2019

EncoderMap(II): Visualizing Important Molecular Motions with Improved Generation of Protein Conformations, T. Lemke, A. Berg, A. Jain, C.Peter, J. Chem. Inf. Model., 2019. [doi]

Anisotropic Extended-Chain Polymer Nanocrystals, C. Rank, M. Häußler, P. Rathenow, M. King, C. Globisch, C. Peter, S. Mecking, Macromolecules 52 (16), 6142−6148, 2019. [doi]

Simulating and analysing configurational landscapes of protein–protein contact formation, A. Berg, C. Peter, Interface Focus 9 (3), 20180062, 2019. [doi]

Coarse-Grained Simulation of CaCO3 Aggregation and Crystallization Made Possible by Nonbonded Three-Body Interactions, M. King, S. Pasler, C. Peter, JPCC 123 (5), 3152-3160, 2019. [doi]

EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations,T. Lemke, C. Peter, JCTC 15 (2), 1209-1215, 2019. [doi]

Coarse-Grained Simulations of Peptide Nanoparticle Formation: Role of Local Structure and Nonbonded Interactions, A. Jain, C. Globisch, S. Verma, C. Peter, JCTC 15 (2), 1453-1462, 2019. [doi]

2018

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers, A. Berg, O. Kukharenko, M. Scheffner, C. Peter, PLOS Comput. Biol., 14(11): e1006589, 2018. [doi]

Efficient sampling and characterization of free energy landscapes of ion-peptide systems, T. Lemke, C. Peter, O. Kukharenko, J. Chem. Theory Comput , 14 (11), 5476, 2018. [doi]

Snapshots of a modified nucleotide moving through the confines of a DNA polymerase, H. M. Kropp, S. L. Dürr, C. Peter, K. Diederichs, A. Marx, PNAS,  115 (40), 9992 , 2018. [doi]

The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation, A. Aichem, S. Anders, N. Catone, P. Rößler, S. Stotz, A. Berg, R. Schwab, S. Scheuermann, J. Bialas, M. C. Schütz-Stoffregen, G. Schmidtke, C. Peter, M. Groettrup, S. Wiesner, Nature Communications,  9 (1), 3321 , 2018. [doi]

2017

Neural network based prediction of conformational free energies - a new route towards coarse-grained simulation models, T. Lemke and C. Peter, J. Chem. Theory Comput.,  13 (12), 6213-6221 , 2017. [doi]

Soluble oligomeric nucleants: simulations of chain length, binding strength, and volume fraction effects, G.G. Poon, T. Lemke, C. Peter, V. Molinero, and B. Peters, J. Phys. Chem. Lett.,  8 (23), 5815-5820 , 2017. [doi]

Evaluation and Optimisation of Interface Force Fields for Water on Gold Surfaces, A. Berg, C. Peter, and K. Johnston, J. Chem. Theory Comput., 13 (11), 5610-5623 , 2017. [doi]

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales, B. Mukherjee, C. Peter, and K. Kremer, The Journal of Chemical Physics, 147, 114501 , 2017. [doi]

Combining Experimental and Simulation Techniques to Understand Morphology Control in Pentapeptide Nanostructures, N. K. Mishra, A. Jain, C. Peter, and S. Verma, J. Phys. Chem. B, , 121 (34),  8155–8161 , 2017. [doi]

Multiskalensimulation von Bio- und Biomaterialsystemen (Trendberichte 2016 - Theoretische Chemie 2016 ),  C. Peter,  Nachrichten aus der Chemie, 65, March 2017, wwww.gdch.de/nachrichten

2016

Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction, M. A. Hanebuth, R. Kityk, S. J. Fries, A. Jain, A. Kriel, V. Albanese, T. Frickey, C. Peter, M. P. Mayer, J. Frydman, and E. Deuerling, Nat Commun.  7, 13695, 2016.[doi]

Representing environment-induced helix-coil transitions in a coarse grained peptide model, C. Dalgicdir, C. Globisch, M. Sayar & C. Peter, Eur Phys J Special Topics, 225 (8-9), 1463-1481, 2016.[doi]

