946
eng
reportzib
0
2006-12-19
2006-12-19
--
Efficient Sampling of the Stationary Distribution of Metastable Dynamical Systems
In this article we aim at an efficient sampling of the stationary distribution of dynamical systems in the presence of metastabilities. In the past decade many sophisticated algorithms have been inven ted in this field. We do not want to simply add a further one. We address the problem that one has applied a sampling algorithm for a dynamical system many times. This leads to different samplings which more or less represent the stationary distribution partially very well, but which are still far away from ergodicity or from the global stationary distribution. We will show how these samplings can be joined together in order to get one global sampling of the stationary distribution.
07-03
946
urn:nbn:de:0297-zib-9467
Marcus Weber
Susanna Kube
Alexander Riemer
Alexander Bujotzek
ZIB-Report
07-03
eng
uncontrolled
dynamical systems
eng
uncontrolled
stationary distribution
eng
uncontrolled
rare events
eng
uncontrolled
metastability
eng
uncontrolled
cluster analysis
Informatik, Informationswissenschaft, allgemeine Werke
Computational Markov chains
Numerical methods (Monte Carlo, series resummation, etc.) [See also 65-XX, 81T80]
ZIB Allgemein
Röblitz, Susanna
Weber, Marcus
https://opus4.kobv.de/opus4-zib/files/946/ZR-07-03.pdf
2646
2012
2012
eng
054111
5
137
article
0
--
--
--
Quantifying the rebinding effect in multivalent chemical ligand-receptor systems
J. Chem. Phys.
yes
Marcus Weber
Alexander Bujotzek
Rainer Haag
Numerical Mathematics
Computational Molecular Design
Weber, Marcus
EyeTracking
Matheon-A19
SFB765-C2
4650
2013
eng
707
715
4
8
article
0
--
--
--
Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor
ACS Chem. Biol.
yes
http://pubs.acs.org/doi/abs/10.1021/cb3006243
Min Shan
Adam Nielsen
Kathryn E. Carlson
Alexander Bujotzek
Anja Wellner
Ronald Gust
Marcus Weber
John A. Katzenellenbogen
Rainer Haag
Numerical Mathematics
Computational Molecular Design
Weber, Marcus
2647
2012
eng
141
154
89
conferenceobject
Springer
0
--
--
--
A meshless discretization method for Markov state models applied to explicit water peptide folding simulations
Meshfree Methods for Partial Differential Equations VI
Lecture Notes in Computational Science and Engineering
yes
Konstantin Fackeldey
Alexander Bujotzek
Marcus Weber
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
Weber, Marcus
Matheon-A19
SFB765-C2
6503
2014
eng
309
313
19
conferenceobject
0
--
--
--
Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach
In this article a method to improve the precision of the classical molecular dynamics force field by solving an approximation problem with scattered quantum mechanical data is presented. This novel technique is based on two steps. In the first step a partition of unity scheme is used for partitioning the state space by meshfree basis functions. As a consequence the potential can be localized for each basis function. In a second step, for one state in each meshfree basis function, the precise QM-based charges are computed. These local QM-based charges are then used, to optimize the local potential function. The performance of this method is shown for the alanine tripeptide.
Progress in Industrial Mathematics at ECMI 2012
10.1007/978-3-319-05365-3_42
Mathematics in Industry
Konstantin Fackeldey
Konstantin Fackeldey
Alexander Bujotzek
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
SFB765-C2
4658
2014
deu
781
804
3
52
article
0
--
--
--
ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling
Journal of Mathematical Chemistry
10.1007/s10910-013-0265-1
yes
urn:nbn:de:0297-zib-42570
Alexander Bujotzek
Adam Nielsen
Ole Schütt
Adam Nielsen
Konstantin Fackeldey
Marcus Weber
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
Weber, Marcus
BMS-Nielsen
Matheon-A19
MIP_FORMATION
NAMPAR
Salsa-Klimm
SFB1114-A5
SFB765-C2
4257
eng
reportzib
0
2013-09-27
2013-09-27
--
Efficient Conformational Analysis by Partition-of-Unity Coupling
Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.
Math Chem
1438-0064
urn:nbn:de:0297-zib-42570
Alexander Bujotzek
Konstantin Fackeldey
Ole Schütt
Adam Nielsen
Konstantin Fackeldey
Marcus Weber
ZIB-Report
13-58
eng
uncontrolled
Markov State Models
eng
uncontrolled
Meshfree
eng
uncontrolled
Molecular Simulation
eng
uncontrolled
Partition of Unity
MATHEMATICAL SOFTWARE
Markov processes (NEW)
General theory and mathematical aspects
Markov processes
Computational methods
Numerical Mathematics
Computational Molecular Design
Fackeldey, Konstantin
Weber, Marcus
BMS-Nielsen
Matheon-A19
MIP_FORMATION
NAMPAR
Salsa-Klimm
SFB1114-A5
SFB765-C2
https://opus4.kobv.de/opus4-zib/files/4257/MolPyPUM.pdf
4965
2013
eng
doctoralthesis
0
--
--
--
Molecular Simulation of Multivalent Ligand-Receptor Systems
http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094981
Marcus Weber
Alexander Bujotzek
Marcus Weber
Numerical Mathematics
Computational Molecular Design
Matheon-A19
SFB765-C2
Freie Universität Berlin