Institute of Visual Computing (IVC)
Unit
Dr Karl Kirschner, Dr Karl Kirschner
Research fields
- Computational Chemistry
Location
Sankt Augustin
Room
C 228
Address
Grantham-Allee 20
53754, Sankt Augustin
Telephone
+49 2241 865 267Profile
Please see English version for complete information.
Aufgabengebiete
- Institut für Visual Computing
- Visual Computing in der Theoretischen Chemie
- Projekt FLOW: Newtonsche molekulare Modellierung. Um zuverlässige und akkurate Kräftefelder zu generieren, muss eine große Menge von Molekülen analysiert werden. Diese großen Datenmengen werden mithilfe des hochauflösenden HORNET Displays visualisiert und analysiert.
Curriculum vitae
Kurzlebenslauf
- 1999 Promotion in physikalischer Chemie an der University of Georgia (USA)
- Veröffentlichungen (peer-reviewed publications): insgesamt 48 in ca. 23 verschiedenen Fachzeitschriften, 2 Buchkapitel
- 2 U.S. Patent für einen pharmakologisch aktiven Wirkstoff, der Brustkrebs am Tiermodell (Maus) hemmt
- Forschungsinteressen im Gebiet der Theoretischen Chemie (siehe auch ausführlicher Lebenslauf-Research Highlights):
- Force-field development for molecular modeling (e.g. Glycam06, Wolf2Pack)
- Biological modeling and drug design (e.g carbohydrates, lipids, breast cancer, ribosome)
- Modeling molecular nonbonded clusters (e.g. water clusters)
- Betreuung von Studierenden in Forschungsprojekten: Insgesamt 44 Undergraduate students, 2 Master students, 2 Doctoral students
- Bisherige Lehrveranstaltungen u.a. Physical Chemistry, Introduction to computational chemistry methods und The history of America's Adirondack Park
Research Projects
Bio-chemical research is increasingly dependent on accurate computer modelling and analysis. This field of research is by its very nature highly interdisciplinary, as basic physical laws must be implemented algorithmically in order to make relevant contributions in life science applications. The project and the associated initiative UMMBAS bundles the strong cross-disciplinary expertise at the H-BRS in method development, visualisation and the application of computer-based procedures for deciphering material science and biochemical issues.
Project management at the H-BRS
Prof. Dr Matthias PrellerPublications
Publications since 2015 (67 total since 1993)
- A Hagg and 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
- 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
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W Fiedler, F Freisleben, J Wellbrock, & Kirschner, Karl N. “Mebendazole’s Conformational
Space and Its Predicted Binding to Human Heat-Shock Protein 90”. Journal of Chemical
Information and Modeling 62.15 (2022), 3604–3617 https://doi.org/10.3390/ijms221910670 -
R Strickstrock, M Hülsmann, D Reith, and KN Kirschner. “Optimizing Lennard-Jones
parameters by coupling single molecule and ensemble target data”. Computer Physics
Communications 274 (2022), 108285 https://doi.org/10.1016/j.cpc.2022.108285 - F. Freisleben, F. Modemann, J. Muschhammer, H. Stamm, F. Brauneck, A. Krispien, C. Bokemeyer, K.N. Kirschner, J. Wellbrock, & W. Fiedler. "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
- 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
- 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, doi: 10.1109/EDUCON45650.2020.9125242. (Won Best Paper.)
- 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
- 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
- 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
- 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 https://www.bloodadvances.org/content/3/3/242
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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