Items where Subject is "Physical Sciences > Chemistry"

Article

Agarwal, A. and Wang, H. and Schütte, Ch. and Delle Site, L. (2014) Chemical potential of liquids and mixtures via Adaptive Resolution Simulation. Journal of Chemical Physics, 141 (3). ISSN 0021-9606

Doerr, S. and Harvey, M. J. and Noé, F. and De Fabritiis, G. (2016) HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput., 12 . pp. 1845-1852.

Doll, J. D. and Plattner, N. and Freeman, D. L. and Liu, Y. and Dupuis, P. (2012) Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods. The Journal of Chemical Physics, 137 (20). p. 204112. ISSN 00219606

Dommert, F. and Wendler, K. and Berger, R. and Delle Site, L. and Holm, C. (2012) Force fields for studying structure and dynamics of imidazolium based ionic liquids - a critical review of recent developments. ChemPhysChem, 13 . p. 1625.

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

Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online)

Lee, M. W. and Plattner, N. and Meuwly, M. (2012) Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Physical Chemistry Chemical Physics, 14 (44). pp. 15464-15474. ISSN 1463-9076

Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2018) VAMPnets: Deep learning of molecular kinetics. Nat. Comm., 9 . p. 5.

Noé, F. and Clementi, C. (2017) Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Curr. Opin. Struct. Biol., 43 . pp. 141-147.

Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104.

Olsson, Simon and Noé, F. (2017) Mechanistic models of chemical exchange induced relaxation in protein NMR. J. Am. Chem. Soc., 139 . pp. 200-210.

Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270.

Paul, F. and Noé, F. and Weikl, T. (2018) Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B .

Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095).

Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297

Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934.

Plattner, N. and Bandi, T. and Doll, J. D. and Freeman, D. and Meuwly, M. (2008) MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates. Molecular Physics, 106 (12). pp. 1675-1684. ISSN 0026-8976

Plattner, N. and Doll, J. D. and Dupuis, P. and Wang, H. and Liu, Y. and Gubernatis, J. E. (2011) An infinite swapping approach to the rare-event sampling problem. The Journal of Chemical Physics, 135 (13). p. 134111. ISSN 00219606

Plattner, N. and Lee, M. W. and Meuwly, M. (2010) Structural and spectroscopic characterization of mixed planetary ices. Faraday discussions, 147 . 217-230; discussion 251. ISSN 1359-6640

Plattner, N. and Meuwly, M. (2012) Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin. Biophysical Journal, 102 (2). pp. 333-341. ISSN 00063495

Plattner, N. and Doerr, S. and De Fabritiis, G. and Noé, F. (2017) Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat. Chem., 9 . pp. 1005-1011.

Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690

Schror, M. and Mey, A.S.J.S. and Noé, F. and MacPhee, C. (2015) Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. J. Chem. Phys. Lett., 6 . pp. 1076-1081.

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.

Wieczorek, M. and Sticht, J. and Stolzenberg, S. and Günther, S. and Wehmeyer, C. and El Habre, Z. and Àlvaro-Benito, M. and Noé, F. and Freund, C. (2016) MHC class II complexes sample intermediate states along the peptide exchange pathway. Nature Communications, 7 . p. 13224.

Book Section

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