Dr Karl Kirschner

International ChairTeacherScience StaffInstitute for Visual Computing

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 (56 total since 1993)

  1. 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, Manuscript ID ct-2019-000166
     
  2. 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
     
  3. 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
     
  4. 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 
     
  5. 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
     
  6. 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
     
  7. 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
     
  8. 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
     
  9. 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

  1. Advanced Research Strategies and Dissemination (Department of EMT, master's course)
  2. Methods Training (Department of EMT, bachelor's course)
  3. Technikjournal  (Department of EMT, bachelor's course)
  4. 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.