Breaking a virus: Identifying molecular level failure modes of a viral capsid by multiscale modeling, V. Krishnamani, C. Globisch, C. Peter & M. Deserno, Eur Phys J Special Topics, 225 (8-9), 1757-1774, 2016.[doi]

Modern simulation approaches in soft matter science: From fundamental understanding to industrial applications, L. Delle Site, M. Deserno, B. Dünweg, C. Holm, C. Peter & H. Pleiner, Eur Phys J Special Topics, 225 (8-9), 1317-1321, 2016. [doi]

Systematic comparison of model polymer nanocomposite mechanics, S. Xiao, C. Peter & K. Kremer, Bioinspiration & Biomimetics, 11, 5, 2016.[doi]

Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides, O. Kukharenko, K. Sawade, J. Steuer & C. Peter, J Chem Theory Comput, 12 (10), 4726, 2016.[doi]

2015

EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Lables, M.J. Schmidt, A. Fedoseev, D. Bücker, J. Borbas, C. Peter, M. Drescher & D. Summerer, ACS Chem Biol, 10, 2764-2771, 2015. [doi]

Relative resolution: A hybrid formalism for fluid mixtures, A. Chaimovich, C. Peter & K. Kremer, J Chem Phys, 143, 243107, 2015.[doi]

Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems, A. Debnath, S. Wiegand, H. Paulsen, K. Kremer & C. Peter, Phys Chem Chem Phys, 17, 22054-22063, 2015.[doi]

Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces, C. Dalgicdir, C. Globisch, C. Peter & M. Sayar, PLoS Comput Biol, 11, e1004328, 2015.[doi]

Molecular simulation of oligo-glutamates in a calcium-rich aqueous solution: insights into peptide-induced polymorph selection, J. Kahlen, C. Peter & D. Donadio, CrystEngComm, 17, 6863-6867, 2015.[doi]

2014

Molecular Dynamics Simulations of Peptides at the Air–Water Interface: Influencing Factors on Peptide-Templated Mineralization, A. Jain, M. Jochum & C. Pete, Langmuir, 30, 15486–15495, 2014.[doi]

Sticky water surfaces: Helix–coil transitions suppressed in a cell-penetrating peptide at the air-water interface, D. Schach et al., J Chem Phys, 141, 22D517, 2014.[doi]

Computer Simulations of Soft Matter: Linking the Scales, R. Potestio, C. Peter & K. Kremer, Entropy, 16, 4199–4245, 2014. [doi]

Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields, J. Kahlen, L. Salimi, M. Sulpizi, C. Peter, D. Donadio, J Phys Chem B, 118, 3960-3972, 2014. [doi]

2013

Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications, M. Deserno, K. Kremer, H. Paulsen, C. Peter, F. Schmid, Adv Polym Sci, Springer Verlag, 2013. [doi]

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition, C. Dalgicdir, O. Sensoy, C. Peter, M. Sayar, J Chem Phys 139, 234115, 2013. [doi]

Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation, C. Globisch, V. Krishnamani, M. Deserno, C. Peter, PLoS ONE, 8, e60582, 2013. [doi]

Dual translocation pathways in smectic liquid crystals facilitated by molecular flexibility, B. Mukherjee, C. Peter, K. Kremer, Physical Review E, 88, 010502(R), 2013. [doi]

Understanding the Control of Mineralization by Polyelectrolyte Additives: Simulation of Preferential Binding to Calcite Surfaces, J.W. Shen, C. Li, N.F.A. van der Vegt, C. Peter, J Phys Chem C, 117, 6904-6913, 2013. [doi]

2012

Structure-based coarse-graining in liquid slabs, M. Jochum, D. Andrienko, K. Kremer, C. Peter, J Chem Phys, 137, 064102, 2012. [doi]


Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26–49: β-Barrel Stability of the Hexamer and Pentamer Geometries, T, Bereau, C. Globisch, M. Deserno, C. Peter, J Chem Theory Comput, 8, 3750–3758, 2012. [doi]

Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions, B. Mukherjee, L. Delle Site, K. Kremer, C. Peter, J Phys Chem B, 116, 8474-8484, 2012. [doi]

