SFB 716:  Dynamic Simulation of Systems with Large Particle Numbers

• Subject Area: Chemistry ; Biology ; Computer Science, Systems and Electrical Engineering ; Mechanical and Industrial Engineering ; Materials Science and Engineering ; Mathematics ; Physics ; Thermal Engineering/Process Engineering
• Term: from 2007 to 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 17546514

• Final Report Year: 2019

Final Report Abstract

Simulations are an ideal tool for solving complex problems in the field of condensed matter, material properties, and biochemical or engineering processes. Most of these questions cannot be answered at all or require an immense effort via theoretical descriptions or experiments. Simulations of certain models can be performed on many different scales, depending on which problem is to be solved. In the SFB 716, a wide variety of problems from the field of natural and engineering science at the University of Stuttgart have been investigated by means of particle methods, both on the atomistic length scale in proteins or DNA, but also on the macroscopic (millimeter) scale, such as in the case of fracture processes in granular solids or particle aggregation in turbulent flows. A major advantage of particle simulations is that they fill the gap between quantum-mechanical ab initio methods and macroscopic continuum methods without phenomenological assumptions. They have therefore been successfully used in multiscale hybrid simulations. The big challenge of the SFB was to develop accurate and efficient force fields, to investigate new coarse-graining strategies, to develop new algorithms, to adopt software for modern and optimized hardware architectures, and finally, to take advantage of the enormous amounts of simulation data by suitable visualization methods and data reduction mechanisms, and to analyze them to gain further knowledge. As part of the cooperation between the project leaders and staff, which came from six different faculties, a far-reaching understanding of the physicochemical basics as well as application-relevant questions has been achieved, but also many new solution strategies have been developed. Over the last twelve years, the SFB 716 has been involved intensively in the development, optimization and validation of particle simulation algorithms, program codes, visualization methods and force fields. Furthermore, we focused on the transference of our simulation results to experimentally accessible systems, and thus compare our models to real world experimental data. For this purpose, in particular the simulation program packages IMD, Pasimodo, ESPResSo, as well as the visualization framework MegaMol have been further extended, but new methodologies have also been integrated, validated, and optimized for other software environments. The application spectrum of the methods ranged from the agglomeration of soot particles, gold nanoparticles, or supramolecular complexes, to the material strength determination of copper-based alloys, the laser ablation of materials, up to protein interactions, the sequencing of DNA in nanopores, or investigations of certain DNA conformations to only name a few examples. In addition, many new algorithms have been developed in the HPC area, and interactive visualization techniques and novel data analysis have been implemented. In addition, the SFB 716 has also contributed significantly to the development of particle methods in the SimTech Cluster of Excellence, and members of the SFB have been actively teaching in the Elite Bachelor's and Master's courses "Simulation Technology". Ultimately, SFB 716 members have thus also contributed to the success of the new cluster of excellence "Daten-integrierte Simulationswissenschaft" that successfully attracted funding in the new excellence strategy 2018.

