Institute of Visual Computing (IVC)

Karl Kirschner Portrait

Dr Karl Kirschner

Research Scientist/Mentor and Teacher/International Chair (2017-'19)

karl.kirschner@h-brs.de

Unit

Institute of Technology, Resource and Energy-efficient Engineering (TREE), Institute of Visual Computing (IVC)

Location

Sankt Augustin

Room

C 228

Address

Grantham-Allee 20

53757, Sankt Augustin

Telephone

+49 2241 865 267

Memberships

Publications

Publications since 2015 (67 total since 1993)

  1. A Hagg & KN Kirschner. “Open-Source Machine Learning in Computational Chemistry”.
    Journal of Chemical Information and Modeling 63.15 (2023), 4505–4532 https://doi.org/10.1021/acs.jcim.3c00643

  2. M Müller, A Hagg, R Strickstrock, M Hülsmann, A Asteroth, KN Kirschner, & D Reith.

    “Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-
    Enhanced, Surrogate-Assisted Global Optimization”. Journal of Chemical Information and
    Modeling 63.7 (2023), 1872–1881 https://doi.org/10.1021/acs.jcim.2c01231

  3. Strickstrock, R.; Hülsmann, M.; Reith, D. & Kirschner, K. N., Optimizing Lennard-Jones parameters by coupling single molecule and ensemble target data Computer Physics Communications, 2022, 274, 108285. https://doi.org/10.1016/j.cpc.2022.108285

  4. Freisleben, F.; Modemann, F.; Muschhammer, J.; Stamm, H.; Brauneck, F.; Krispien, A.; Bokemeyer, C.; Kirschner, K. N.; Wellbrock, J. & Fiedler, W. "Mebendazole Mediates Proteasomal Degradation of GLI Transcription Factors in Acute Myeloid Leukemia," International Journal of Molecular Sciences, 2021, 22, 10670. https://doi.org/10.3390/ijms221910670

  5. Cesari, A.; Uccello Barretta, G.; Kirschner, K.N.; Pappalardo, M.; Basile, L.; Guccione, S.; Russotto, C.; Lauro, M. R.; Cavaliere, F. & Balzano, F. “Interaction of natural flavonoid eriocitrin with β-cyclodextrin and hydroxypropyl-β-cyclodextrin: an NMR and molecular dynamics investigation,” New J. Chem., The Royal Society of Chemistry, 2020, 44, 16431-16441 https://pubs.rsc.org/en/content/articlelanding/2020/nj/d0nj02022b#!divAbstract

  6. K.N. Kirschner, S. Keil, K. Seuser, and C. Siefer, “Teaching Technical Journalism with an Engineering Foundation,” in 2020 IEEE Global Engineering Education Conference (EDUCON), Porto, Portugal, 2020, pp. 808-813, 10.1109/EDUCON45650.2020.9125242. (Won Best Paper)

  7. K.N. Kirschner, D. Reith, and W. Heiden, “The performance of Dunning, Jensen, and Karlsruhe basis sets on computing relative energies and geometries,” Soft Materials, 2020, 18, 200-214 https://www.tandfonline.com/doi/full/10.1080/1539445X.2020.1714656

  8. Schenk, M.R.; Köddermann, T.; Kirschner, K.N.; Knauer, S. & Reith, D.
    “Molecular Dynamics in the Energy Sector: Experiment and Modeling of the CO2/CH4 Mixture,” Journal of Chemical & Engineering Data, 2020, 65, 1117-1123 https://pubs.acs.org/doi/10.1021/acs.jced.9b00503

  9. Krämer, A.; Pickard, F.; Huang, J.; Venable, R.; Reith, D.; Kirschner, K.; Pastor, R. & Brooks, B. “Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects,” J. Chem. Theory Comput., 2019, 15 (6), 3854-3867  https://pubs.acs.org/doi/10.1021/acs.jctc.9b00016

  10. Mitchell, S. R.; Larkin, K.; Grieselhuber, N. R.; Lai, T.-H.; Cannon, M.; Orwick, S.; Sharma, P.; Asemelash, Y.; Zhang, P.; Goettl, V. M.; Beaver, L.; Mims, A.; Puduvalli, V. K.; Blachly, J. S.; Lehman, A.; Harrington, B.; Henderson, S.; Breitbach, J. T.; Williams, K. E.; Dong, S.; Baloglu, E.; Senapedis, W.; Kirschner, K.; Sampath, D.; Lapalombella, R. & Byrd, J. C. “Selective targeting of NAMPT by KPT-9274 in acute myeloid leukemia, Blood Advances, American Society of Hematology, 2019, 3, 242-255  http://www.bloodadvances.org/content/3/3/242

  11.  A. Bernardi, R. Faller, D. Reith, and K.N. Kirschner, “ACPYPE update for nonuniform 1-4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS,” SoftwareX, 2019, 10, 100241 https://www.sciencedirect.com/science/article/pii/S2352711018300736

  12. K. Kirschner, J. Bode, and D. Reith, “The International Chair - Concept and Benefits of a New Interdisciplinary Faculty Position,” in 2019 IEEE Global Engineering Education Conference (EDUCON), 2019, 775-780 https://ieeexplore.ieee.org/document/8725255

