Recent publications

2012 :

• Impact of anisotropic atomic motions in proteins on powder-averaged incoherent neutron scattering intensities G.R. Kneller and G. Chevrot, J Chem Phys 137, 225101 (2012) (PDF).

• Screwfit: Combining localization and description of protein secondary structure. P. Calligari and G. R. Kneller. Acta Crystallographica D, 68(12):1690–1693, 2012 (PDF) (Editor's link)

• nMoldyn 3: A parallel program package for spectroscopy-oriented analysis of Molecular Dynamics simulations.
  K. Hinsen, E. Pellegrini,  S. Stachura, and G. R. Kneller, J. Comp. Chem. (2012, in press) (PDF)

• A minimal model for the diffusion-relaxation backbone dynamics of proteins.
  G. R. Kneller, K. Hinsen and P. Calligari, J. Chem. Phys.  136  191101  (2012) (PDF)

• Functional domain motions in proteins on the 1 - 100 ns timescale: Comparison of neutron spin echo spectroscopy of phosphoglycerate kinase with molecular dynamics simulation.
  N. Smolin, R. Biehl, G. R. Kneller, D. Richter, J. C. Smith, Biophys. J.  102  1108-1117 (2012) (PDF)

2011 :

• Consistent picture of lateral subdiffusion in lipid bilayers: molecular dynamics simulation and exact results.
  G. R. Kneller, K. Baczynski and M. Pasenkiewicz-Gierula, J. Chem. Phys.  135  141105  (2011) (PDF)
  

• Generalized Kubo relations and conditions for anomalous diffusion: Physical insights from a mathematical theorem.
  G. R. Kneller, J. Chem. Phys.  134  224106  (2011) (PDF)
  

• From NMR relaxation to fractional Brownian dynamics in proteins : Results from a virtual experiment.
  P. Calligari, V. Calandrini, G. R. Kneller and D. Abergel, J. Phys. Chem. B.  115, 12370--12379 (2011) (PDF)
  

• Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules.
  G. Chevrot, P. Calligari, K. Hinsen and G. R. Kneller, J. Chem. Phys.  135  084110  (2011) (PDF)

• nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions.
  V. Calandrini, E. Pellegrini, P. Calligari, K. Hinsen and G. R. Kneller, Collection SFN 12, 201--232 (2011) (PDF)

2010 :

• Fractional protein dynamics seen by NMR spectroscopy: Relating molecular dynamics simulation and experiment
  V. Calandrini and D. Abergel and G. R. Kneller, J. Chem. Phys.  133  145101  (2010) (PDF)
  

• Self-similar dynamics of proteins under hydrostatic pressure - computer simulations and experiments
  G. R. Kneller and V. Calandrini, Biochimica et Biophysica Acta 1804  56-62  (2010) (PDF)

• Comment on ``Fast Determination of the Optimal Rotational Matrix for Macromolecular Superpositions'' [J. Comp. Chem. 31, 1561 (2010)].
  G. R. Kneller, J. Comp. Chem. 32,  183-184 (2011), published online Aug. 2010. (PDF)
  

2009 :

• A least-constraint principle for population dynamics and reaction kinetics: Modeling entropy-controlled chemical hypercycles
  D. Horvath and G. R. Kneller, J. Chem. Phys.  131, 171101 (2009) (PDF)

• Group-1 and group-2 neuraminidases: Screw motion analysis reveals fine structural changes induced by binding with oseltamivir.
  P. A. Calligari, G. R. Kneller, A. Giansanti, P. Ascenzi, A. Porrello and A. Bocedi, Biophys. Chem.  141  117-123 (2009) (PDF)

• Rigid Molecule Approximation in Memory Function-based Models for Molecular Liquids: Application to Liquid Water
  V. Calandrini, G. Sutmann, A. Deriu and G. R. Kneller, Z. Phys. Chem.  223  957-978  (2009) (PDF)

• New Trends in High-pressure Molecular Biophysics
  R. Fourme and I. Ascone and G. R. Kneller, Synchrotron Radiation News  22  39-41  (2009) (PDF)

• Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study
  G. R. Kneller and K. Hinsen, J .Chem. Phys.  131  171101  (2009) (PDF)

2008 :

• Influence of pressure on the fractional relaxation dynamics in proteins: A simulation study
  V. Calandrini and G. R. Kneller, J. Chem. Phys.  128  065102  (2008) (PDF)
  

• Protein dynamics from a NMR perspective: Networks of coupled rotators and fractional Brownian dynamics
  V. Calandrini and D. Abergel and G. R. Kneller, J .Chem. Phys.  128  145102  (2008) (PDF)
  

• Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering
  V. Calandrini and V. Hamon and K. Hinsen and P. Calligari and M.-C. Bellissent-Funel and G. R. Kneller, Chem. Phys.  345  289-297  (2008) (PDF)
  