Publications

• "Femtosecond laser ablation of aluminium," Applied Surface Science, vol. 255, pp. 9742-9744, 2009
  S. Sonntag, J. Roth, F. Gaehler and H.-R. Trebin
  (See online at https://doi.org/10.1016/j.apsusc.2009.04.062)
• "Interactive visualization of molecular surface dynamics," IEEE transactions on visualization and computer graphics, vol. 15, pp. 1391-1398, 2009
  M. Krone, K. Bidmon and T. Ertl
  (See online at https://doi.org/10.1109/TVCG.2009.157)
• "Implicit method for simulating electrohydrodynamics of polyelectrolytes," Physical review letters, vol. 105, p. 148301, 2010
  O. A. Hickey, C. Holm, J. L. Harden and G. W. Slater
  (See online at https://doi.org/10.1103/PhysRevLett.105.148301)
• "Applying ICC* to DNA translocation. Effect of dielectric boundaries," Computer Physics Communications, vol. 182, pp. 33-35, 1 2011
  S. Kesselheim, M. Sega and C. Holm
  (See online at https://doi.org/10.1016/j.cpc.2010.08.014)
• "Simulation of crack propagation in alumina with ab initio based polarizable force field," The Journal of chemical physics, vol. 136, p. 084707, 2012
  S. Hocker, P. Beck, S. Schmauder, J. Roth and H.-R. Trebin
  (See online at https://doi.org/10.1063/1.3685900)
• "Visualization of electrostatic dipoles in molecular dynamics of metal oxides," IEEE Transactions on Visualization and Computer Graphics, vol. 18, pp. 2061-2068, 2012
  S. Grottel, P. Beck, C. Müller, G. Reina, J. Roth, H.-R. Trebin and T. Ertl
  (See online at https://doi.org/10.1109/TVCG.2012.282)
• "A quadratically-converging nudged elastic band optimizer," Journal of chemical theory and computation, vol. 9, pp. 3498-3504, 2013
  M. U. Bohner, J. Meisner and J. Kästner
  (See online at https://doi.org/10.1021/ct400323z)
• "Atomistic visualization of mesoscopic whole-cell simulations using raycasted instancing," in Computer Graphics Forum, vol.32, pp. 195-206, 2013
  M. Falk, M. Krone and T. Ertl
  (See online at https://doi.org/10.1111/cgf.12197)
• "Fluorescent nanodiamonds derived from HPHT with a size of less than 10 nm," Diamond and Related Materials, vol. 37, pp. 80-86, 2013
  J.-P. Boudou, J. Tisler, R. Reuter, A. Thorel, P. A. Curmi, F. Jelezko and J. Wrachtrup
  (See online at https://doi.org/10.1016/j.diamond.2013.05.006)
• "Optically controlled switching of the charge state of a single nitrogen-vacancy center in diamond at cryogenic temperatures," Physical review letters, vol. 110, p. 167402, 2013
  P. Siyushev, H. Pinto, M. Vörös, A. Gali, F. Jelezko and J. Wrachtrup
  (See online at https://doi.org/10.1103/physrevlett.110.167402)
• "Tracer diffusion in a crowded cylindrical channel," Physical Review E, vol. 87, p. 062709, 2013
  R. Chakrabarti, S. Kesselheim, P. Košovan and C. Holm
  (See online at https://doi.org/10.1103/PhysRevE.87.062709)
• "Mobility reversal of polyelectrolyte-grafted colloids in monovalent salt solutions," Physical review letters, vol. 113, p. 238301, 2014
  S. Raafatnia, O. A. Hickey and C. Holm
  (See online at https://doi.org/10.1103/PhysRevLett.113.238301)
• "Modeling nanoparticle agglomeration using local interactions," Aerosol Science and Technology, vol. 48, pp. 842-852, 2014
  G. Inci, A. Arnold, A. Kronenburg and R. Weeber
  (See online at https://doi.org/10.1080/02786826.2014.932942)
• "Molecular-sized fluorescent nanodiamonds," Nature nanotechnology, vol. 9, p. 54, 2014
  I. I. Vlasov, A. A. Shiryaev, T. Rendler, S. Steinert, S.-Y. Lee, D. Antonov, M. Vörös, F. Jelezko, A. V. Fisenko, L. F. Semjonova, J. Biskupek, U. Kaiser, O. Lebedev, I. Sildos, P. Hemmer, V. Konov, A. Gali and J. Wrachtrup
  (See online at https://doi.org/10.1038/nnano.2013.255)
• "Origin of Current Blockades in Nanopore Translocation Experiments," Physical Review Letters, vol. 112, no. 1, p. 018101, 2014
  S. Kesselheim, W. Müller and C. Holm
  (See online at https://doi.org/10.1103/physrevlett.112.018101)
• "Effective potentials between gold nano crystals-- functional dependence on temperature," Molecular Simulation, vol. 41, pp. 1153-1158, 2015
  G. Bauer, A. Lange, N. Gribova, C. Holm and J. Gross
  (See online at https://doi.org/10.1080/08927022.2014.951521)
• "MD-Simulations on Metallic Alloys," in High Performance Computing in Science and Engineering ‘14, Springer, pp. 153-162, 2015
  M. Hummel, A.-P. Prskalo, P. Binkele and S. Schmauder
  (See online at https://doi.org/10.1007/978-3-319-10810-0_11)
• "MegaMol—a prototyping framework for particlebased visualization," IEEE transactions on visualization and computer graphics, vol. 21, pp. 201-214, 2015
  S. Grottel, M. Krone, C. Müller, G. Reina and T. Ertl
  (See online at https://doi.org/10.1109/TVCG.2014.2350479)
• "Peptides in the presence of aqueous ionic liquids: tunable co-solutes as denaturants or protectants?," Physical Chemistry Chemical Physics, vol. 17, pp. 26049- 26053, 2015
  V. Lesch, A. Heuer, V. A. Tatsis, C. Holm and J. Smiatek
  (See online at https://doi.org/10.1039/C5CP03838C)
• "Threading DNA through nanopores for biosensing applications," Journal of physics: condensed Matter, vol. 27, p. 273101, 2015
  M. Fyta
  (See online at https://doi.org/10.1088/0953-8984/27/27/273101)