  13. K. N. Kirschner, W. Heiden, and D. Reith. “Small alcohols revisited: CCSD(T) relative potential energies for the minima, first- and second-order saddle points, and torsion-coupled surfaces,” ACS Omega, 3(1):419–432, 2018 https://pubs.acs.org/doi/abs/10.1021/acsomega.7b01367

  14. A. Bernardi, K.N. Kirschner, and R. Faller. “Structural analysis of human glycoprotein butyrylcholinesterase using atomistic molecular dynamics: The importance of glycosylation site ASN241,” PLOS ONE, 12(11):1–17, 11 2017 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187994 

  15. T. Köddermann, M.R. Schenk, M. Hülsmann, A. Krämer, K.N. Kirschner, and D. Reith. “Molecular dynamics simulation of membrane free energy profiles using accurate force field for ionic liquids.” In Scientific Computing and Algorithms in Industrial Simulations. Springer, Cham, 2017 https://link.springer.com/chapter/10.1007/978-3-319-62458-7_14

  16. K. N. Kirschner, W. Heiden, and D. Reith. “Relative electronic and free energies of octane’s unique conformations. Molecular Physics, 115(9-12):1155–1165, 2017 https://www.tandfonline.com/doi/abs/10.1080/00268976.2016.1262076

  17. R. Elfgen, M. Hülsmann A. Krämer, T. Köddermann, K.N. Kirschner, and D. Reith. “Optimized atomistic force fields for aqueous solutions of magnesium and calcium chloride: Analysis, achievements and limitations,” The European Physical Journal Special Topics, 225(8):1391–1409, 2016 https://link.springer.com/article/10.1140/epjst/e2016-60112-7

  18. M. Hülsmann, K.N. Kirschner, A. Krämer, D.D. Heinrich, O. Krämer-Fuhrmann, and D. Reith. “Optimizing molecular models through force-field parameterization via the efficient combination of modular program packages. In Q. R. Snurr, S. C. Adjiman, and A. D. Kofke, editors, Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2015, pages 53–77. Springer Singapore, Singapore, 2016 https://link.springer.com/chapter/10.1007/978-981-10-1128-3_4

  19. K.N. Kirschner, D. Reith, O. Jato, and A. Hinkenjann. “Visualizing potential energy curves and conformations on ultra high-resolution display walls,” Journal of Molecular Graphics and Modelling, 62:174–180, 2015 https://www.sciencedirect.com/science/article/pii/S1093326315300577

Further Information

H-BRS courses that I teach or have taught

  1. Scientific Programming in Python (Department of Computer Science, bachelor's course)
  2. Scientific Writing (Department of Computer Science, master's course)
  3. Molecular Modeling (Department of Computer Science, bachelor's course)
  4. Advanced Research Strategies and Dissemination (Department of EMT, master's course)
  5. Methods Training (Department of EMT, bachelor's course)
  6. Technikjournal  (Department of EMT, bachelor's course)
  7. Project Seminar: Computational Chemistry (Department of Computer Science, bachelor's course)
  8. Literature Seminar: Mahcine Learning in Computational Chemistry (Department of Computer Science, bachelor's course)

Previously taught courses

  1.  B-IT, University of Bonn: CHM 24 (2012) & CHM 33 (2013), LC, 3 Credits, Bachelor, Chemistry: Molecular Modeling using Quantum Mechanics, Molecular Mechanics, and Molecular Dynamics
  2. Hamilton College: Chemistry 321, Physical Chemistry I: Quantum Mechanics, Bachelor course
  3. Hamilton College: Chemistry 321L, Physical Chemistry I Lab: Introduction to Computational Chemistry - Classical Methodologies, Bachelor course
  4. Hamilton College: Chemistry 322, Physical Chemistry II: Thermodynamics & Kinetics, Bachelor course
  5. Hamilton College: Chemistry 322L, Physical Chemistry I Lab: Introduction to Computational Chemistry - Quantum Methodologies, Bachelor course
  6. Hamilton College: Sophomore Seminar 220, Forever Wild, The Cultural and Natural Histories of the Adirondack Park, Bachelor course

H-BRS master theses that I supervised

  1. Abanoub Abdelmalak - Master of Science in Autonomous Systems: "3-D Molecular Conformation Generation Using Machine Learning" University of Applied Science, Bonn-Rhein-Sieg, 2023

  2. Lena Riem - Master of Science in Computer Science: "Geometric Deep Learning on Small Molecule Properties" University of Applied Science, Bonn-Rhein-Sieg, 2022

  3. Vishwas Sharma - Master of Science in Autonomous Systems: "Learning Simulation for Plastic Sheet Extrusion in Blow Molding Machine " University of Applied Science, Bonn-Rhein-Sieg, 2022

  4. Robin Strickstrock – Master of Engineering: “Coupling of atomistic QM data and macroscopic experimental data for optimizing Lennard-Jones parameters” University of Applied Science, Bonn-Rhein-Sieg, 2018

Since 2005, I have supervised or mentored students in 15 bachelor theses, 4 master theses and 2 PhD theses in the United States and Germany. During my career, I have mentored over 50 students during their studies, summer research programs and student exchanges.

I am also responsible for the Chemical Computing Group Graudate Studuent Awards that are given by the Computers in Chemistry division of the American Chemical Society. Each application is reviewed by three experts, and are given twice a year. https://www.acscomp.org/awards/chemical-computing-group-excellence-award

Links

Weiterführende Links

Google Scholar
Research Gate
GitLab
GitHub
LinkedIn