Dr Karl Kirschner

Research MentorScience StaffTeacherInternational Chair

Field of research

I am interested in understanding the behavior of molecules through the use of computational chemistry. One long-term goal is the optimization of force-field parameters for use in molecular dynamics simulations. As part of this goal, I investigate the potential energy and conformations of small molecules using rigorous quantum mechanical methods. Other systems that I am interested in are biological (e.g. carbohydrates, proteins, lipids), drug and drug-like molecules, and nonbonded clusters (e.g. water clusters, hydration of environmentally relevant molecules). To support this work, my students and I write software in Python3. For examples of my research, please refer to my publication list.

Contact

Karl Kirschner
Email: 
karl.kirschner [at] h-brs.de

Sankt Augustin

Grantham-Allee 20
53757
Sankt Augustin
Room: 
C 228

Publications

Publications since 2015 (61 total since 1993)

  1. 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), accepted Feb. 2020

  2. 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, accepted, Feb. 2020 https://www.tandfonline.com/doi/full/10.1080/1539445X.2020.1714656

  3. 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

  4. 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

  5.  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

  6. 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

  7. 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

  8. 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 

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

More infos

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. Advanced Research Strategies and Dissemination (Department of EMT, master's course)
  4. Methods Training (Department of EMT, bachelor's course)
  5. Technikjournal  (Department of EMT, bachelor's course)
  6. Project Seminar: 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. 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 13 bachelor theses, 2 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