B 4 - Simulation of primary electronic dynamics in macromolecules after femtosecond x-ray pulses

The aim of the project is to develop methods for extracting structural information from single molecule scattering images collected by ultra-short (femtosecond) free electron laser pulses. To reach this goal, we will develop new methods to (a) simulate the primary (few 10 fs) electronic and nuclear dynamcis following x-ray absorption, and (b) to extract structural information from diffraction images.

Members of this project:

Prof. Dr. Helmut Grubmüller
Marco Dalla-Sega

Publications:

Ardenne, B., Mechelke, M. and Grubmüller, H. (2018)
Structure determination from single molecule X-ray scattering with three photons per image
Nature comm., 9: 2375, DOI:10.1038/s41467-018-04830-4

Yin, Z., Inhester, L., Thekku Veedu, S., Quevedo, W., Pietzsch, A., Wernet, P., Groenhof, G., Föhlisch, A., Grubmüller, H. and Techert, S. (2017)
Cationic and Anionic Impact on the Electronic Structure of Liquid Water
J. Phys. Chem. Lett., 8: 3759−3764, DOI:10.1021/acs.jpclett.7b01392

Walczak, M. and Grubmüller, H. (2016)
BASDet:Bayesian approach(es) for structure determination from single molecule X-ray diffraction images
Computer Physics Communications, 201: 159-166

Wiederschein, F., Vöhringer-Martinez, E., Beinsen, A., Postberg, F., Schmidt, J., Srama, R., Stolz, F., Grubmüller, H. and Abel, B. (2015)
Charge separation and isolation in strong water droplet impacts
Phys.Chem.Chem.Phys., 17: 6858, DOI:10.1039/c4cp05618c

Walczak, M. (2014)
Bayesian structure reconstruction from single molecule X-ray scattering data
Georg-August University Göttingen,

Walczak, M. and Grubmüller, H. (2014)
Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images
Phys. Rev. E, 90(2): 022714, DOI:10.1103/PhysRevE.90.022714

Groenhof, G. (2013)
Introduction to QM/MM Simulations
Monticelli, L. & Salonen, E.Biomolecular SimulationsChapter3Humana Press,, 924, DOI:10.1007/978-1-62703-017-5

Hoefling, M. and Grubmüller, H. (2013)
In silico FRET from simulated dye dynamics
Comput. Phys. Commun.Elsevier B.V.,, 184(3): 841-852, DOI:10.1016/j.cpc.2012.10.018

Inhester, L. (2013)
Auger decay in double core ionized molecules
Georg-August University Göttingen,

Inhester, L., Groenhof, G. and Grubmüller, H. (2013)
Core hole screening and decay rates of double core ionized first row hydrides.
J. Chem. Phys., 138(16): 164304, DOI:10.1063/1.4801660

Inhester, L., Burmeister, C. F., Groenhof, G. and Grubmüller, H. (2012)
Auger spectrum of a water molecule after single and double core ionization.
J. Chem. Phys., 136(14): 144304, DOI:10.1063/1.3700233

van den Bogaart, G., Thutupalli, S., Risselada, J. H., Meyenberg, K., Holt, M., Riedel, D., Diederichsen, U., Herminghaus, S., Grubmüller, H. and Jahn, R. (2011)
Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation.
Nat. Struct. Mol. Biol.Nature Publishing Group,, 18(7): 805-12, DOI:10.1038/nsmb.2061

Boggio-Pasqua, M. and Groenhof, G. (2011)
Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group.
J. Phys. Chem. B, 115(21): 7021-8, DOI:10.1021/jp108977x

Groenhof, G., Schäfer, L. V., Boggio-Pasqua, M., Grubmüller, H. and Robb, M. A. (2008)
Arginine52 controls the photoisomerization process in photoactive yellow protein
Journal of the American Chemical Society, 130: 3250-3251, DOI:10.1021/ja078024u

Puchner, E. M., Alexandrovich, A., Kho, A. L., Hensen, U., Schäfer, L. V., Brandmeier, B., Gräter, F., Grubmüller, H., Gaub, H. E. and Gautel, M. (2008)
Mechanoenzymatics of titin kinase.
Proceedings of the National Academy of Sciences of the United States of America, 105: 13385-13390, DOI:10.1073/pnas.0805034105