A Chemically Accurate Implicit-Solvent Coarse-Grained Model for Polystyrenesulfonate Solutions, C. Li, J.-W. Shen, C. Peter, N.F.A. van der Vegt, Macromolecules, 45, 2551, 2012. [doi]

Multiscale simulation of peptides: Consistent conformational sampling in atomistic and coarse-grained models, O. Bezkorovaynaya, A. Lukyanov, K. Kremer, C. Peter, J Comp Chem, 33, 937, 2012. [doi]

Soft Matter, Fundamentals and Coarse Graining Strategies, C. Peter, in "Hierarchical Methods for Dynamics in Complex Molecluar Systems" eds. J. Grotendorst, G. Sutmann, G. Gompper, Norbert Attig, Stefan Blügel, Dominik Marx, IAS Series, Forschungszentrum Jülich, 10, 195, 2012. [pdf]

2011

Transferability of coarse grained potentials:implicit solvent models for hydrated ions, J.-W. Shen, C. Li, N.F.A. van der Vegt, C. Peter, J. Chem. Theory Comput., 7, 1916, 2011 [doi]

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models, O. Engin, A. Villa, C. Peter, M Sayar, Macromol. Theory Simul., 20, 451, 2011 [doi]

Hybrid Simulations: Combining Atomistic and Coarse-Grained Force Fields using Virtual Sites, A.J. Rzepiela, M. Louhivuori, C. Peter, and S.J. Marrink, Phys. Chem. Chem. Phys., 13, 10437, 2011 [doi]

Multiscale Modelling of Mesoscopic Phenomena triggered by Quantum Events: Light-Driven Azo-Materials and Beyond, M. Böckmann, D. Marx, C. Peter, L. Delle Site, K. Kremer, N.L. Doltsinis, Phys. Chem. Chem. Phys., 13, 7604, 2011 [doi]

2010

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water, A. Villa, C. Peter, N.F.A. van der Vegt, J. Chem. Theory Comput., 6, 2434, 2010 [doi]

Multiscale simulation of soft matter systems, C. Peter, K. Kremer, Faraday Discuss., 144, 9, 2010 [doi]

2009

Multiskalensimulationen in der Materialwissenschaft, C. Peter, K. Kremer, Natur und Geist (Forschungsmagazin der Uni Mainz), 25, 14, 2009 [pdf]

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back, C. Peter, K. Kremer, Soft Matter, 5, 4357, 2009 [doi]

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model, A. Villa, N.F.A. van der Vegt, C. Peter, Phys. Chem. Chem. Phys., 11, 2068, 2009 [doi] 

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation, A. Villa, C. Peter, N.F.A. van der Vegt, Phys. Chem. Chem. Phys., 11, 2077, 2009 [doi]

Soft Matter, Fundamentals and Coarse Graining Strategies, C. Peter, K. Kremer, in "Multiscale Simulation Methods in Molecular Sciences" eds. Johannes Grotendorst, Norbert Attig, Stefan Blügel, Dominik Marx, Forschungszentrum Jülich, 42, 337, 2009 [pdf]

2008

Structure-based coarse- and fine-graining in soft matter simulations, N.F.A. van der Vegt, C. Peter, K.Kremer, in Coarse-Graining of Condensed Phase and Biomolecular Systems, ed. G.A. Voth, Chapman and Hall/CRC Press, 2008

Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal, C. Peter, L. Delle Site, K. Kremer, Soft Matter, 4, 859-869, 2008 [doi]

Modeling Solubilities of Additives in Polymer Microstructures: Single Step Perturbation Method based on a Soft-Cavity Reference State, T. Ozal, C. Peter, B. Hess, N.F.A. van der Vegt, Macromolecules, 41, 5055-5061, 2008 [doi]

Fast-growth thermodynamic integration: Calculating excess chemical potentials of additive molecules in polymer microstructures, B. Hess, C. Peter, T. Ozal, N.F.A. van der Vegt, Macromolecules, 41, 2283-2289, 2008 [doi]

2007

An atomistic force field for azobenzene compounds adapted for QM/MM simulations with applications to liquids and liquid crystals, M. Böckmann, C. Peter, L. Delle Site, N.L. Doltsinis, K. Kremer, D. Marx, J. Chem. Theory Comput., 3, 1789-1802, 2007 [doi]

