Number of items: **32**.

## 2014

Chodera, J. D. and Noé, F.
(2014)
*Markov state models of biomolecular conformational dynamics.*
Curr. Opin. Struct. Biol., 25
.
pp. 135-144.

Mey, A.S.J.S. and Wu, H. and Noé, F.
(2014)
*xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states.*
Phys. Rev. X, 4
(4).
041018.

Nüske, F. and Keller, B. and Pérez-Hernández, G. and Mey, A.S.J.S. and Noé, F.
(2014)
*Variational Approach to Molecular Kinetics.*
J. Chem. Theory Comput., 10
.
pp. 1739-1752.

Prinz, J.-H. and Chodera, J. D. and Noé, F.
(2014)
*Spectral rate theory for two-state kinetics.*
Phys Rev X, 4
.
011020.

Wu, H. and Noé, F.
(2014)
*Optimal estimation of free energies and stationary densities from multiple biased simulations.*
SIAM Multiscale Model. Simul., 12
.
pp. 25-54.

## 2013

Noé, F. and Nüske, F.
(2013)
*A variational approach to modeling slow processes in stochastic dynamical systems.*
SIAM Multiscale Model. Simul., 11
.
pp. 635-655.

Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard
(2013)
*Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein.*
Biophys. J., 104
.
pp. 63-74.

Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F.
(2013)
*Identification of slow molecular order parameters for Markov model construction.*
J. Chem. Phys., 139
.
015102.

Schaller, Christoph
(2013)
*STORMicroscopy: A Mathematical Analysis.*
Masters thesis, FU Berlin.

Schöneberg, J. and Noé, F.
(2013)
*ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments.*
PLoS ONE, 8
.
e74261.
ISSN 1932-6203

Steger, Katrin and Bollmann, Stefan and Noé, F. and Doose, S.
(2013)
*Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale.*
Phys. Chem. Chem. Phys., 15
.
pp. 10435-10445.

Trendelkamp-Schroer, B. and Noé, F.
(2013)
*Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution.*
J. Phys. Chem., 138
.
p. 164113.

## 2012

Faelber, K. and Held, M. and Gao, S. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O.
(2012)
*Structural insights into dynamin-mediated membrane fission.*
Structure, 20
.
1621-1628.

Held, M. and Imhof, P. and Keller, B. and Noé, F.
(2012)
*Modulation of a ligand’s energy landscape and kinetics by the chemical environment.*
J. Phys. Chem. B, 116
.
pp. 13597-13607.

Keller, B. and Prinz, J.-H. and Noé, F.
(2012)
*Markov models and dynamical fingerprints: unraveling the complexity of molecular kinetics.*
Chem. Phys., 396
.
pp. 92-107.

Nüske, F.
(2012)
*A variational approach for conformation dynamics.*
Masters thesis, FU Berlin.

Prinz, J.-H.
(2012)
*Advanced estimation methods for Markov models of dynamical systems.*
PhD thesis, FU Berlin.

Sadiq, S. K. and Noé, F. and de Fabritiis, G.
(2012)
*Kinetic characterization of the critical step in HIV-1 protease maturation.*
Proc. Natl. Acad. Sci. USA, 109
.
pp. 20449-20454.

## 2011

Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch.
(2011)
*Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems.*
J. Chem. Phys., 135
(1).
014112.

Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E.
(2011)
*Markov State Models Based on Milestoning.*
J. Chem. Phys., 134
(20).
p. 204105.

Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F.
(2011)
*Markov models of molecular kinetics: Generation and Validation.*
J. Chem. Phys., 134
.
p. 174105.

Chodera, J. D. and Swope, W. D. and Noé, F. and Prinz, J.-H. and Shirts, M. R. and Pande, V. S.
(2011)
*Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures.*
J. Chem. Phys., 134
(24).
p. 244107.

Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred
(2011)
*An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles.*
J. Chem. Theo. Comput., 7
.
pp. 1032-1044.

Noé, F. and Doose, S. and Daidone, I. and Löllmann, M. and Chodera, J. D. and Sauer, M. and Smith, J. C.
(2011)
*Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.*
Proc. Natl. Acad. Sci. USA, 108
.
pp. 4822-4827.

Prinz, J.-H. and Chodera, J. D. and Pande, V. S. and Swope, W. D. and Smith, J. C. and Noé, F.
(2011)
*Optimal use of data in parallel tempering simulations for the
construction of discrete-state Markov models of biomolecular
dynamics.*
J. Chem. Phys., 134
(24).
p. 244108.

Prinz, J.-H. and Held, M. and Smith, J. C. and Noé, F.
(2011)
*Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes.*
Multiscale Model. Simul., 9
.
pp. 545-567.

Prinz, J.-H. and Keller, B. and Noé, F.
(2011)
*Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables.*
Phys. Chem. Chem. Phys., 13
.
pp. 16912-16927.

Wu, H. and Noé, F.
(2011)
*Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations.*
Phys. Rev. E, 83
(3).
036705.

Wu, H. and Noé, F.
(2011)
*A flat Dirichlet process switching model for Bayesian estimation of hybrid systems.*
Procedia Computer Science, 4
.
pp. 1393-1402.

## 2010

Seibert, Johannes
(2010)
*Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution.*
Masters thesis, FU Berlin.

Kavalar, Martin
(2010)
*Conformational Dynamics of a Peptide Ligand in Solvent and in Complex with a MHC-I Protein.*
Masters thesis, FU Berlin.

Wu, H. and Noé, F.
(2010)
*Probability Distance Based Compression of Hidden Markov Models.*
Multiscale Model. Simul., 8
.
pp. 1838-1861.

This list was generated on **Wed Sep 20 14:44:04 2017 CEST**.