Zobrazeno 1 - 10
of 329
pro vyhledávání: '"Keller, Bettina"'
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studyin
Externí odkaz:
http://arxiv.org/abs/2312.12948
Autor:
Ghysbrecht, Simon, Keller, Bettina G.
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accura
Externí odkaz:
http://arxiv.org/abs/2312.10520
Autor:
Heinz, Frederick, Proksch, Jonas, Schmidt, Robert F., Koksch, Beate, Gradzielski, Michael, Keller, Bettina G.
Biocompatible and functionalizable hydrogels have a wide range of (potential) medicinal applications. In contrast to conventional hydrogels formed by interconnected or interlocked polymer chains, self-assembled hydrogels form from small building bloc
Externí odkaz:
http://arxiv.org/abs/2310.09142
The critical step in a molecular process is often a rare-event and has to be simulated by an enhanced sampling protocol. Recovering accurate dynamical estimates from such biased simulation is challenging. Girsanov reweighting is a method to reweight
Externí odkaz:
http://arxiv.org/abs/2303.14696
We review clustering as an analysis tool and the underlying concepts from an introductory perspective. What is clustering and how can clusterings be realised programmatically? How can data be represented and prepared for a clustering task? And how ca
Externí odkaz:
http://arxiv.org/abs/2212.01248
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is heavily limited
Externí odkaz:
http://arxiv.org/abs/2211.00566
Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential $\tilde{V}(x)$ from trajectories that have been generated at a different potential $V(x)$. In this article, we present Girsano
Externí odkaz:
http://arxiv.org/abs/2209.10544
Publikováno v:
J. Chem. Theory Comput. (2022)
Two of the most widely used Langevin integrators for molecular dynamics simulations are the GROMACS Stochastic Dynamics (GSD) integrator and the splitting method BAOAB. In this letter, we show that the GROMACS Stochastic Dynamics integrator is equal
Externí odkaz:
http://arxiv.org/abs/2204.02105
Autor:
Loges, Anselm, Manni, Marco, Louvel, Marion, Wilke, Max, Jahn, Sandro, Welter, Edmund, Borchert, Manuela, Qiao, Shilei, Klemme, Stephan, Keller, Bettina G., John, Timm
Publikováno v:
In Geochimica et Cosmochimica Acta 1 February 2024 366:167-181
Publikováno v:
J. Chem. Phys, 154, (2021), 094102
Path reweighting is a principally exact method to estimate dynamic properties from biased simulations - provided that the path probability ratio matches the stochastic integrator used in the simulation. Previously reported path probability ratios mat
Externí odkaz:
http://arxiv.org/abs/2011.12849