Solvent Reorganization Contributions in Solute Transfer Thermodynamics: Inferences from the Solvent Equation of State, C. Peter, N.F.A. van der Vegt, J. Phys. Chem. B., 111, 7836-7842, 2007 [doi]

2005

Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation, S.-T. D. Hsu, C. Peter, W. F. van Gunsteren, A. M. J. J. Bonvin, Biophys. J., 88, 15-24, 2005 [doi: 10.1529/biophysj.104.044933]

Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations, C. Peter, G. Hummer, Biophys. J.89, 2222-2234, 2005 [doi]

The GROMOS software for biomolecular simulation: GROMOS05, M. Christen, P.H. Hunenberger, D. Bakowies, R. Baron, R. Burgi, D.P. Geerke, T.N. Heinz, M.A. Kastenholz, V. Krautler, C. Oostenbrink, C. Peter, D. Trzesniak, W.F. van Gunsteren, J. Comp. Chem., 26, 1719-1751, 2005

2004

Estimating entropies from molecular dynamics simulations, C. Peter, C. Oostenbrink, A. van Dorp und W.F. van Gunsteren, J. Chem. Phys., 120, 2652-2661, 2004

2003

A fast-Fourier-transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: algorithm and application to ionic solvation and ion-ion interaction, C. Peter, W.F. van Gunsteren, P.H. Hünenberger, J. Chem. Phys., 119, 12205-12223, 2003

Influence of cutoff truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study, M. Bergdorf, C. Peter, P.H. Hünenberger, J. Chem. Phys., 119, 9129-9144, 2003

Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra?, C. Peter, M. Rueping, H.J. Wörner, B. Jaun, D. Seebach, W.F. van Gunsteren, Chem. Eur. J., 9, 5838-5849, 2003

A critical analysis of various aspects of biomolecular simulation: from electrostatic forces, NMR spectra, and entropy to peptide folding, C. Peter, Dissertation, Naturwissenschaften ETH Zurich, Nr. 15160, 2003

Phase Behavior of n-Alkyl-Substituted Polysilanes, C. Müller, C. Peter, H. Frey, C. Schmidt, in Silicon Chemistry: From the Atom to Extended Systems, eds. P. Jutzi, and U. Schubert, Wiley-VCh, Weinheim, 2003

2002

The Unfolded State of Peptides, X. Daura, A. Glättli, P. Gee, C. Peter, W.F. van Gunsteren, Adv. Prot. Chem., 62, 341-360, 2002

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides, K.A. Feenstra, C. Peter, R.M. Scheek, W.F. van Gunsteren und A.E. Mark, J. Biomol. NMR, 23, 181 - 194, 2002

Solving the Poisson equation for solute-solvent systems using fast Fourier transforms, C. Peter, W.F. van Gunsteren, P.H. Hünenberger, J. Chem. Phys., 116, 7434-7451, 2002

Solitons and production of defects in flow-aligning nematic liquid crystals under simple shear flow, Y.L. Yang, K.F. Luo, C. Schmidt, C. Peter, Prog. Natl. Sci., 12, 188-197, 2002

2001

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations, C. Peter, X. Daura, W.F. van Gunsteren, J. Biomol. NMR, 20, 297-310, 2001

Molecular Dynamics Simulation of Biomolecular Systems, W.F. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glättli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares, H. Yu, CHIMIA, 55, 856-860, 2001

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering and visualization, F.A. Hamprecht, C. Peter, X. Daura, W. Thiel, W.F. van Gunsteren, J. Chem. Phys., 144, 2079-2089, 2001

Reply to the comment on the communication by van Gunsteren et al., W.F. van Gunsteren, R. Bürgi, C. Peter, X. Daura, Angew. Chemie Intl. Ed. , 40, 4616-4618, 2001

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State, W.F. van Gunsteren, R. Bürgi, C. Peter, X. Daura , Angew. Chemie Intl. Ed., 40, 351-355, 2001

2000

Peptides of Aminoxy Acids: a Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions, C. Peter, X. Daura, W.F. van Gunsteren, J. Am. Chem. Soc., 122, 7461-7466, 2000