Publications

last updated 2015


Protein Conformational Plasticity and Complex Ligand-Binding Kinetics Explored by Atomistic Simulations and Markov Models
N. Plattner and F. Noé, Nat. Commun., 6, 7653, (2015).

Crystal Structure of the Dynamin Tetramer
T. F. Reubold, K. Faelber, N. Plattner, Y. Posor, K. Ketel, U. Curth, J. Schlegel, R. Anand, D. Manstein, F. Noé, V. Haucke, O. Daumke and S. Eschenburg, Nature, 525, 404-408, (2015).

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
M. K. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Perez-Hernandez, M. Hoffmann, N. Plattner, C. Wehmeyer, J.-H. Prinz, and F. Noé, J. Chem. Theory Comput., 11, 5525-5542, (2015).


Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules
F. H├ędin, N. Plattner, J. D. Doll and M. Meuwly, J. Chem. Theory Comput., 10, 4284-4296, (2014).

The Effect of Classical and Quantum Dynamics on Vibrational Frequency Shifts of H2 in Clathrate Hydrates
N. Plattner and M. Meuwly, J. Chem. Phys., 140, 024311, (2014).


Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping
N. Plattner, J. D. Doll and M. Meuwly, J. Chem. Theory Comput., 9, 4215-4224, (2013).

Projected and Hidden Markov Models for Calculating Kinetics and Metastable States of Complex Molecules
F. Noé, H. Wu, J.-H. Prinz and N. Plattner, J. Chem. Phys., 139, 184114, (2013).


On the Infinite Swapping Limit for Parallel Tempering
P. Dupuis, Y. Liu, N. Plattner and J. D. Doll , SIAM J. Multiscale Model. Simul., 10, 986-1022, (2012).

Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin
N. Plattner and M. Meuwly, Biophys. J., 102, 333-341, (2012).

Structure, Spectroscopy and Dynamics of Layered H2O and CO2 ices
M. W. Lee, N. Plattner and M. Meuwly, Phys. Chem. Chem. Phys., 14, 15464-15474, (2012).

Rare-event sampling: Occupation-based Performance Measures for Parallel Tempering and Infinite Swapping Monte Carlo methods
J. D. Doll, N. Plattner, D. L. Freeman, P. Dupuis and Y. Liu, J. Chem. Phys., 137, 204112, (2012).

Numerical Investigation of the Cumulant Expansion for Fourier Path Integrals
N. Plattner, S. Kunikeev, D.L. Freeman and J.D. Doll, LNCS, 7134, 13-22, (2012).


An Infinite Swapping Approach to the Rare-event Sampling Problem
N. Plattner, J. D. Doll P. Dupuis, Y. Liu, H. Wang and J. E. Gubernatis, J. Chem. Phys., 135, 134111, (2011).


Structural and Spectroscopic Characterization of Mixed Planetary Ices
N. Plattner, M. W. Lee and M. Meuwly, Faraday Discuss., 147, 217-230, (2010).

Spatial Averaging for Small Molecule Diffusion in Condensed Phase Environments
N. Plattner, J. D. Doll and M. Meuwly, J. Chem. Phys., 133, 044506, (2010).


Higher Order Multipole Moments for Molecular Dynamics Simulations
N. Plattner and M. Meuwly, J. Mol. Model., 15, 687-694, (2009).

Application of Multipolar Charge Models and Molecular Dynamics Simulations to Study Stark Shifts in Non-Uniform Electric Fields
M. Devereux, N. Plattner and M. Meuwly, J. Phys. Chem. A, 113, 13199-12909, (2009).

A Spatial Averaging Approach to Rare-Event Sampling
J. D. Doll, J. E. Gubernatis, N. Plattner, M. Meuwly, P. Dupuis and H. Wang, J. Chem. Phys., 131, 104107, (2009).


The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin
N. Plattner and M. Meuwly, Biophys. J., 94, 2505-2515, (2008).

Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry
N. Plattner and M. Meuwly, ChemPhysChem, 9, 1271-1277, (2008).

MD Simulations using Distributed Multipole Electrostatics: Structural and Spectroscopic Properties of CO- and Methane-Containing Clathrates
N. Plattner, T. Bandi, J.D. Doll, D.L. Freeman and M. Meuwly, Mol. Phys., 106, 1675-1684, (2008).