, W. Cavalcanti. Semantic interoperability and characterization of data provenance in computational molecular engineering. Journal of Chemical & Engineering Data 65(3):1313-1329, 2020

2019

B. Stevens, M. Satoh, L. Auger, J. Biercamp, C.S. Bretherton, X. Chen, P. Düben, F. Judt, M. Khairoutdinov, D. Klocke, C. Kodama, L. Kornblueh, S.-J. Lin, P. Neumann, W.M. Putman, N. Röber, R. Shibuya, B. Vanniere, P.L. Vidale, N. Wedi, L. Zhou. DYAMOND: the DYnamics of the Atmospheric general circulation Modeled On Non-hydrostatic Domains. Progress in Earth and Planetary Science 6(1):61, 2019.

P. Neumann, P. Düben, P. Adamidis, P. Bauer, M. Brueck, L. Kornblueh, D. Klocke, B. Stevens, N. Wedi and J. Biercamp. Assessing the Scales in Numerical Weather and Climate Predictions: Will Exascale be the Rescue? Philosophical Transactions of the Royal Society A 377(2142), 20180148, 2019.

D. Groen, J. Knap, P. Neumann, D. Suleimenova, L. Veen and K. Leiter. Mastering the scales: a survey on the benefits of multiscale computing software. Philosophical Transactions of the Royal Society A 377(2142), 20180147, 2019.

N. Tchipev, S. Seckler, M. Heinen, J. Vrabec, M. Horsch, M. Bernreuther, C.W. Glass, C. Niethammer, N. Hammer, B. Krischok, M. Resch, D. Kranzlmüller, H. Hasse, H.-J. Bungartz and P. Neumann. TweTriS: Twenty Trillion-atom Simulation. International Journal of High Performance Computing Applications 33(5):838-854, 2019.

2018

J. Vrabec, M. Bernreuther, H.-J. Bungartz, W.-L. Chen, W. Cordes, R. Fingerhut, C.W. Glass, J. Gmehling, R. Hamburger, M. Heilig, M. Heinen, M.T. Horsch, C.-M. Hsieh, M. Hülsmann, P. Jäger, P. Klein, S. Knauer, T. Köddemann, A. Köster, K. Langenbach, S.-T. Lin, P. Neumann, J. Rarey, D. Reith, G. Rutkai, M. Schappals, M. Schenk, A. Schedemann, M. Schönherr, S. Seckler, S. Stephan, K. Stöbener, N. Tchipev, A. Wafai, S. Werth and H. Hasse. SkaSim – Skalierbare HPC-Software für molekulare Simulationen in der chemischen Industrie. Chemie Ingenieur Technik 90(3), pp. 295-306, 2018.

P. Solin, J.L. Galán-García, V. Dolejší, P. Neumann, P. Svacek, J. Kruis and V. John. Recent Advances in Computing. Editorial. Applied Mathematics and Computation 319, p. 1, 2018.

2017

C. Riesinger, A. Bakhtiari, M. Schreiber, P. Neumann and H.-J. Bungartz. A holistic scalable implementation approach of the lattice Boltzmann method for CPU/GPU heterogeneous clusters. Computation 5(4):48, 2017.

J.E. Neumann, A.K. Wefers, S. Lambo, E. Bianchi, M. Bockstaller, M.M. Dorostkar, V. Meister, P. Schindler, A. Korshunov, K. von Hoff, J. Nowak, M. Warmuth-Metz, M.R. Schneider, I. Müller-Renner, D.J. Merk, M. Shakarami, T. Sharma, L. Chavez, R. Glass, J.A. Chan, M.M. Taketo, P. Neumann, M. Kool and U. Schüller. A mouse model for embryonal tumors with multilayered rosettes uncovers the therapeutic potential of Sonic-hedgehog inhibitors. Nature Medicine 23(10), pp. 1191-1202, 2017.

P. Neumann and X. Bian. MaMiCo: Transient Multi-Instance Molecular-Continuum Flow Simulation on Supercomputers. Computer Physics Communications 220, pp. 390-402, 2017.

R. Wittmann, H.-J. Bungartz and P. Neumann. High Performance Shallow Water Kernels for Parallel Overland Flow Simulations Based on FullSWOF2D. Computers and Mathematics with Applications 74(1), pp. 110-125, 2017.

P. Neumann, C. Kowitz, F. Schranner and D. Azarnykh. Interdisciplinary Teamwork in HPC Education: Challenges, Concepts, and Outcomes. Journal of Parallel and Distributed Computing 105, pp. 83-91, 2017.

2016

A. Atanasov, B. Uekermann, C.A. Pachajoa Mejía, H.-J. Bungartz and P. Neumann. Steady-State Anderson Accelerated Coupling of Lattice Boltzmann and Navier-Stokes Solvers. Computation 4(4), pp. 1-19, 2016.

P. Neumann. On Transient Hybrid Lattice Boltzmann—Navier-Stokes Flow Simulations. Journal of Computational Science 17, pp. 482-490, 2016.

