Browse by Projects

B

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355

D

Donati, Luca and Weber, Marcus and Keller, Bettina (2022) A review of Girsanov reweighting and of square root approximation for building molecular Markov state models. J. Math. Phys., 63 (12). pp. 1-22.

Donati, Luca and Weber, Marcus and Keller, Bettina G. (2021) Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux. J. Phys.: Condens. Matter, 33 . pp. 1-15.

Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X

Donati, Luca and Keller, Bettina G. (2018) Girsanov reweighting for metadynamics simulations. J. Chem. Phys. 149, 149 . pp. 1-16.

Donati, L. and Keller, B. (2018) Girsanov reweighting for metadynamics simulations. Journal of Chemical Physics, 149 (7). 072335. ISSN 0021-9606

Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. Journal of Chemical Physics, 146 (24). p. 244112. ISSN 0021-9606

F

Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M. (2019) From Metastable to Coherent Sets – time-discretization schemes. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (1). 012101. ISSN 1054-1500 (print); 1089-7682 (online)

G

Ghysbrecht, Simon and Keller, Bettina G. (2024) Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. Journal of Computational Chemistry, 45 (16). pp. 1317-1427.

H

Hassan, Irtaza and Ferraro, Federica and Imhof, Petra (2021) Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021, 26 (8). pp. 1-24.

Hartmann, C. and Neureither, L. and Sharma, U. (2020) Coarse-graining of non-reversible stochastic differential equations: quantitative results and connections to averaging. SIAM Journal on Mathematical Analysis, 52 (3). pp. 2689-2733.

Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2020) Coarse-graining of non-reversible stochasticdifferential equations: quantitative results and connections to averaging. SIAM Journal on Numerical Analysis, 52 (3). pp. 2689-2733. ISSN 0036-1429

Hartmann, C. and Schütte, Ch. and Zhang, W. (2019) Jarzysnki equality, fluctuation theorems and variance reduction: Mathematical analysis and numerical algorithms. J. Stat. Phys., 175 (6). pp. 1214-1261. ISSN 0022-4715; ESSN: 1572-9613

Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P. (2018) The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation. Chem. Phys. Lett. . pp. 1-26. ISSN 0009-2614

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355

K

Keller, Bettina G. and Bolhuis, Peter G. (2024) Dynamical Reweighting for Biased Rare Event Simulations. Annual Review of Physical Chemistry, 75 (1). pp. 137-162.

Kieninger, Stefanie and Keller, Bettina (2022) GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J. Chem. Theory Comput., 18 (10).

Kieninger, S. and Keller, B. (2021) Path probability ratios for Langevin dynamics—Exact and approximate. The Journal of Chemical Physics, 154 . pp. 1-21.

Kieninge, Stefanie and Donati, Luca and Keller, Bettina (2020) Dynamical reweighting methods for Markov models. Current Opinion in Structural Biology, 61 . pp. 124-131. ISSN 0959-440X

Keller, B.G. and Aleksic, S. and Donati, L. (2019) Markov State Models in drug design. In: Biomolecular Simulations in Structure-based Drug Discovery. Methods and Principles in Medicinal Chemistry, 75 . Wiley-Interscience, Weinheim, pp. 67-86. ISBN 978-3-527-34265-5

L

Lemke, O. and Keller, B.G. (2016) Density-based cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104).

M

Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U. (2017) Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat. Chem. Biol., 13 . pp. 1172-1178.

N

Neureither, L. and Hartmann, C. (2019) Time scales and exponential trends to equilibrium: Gaussian model problems. In: Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017. Springer Proceedings in Mathematics & Statistics, 282 . Springer, pp. 391-410. ISBN 978-3-030-15095-2

Q

Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 1-19. ISSN 1064-8275 (print) (In Press)

S

Sechi, Renata and Sikorski, Alexander and Weber, Marcus (2021) Estimation of the Koopman Generator by Newton's Extrapolation. Multiscale Modeling & Simulation, 19 (2). pp. 758-774.

Stensitzki, T. and Yang, Y. and Kozich, V. and Ahmed, A.A. and Kössl, F. and Kühn, O. and Heyne, K. (2018) Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation. Nature Chemistry, 10 . pp. 126-131.

T

Trung, Minh Nguyen and Kieninger, Stefanie and Fandi, Zeinab and Qiu, Danye and Liu, Guizhen and Mehendale, Neelay K. and Saiardi, Adolfo and Jessen, Henning and Keller, Bettina and Fiedler, Dorothea (2022) Stable Isotopomers of myo-Inositol Uncover a Complex MINPP1-Dependent Inositol Phosphate Network. ACS Cent. Sci., 8 (12). pp. 1683-1694.

V

Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590.

W

Witek, J. and Wang, S. and Schroeder, B. and Lingwood, R. and Dounas, A. and Roth, H.-J. and Fouché, M. and Blatter, M. and Lemke, O. and Keller, B. and Riniker, S. (2019) Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model., 59 (1). pp. 294-308. ISSN 1549-9596, ESSN: 1549-960X

Z

Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365-394. ISSN 1359-6640