• "Atomistic modeling of flexoelectricity in periclase," Physical Review B, vol. 93, p. 024105, 2016
  A. Chatzopoulos, P. Beck, J. Roth and H.-R. Trebin
  (See online at https://doi.org/10.1103/PhysRevB.93.024105)
• "Binding of solvent molecules to a protein surface in binary mixtures follows a competitive langmuir model," Langmuir, vol. 32, pp. 8960-8968, 2016
  T. Kulschewski and J. Pleiss
  (See online at https://doi.org/10.1021/acs.langmuir.6b02546)
• "Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides," Nanoscale, vol. 8, pp. 10105-10112, 2016
  G. Sivaraman, R. G. Amorim, R. H. Scheicher and M. Fyta
  (See online at https://doi.org/10.1039/c6nr00500d)
• "Laser ablation of Al--Ni alloys and multilayers," Applied Physics A, vol. 122, p. 500, 2016
  J. Roth, H.-R. Trebin, A. Kiselev and D.-M. Rapp
  (See online at https://doi.org/10.1007/s00339-016-9754-y)
• "Open boundary conditions for ISPH and their application to micro-flow," Journal of Computational Physics, vol. 307, pp. 614-633, 2016
  M. Hirschler, P. Kunz, M. Huber, F. Hahn and U. Nieken
  (See online at https://doi.org/10.1016/j.jcp.2015.12.024)
• "Synergistic substrate and oxygen activation in salicylate dioxygenase revealed by QM/MM simulations," Angewandte Chemie International Edition, vol. 55, pp. 1168-1172, 2016
  S. Roy and J. Kästner
  (See online at https://doi.org/10.1002/anie.201506363)
• "Langevin dynamics simulation of transport and aggregation of soot nano-particles in turbulent flows," Flow, Turbulence and Combustion, vol. 98, pp. 1065-1085, 2017
  G. Inci, A. Kronenburg, R. Weeber and D. Pflüger
  (See online at https://doi.org/10.1007/s10494-016-9797-3)
• "Molecular dynamics investigations of the strengthening of Al-Cu alloys during thermal ageing," Physical Mesomechanics, vol. 20, pp. 291-304, 2017
  W. Verestek, A.-P. Prskalo, M. Hummel, P. Binkele and S. Schmauder
  (See online at https://doi.org/10.1134/S1029959917030055)
• "Molecular surface maps," IEEE transactions on visualization and computer graphics, vol. 23, pp. 701-710, 2017
  M. Krone, F. Frieß, K. Scharnowski, G. Reina, S. Fademrecht, T. Kulschewski, J. Pleiss and T. Ertl
  (See online at https://doi.org/10.1109/TVCG.2016.2598824)
• "Tailoring spin defects in diamond by lattice charging," Nature Communications, vol. 8, p. 15409, 2017
  F. F. De Oliveira, D. Antonov, Y. Wang, P. Neumann, S. A. Momenzadeh, T. Häußermann, A. Pasquarelli, A. Denisenko and J. Wrachtrup
  (See online at https://doi.org/10.1038/ncomms15409)
• "Three-body effects in triplets of capped gold nanocrystals," Molecular Physics, vol. 115, pp. 1031-1040, 2017
  G. Bauer, N. Gribova, A. Lange, C. Holm and J. Gross
  (See online at https://doi.org/10.1080/00268976.2016.1213909)
• "Aqueous ionic liquids in comparison with standard co-solutes," Biophysical reviews, pp. 1-16, 2018
  E. A. Oprzeska-Zingrebe and J. Smiatek
  (See online at https://doi.org/10.1007/s12551-018-0414-7)
• "Influence of compatible solute ectoine on distinct DNA structures: thermodynamic insights into molecular binding mechanisms and destabilization effects," Physical Chemistry Chemical Physics, vol. 20, pp. 25861-25874, 2018
  E. A. Oprzeska-Zingrebe, S. Meyer, A. Roloff, H.-J. Kunte and J. Smiatek
  (See online at https://doi.org/10.1039/C8CP03543A)
• "Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity," Journal of inorganic biochemistry, vol. 183, pp. 172-178, 2018
  V. Ferrario, N. Hansen and J. Pleiss
  (See online at https://doi.org/10.1016/j.jinorgbio.2018.02.016)
• "Modeling of pore formation in phase inversion processes: Model and numerical results," Journal of Membrane Science, vol. 564, pp. 820-831, 2018
  M. Hopp-Hirschler and U. Nieken
  (See online at https://doi.org/10.1016/j.memsci.2018.07.085)
• "Precipitation strengthening in Cu--Ni--Si alloys modeled with ab initio based interatomic potentials," The Journal of chemical physics, vol. 149, p. 024701, 2018
  S. Hocker, H. Lipp, E. Eisfeld, S. Schmauder and J. Roth
  (See online at https://doi.org/10.1063/1.5029887)
• "Thermodynamic Characterization of the Dimerization of an Anionic Perylene Bisimide Dye Using Molecular Simulation," The Journal of Physical Chemistry C, 2018
  J. Baz and N. Hansen
  (See online at https://doi.org/10.1021/acs.jpcc.8b07400)
• "A particle localization algorithm on unstructured curvilinear polynomial meshes," Computer Physics Communications, vol. 235, pp. 63- 74, 2019
  P. Ortwein, S. M. Copplestone, C.-D. Munz, T. Binder, W. Reschke and S. Fasoulas
  (See online at https://doi.org/10.1016/j.cpc.2018.09.024)
• "A Particle-in-Cell solver based on a high-order hybridizable discontinuous Galerkin spectral element method on unstructured curved meshes," Computer Methods in Applied Mechanics and Engineering, vol. 349, pp. 149-166, 2019
  M. Pfeiffer, F. Hindenlang, T. Binder, S. M. Copplestone, C.-D. Munz and S. Fasoulas
  (See online at https://doi.org/10.1016/j.cma.2019.02.014)
• "Thermophysical properties of glyceline–water mixtures investigated by molecular modelling," Phys. Chem. Chem. Phys., vol. 21, pp. 6467-647 , 2019
  J. Baz, C. Held, J. Pleiss and N. Hansen
  (See online at https://doi.org/10.1039/c9cp00036d)