P. Neumann, H. Flohr, R. Arora, P. Jarmatz, N. Tchipev and H.-J. Bungartz. MaMiCo: Software Design for Parallel Molecular-Continuum Flow Simulations. Computer Physics Communications 200, pp. 324-335, 2016.

2015

P. Neumann and H.-J. Bungartz. Dynamically Adaptive Lattice Boltzmann Simulation of Shallow Water Flows with the Peano Framework. Applied Mathematics and Computation 267, pp. 795-804, 2015.

2014

J. Pöschl, S. Stark, P. Neumann, S. Gröbner, D. Kawauchi, D. Jones, P. Northcott, P. Lichter, S. Pfister, M. Kool and U. Schüller. Genomic and transcriptomic analyses match medulloblastoma mouse models to their human counterparts. Acta Neuropathologica 128(1), pp. 123-136, 2014.

P. Neumann, W. Eckhardt and H.-J. Bungartz. A Radial Distribution Function-Based Open Boundary Force Model for Multi-Centered Molecules. International Journal of Modern Physics C 25(6), 1450008, 2014.

P. Neumann, W. Eckhardt and H.-J. Bungartz. Hybrid Molecular-Continuum Methods: From Prototypes to Coupling Software. Computers and Mathematics with Applications 67(2), pp. 272-281, 2014.

2013

P. Neumann and T. Neckel. A dynamic mesh refinement technique for Lattice Boltzmann simulations on octree-like grids. Computational Mechanics 51(2), pp. 237-253, 2013.

2012

P. Neumann, H.-J. Bungartz, M. Mehl, T. Neckel and T. Weinzierl. A Coupled Approach for Fluid Dynamic Problems Using the PDE Framework Peano. Communications in Computational Physics 12(1), pp. 65-84, 2012.

P. Neumann and T. Rohrmann. Lattice Boltzmann Simulations in the Slip and Transition Flow Regime with the Peano Framework. Open Journal of Fluid Dynamics 2(3), pp. 101-110, 2012.

2011

M. Mehl, T. Neckel and P. Neumann. Navier-Stokes and Lattice-Boltzmann on octree-like grids in the Peano framework. International Journal for Numerical Methods in Fluids 65(1-3), pp. 67-86, 2011.

Publications in Proceedings

2024

R. Horn, P. Neumann. Towards Green HPC Job Outsourcing: Energy Models for Molecular Dynamics Simulations on Three Clusters. ISPDC 2024, pp. 1-8, 2024.

P. Ivanovic, A. Windmann, P. Neumann. SmartShip: Data Decoding Optimization for Onboard AI Anomaly Detection. ISPDC 2024, pp. 1-5, 2024.

A. Das Sharma, R. Horn, P. Neumann. The Error-Energy Tradeoff in Molecular and Molecular-Continuum Fluid Simulations. HPC Asia 2024 (workshop MMCP), pp. 111-121, 2024.

2023

P. Ivanovic, A. Ganbarov, P. Neumann. System Architecture for Real-time Condition Monitoring and Anomaly Detection on Ships. ISPDC proc., pp. 45-52, 2023

L. Viot, Y. Piel, P. Neumann. From Desktop to Supercomputer: Computational Fluid Dynamics Augmented by Molecular Dynamics using MaMiCo and preCICE. ISC HPC workshop proceedings 2023, pp. 567-576, 2023

P. Jarmatz, S. Lerdo, P. Neumann. Convolutional Recurrent Autoencoder for Molecular-Continuum Coupling. ICCS 2023 proceedings, LNCS 10476, pp. 535-549, 2023

V. Jafari, P. Neumann. Fault Tolerance for Ensemble-based Molecular-Continuum Flow Simulations. HPC Asia 2023 proceedings, pp. 35-45, 2023

2022

Y. Schumann, P. Neumann. Towards Data-Driven Inference of Stencils for Discrete Differential Operators. PASC 2022 proceedings, 4, 2022

V. Jafari, N. Wittmer, P. Neumann. Massively Parallel Molecular-Continuum Flow Simulation with Error Control and Dynamic Ensemble Handling. HPC Asia 2022 proceedings, pp. 52-60, 2022

2021

P. Jarmatz, F. Maurer and P. Neumann. MaMiCo: Non-Local Means Filtering with Flexible Data-Flow for Coupling MD and CFD. ICCS 2021 proceedings, LNCS 12746, pp. 576-589, 2021

2020

P. Neumann and N. Wittmer. Open Boundary Modeling in Molecular Dynamics with Machine Learning. ICCS 2020 proceedings, LNCS 12142, pp. 334-347, 2020.

P. Neumann. Sparse Grid Regression for Performance Prediction Using High-Dimensional Run Time Data. Euro-Par 2019: Parallel Processing Workshops, Lecture Notes in Computer Science 11997, pp. 601-612, 2020.

2019

P. Neumann and J. Biercamp. ESiWACE: On European Infrastructure Efforts for Weather and Climate Modeling at Exascale. eScience 2019 proceedings, pp. 498-501, 2019.

P. Jarmatz and P. Neumann. MaMiCo: Parallel Noise Reduction for Multi-Instance Molecular-Continuum Flow Simulation. ICCS 2019 proceedings, LNCS 11539, pp. 451-464, 2019.

F. Gratl, S. Seckler, N. Tchipev, H.-J. Bungartz and P. Neumann. AutoPas: Auto-Tuning for Particle Simulations. IEEE IPDPS workshops proceedings, pp. 748-757, 2019.

2018

J. Behrens, J. Biercamp, H. Bockelmann and P. Neumann. Increasing parallelism in climate models via additional component concurrency. 2018 IEEE 14th International Conference on e-Science, pp. 271–271, 2018.

2017

P. Neumann and M. Zellner. Lattice Boltzmann Flow Simulation on Android Devices for Interactive Mobile-Based Learning. Euro-Par 2016: Parallel Processing Workshops, Lecture Notes in Computer Science 10104, pp. 3-15, 2017.

2016

S. Seckler, N. Tchipev, H.-J. Bungartz and P. Neumann. Load Balancing for Molecular Dynamics Simulations on Heterogeneous Architectures. IEEE 23rd International Conference on High Performance Computing, pp. 101-110, 2016.

2015

N. Tchipev, A. Wafai, C.W. Glass, W. Eckhardt, A. Heinecke, H.-J. Bungartz and P. Neumann. Optimized Force Calculation of Molecular Dynamics Simulations for the Intel Xeon Phi. Euro-Par 2015: Parallel Processing Workshops, Lecture Notes in Computer Science 9523, pp. 774-785, 2015.

P. Neumann, C. Kowitz, F. Schranner and D. Azarnykh. Teamwork Across Disciplines: High-Performance Computing Meets Engineering. Euro-Par 2015: Parallel Processing Workshops, Lecture Notes in Computer Science 9523, pp. 125-134, 2015.

K. Unterweger, R. Wittmann, P. Neumann, T. Weinzierl and H.-J. Bungartz. Integration of FULLSWOF2D and PeanoClaw: Adaptivity and Local Time-stepping for Complex Overland Flows. Proceedings of CE2014, Lecture Notes in Computational Science and Engineering 105, pp. 181-195, 2015.

2014

M. Schreiber, A. Atanasov, P. Neumann and H.-J. Bungartz. Rendering of Feature-Rich Dynamically Changing Volumetric Datasets on GPU. Proceedings of the 2014 International Conference on Computational Science, Procedia Computer Science 29, pp. 648-658, 2014.

2013

P. Neumann and J. Harting. Massively Parallel Molecular-Continuum Simulations with the Macro-Micro-Coupling Tool. Proceedings of the NIC Workshop on Hybrid Particle-Continuum Methods in Computational Materials Physics, NIC Series 46, pp. 211-216, 2013.

S. Grimm, T. Hubauer, T. Runkler, C. Pachajoa, F. Rempe, M. Seravalli and P. Neumann. A CEP Technology Stack for Situation Recognition on the Gumstix Embedded Controller. GI-Jahrestagung, pp. 1925-1930, 2013.

2012

P. Neumann and N. Tchipev. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations. Proceedings of the 11th International Symposium on Parallel and Distributed Computing, pp. 111-118, 2012.

D. Jarema, P. Neumann and T. Weinzierl. A Multiscale Approach for Particle Transport Simulation in Low Reynolds Number Flows. Student Paper Competition of the 12th Copper Mountain Conference on Iterative Methods, 2012.

2011

M. Schreiber, P. Neumann, S. Zimmer and H.-J. Bungartz. Free-Surface Lattice-Boltzmann Simulation on Many-Core Architectures. Proceedings of the 2011 International Conference on Computational Science, Procedia Computer Science 4, pp. 984-993, 2011.

Books and Monographs

H.-J. Bungartz, S. Reiz, B. Uekermann, P. Neumann, W.E. Nagel (Eds.). Software for Exascale Computing – SPPEXA 2016-2019. Lecture Notes in Computational Science and Engineering 136, Springer, 2020.

P. Neumann, J. Kunkel. Chapter 07: High-Performance Techniques for Big Data Processing. In Knowledge Discovery in Big Data from Astronomy and Earth Observation, pp. 137-158, 2020

P. Neumann. Algorithms and HPC Software for Molecular-Continuum Flow Simulation. Habilitation thesis (cumulative), 2019

H.-J. Bungartz, P. Neumann, W.E. Nagel (Eds.). Software for Exascale Computing – SPPEXA 2013-2015. Lecture Notes in Computational Science and Engineering 113, Springer, 2016.

P. Neumann. Hybrid Multiscale Simulation Approaches for Micro- and Nanoflows. Ph.D. thesis, Dr. Hut, 2013.