• Solvent effects in the slow dynamics of proteins
  K. Hinsen and G. R. Kneller, Proteins: Structure, Function, and Genetics  70  1235-1242  (2008) (PDF)
  

• Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures
  G. R. Kneller, J. Chem. Phys.  128 194101 (2008) (PDF)
  

• Scaling laws and memory effects in the dynamics of liquids and proteins
  G. R. Kneller, K. Hinsen, G. Sutmann and V. Calandrini, Physics of Particles and Nuclei Letters  5  189-195 (2008)  (PDF)

• Dynamical heterogeneity of specific amino acids in bacteriorhodopsin
  K. Wood and S. Grudinin and B. Kessler and M. Weik and M. Johnson and G. R. Kneller and D. Oesterhelt and G. Zaccai,
  J. Mol. Biol.  380  581-591  (2008) (PDF)

2007 :

• Estimating the influence of finite instrumental resolution on elastic neutron scattering intensities from proteins
  G. R. Kneller and V. Calandrini, J. Chem. Phys.  126  125107 (2007) (PDF)
  

• Projection formalism for constrained dynamical systems: From Newtonian to Hamiltonian mechanics
  G. R. Kneller, J. Chem. Phys.  127  164114 (2007) (PDF)
  

2006 :

• The role of effective atomic masses in memory function-based models for liquids : A simulation study of liquid water
  V. Calandrini and G. Sutmann and A. Deriu and G. R. Kneller, J. Chem. Phys.  125  236102  (2006) (PDF) 

• Hamiltonian formalism for semiflexible molecules in Cartesian coordinates
  G. R. Kneller, J. Chem. Phys.  125  114107  (2006)  (PDF)

• Simulation studies of structural changes and relaxation processes in lysozyme under pressure
  V. Hamon and P. Calligari and K. Hinsen and G. R. Kneller, Journal of Non-Crystalline Solids 352  4417-4423 (2006)  (PDF)

• Efficient characterisation of protein secondary structure in terms of screw motions
  G. R. Kneller and P. Calligari, Acta Crystallographica D  62  302-311  (2006) (PDF)
  

2005 :

• Linear prediction of force time series to accelerate molecular dynamics simulations
  B. Brutovsky and G. R. Kneller, Computer Physics Communications  169  339-342  (2005) (PDF)
  

• Comment on ``Using quaternions to calculate RMSD'' [J. Comp. Chem. 25, 1849 (2004)]
  G. R. Kneller, J. Comp. Chem.  26  1660-1662  (2005) (PDF)

• Quasielastic neutron scattering and relaxation processes in proteins: {A}nalytical and simulation-based models
  G. R. Kneller, Physical Chemistry Chemical Physics  7  2641 - 2655  (2005) (PDF)
  

• Simulations moléculaires et leur analyse
  G. R. Kneller, J. Phys. IV  130  155-178  (2005) (PDF)

2004 :

• Scaling of the memory function and Brownian motion
  G. R. Kneller and G. Sutmann, J. Chem. Phys.  120  1667-1669  (2004)  (PDF)

• Fractional Brownian dynamics in proteins
  G. R. Kneller and K. Hinsen, J. Chem. Phys.  121  10278-10283  (2004) (PDF)
  

2003 :

• Accelerating molecular dynamics s{I}mulations by linear prediction of time series.
  B. Brutovsky and T. Mülders and G. R. Kneller, J. Chem. Phys.  118  6179-6187  (2003) (PDF)
  

• Mass and size effects on the memory function of tracer particles
  G. R. Kneller and K. Hinsen and G. Sutmann, J. Chem. Phys.  118  5283-5286  (2003) (PDF)
  

• nMoldyn : A Program Package for a Neutron Scattering Oriented Analysis of Molecular Dynamics Simulations
  T. Rog and K. Murzyn and K. Hinsen and G. R. Kneller, J. Comp. Chem.  24  657-667  (2003) (PDF)

Selection of older publications

• Computing memory functions from Molecular Dynamics simulations
  G. R. Kneller and K. Hinsen, J. Chem. Phys.  115  11097-11105  (2001)

• Projection methods for the analysis of complex motions in macromolecules
  K. Hinsen and G. R. Kneller, Mol. Sim.  23  275-292  (2000)

• Harmonicity in slow protein dynamics
  K. Hinsen and A.-J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller, Chem. Phys.  261  25-38  (2000)

• Inelastic neutron scattering from damped collective vibrations of macromolecules
  G. R. Kneller, Chem. Phys.  261  1-24  (2000)

• The influence of molecular flexibility on {DNA} radiosensitivity: {A} simulation study
  D. Viduna and K. Hinsen and G. R. Kneller, Phys. Rev. E  63  3986-3990  (2000)

• A simplified force field for describing vibrational protein dynamics over the whole frequency range
  K. Hinsen and G. R. Kneller, J. Chem. Phys.  111  10766-10769  (1999)

• Transport coefficients of electrolyte solutions from smart {B}rownian {D}ynamics simulations
  M. Jardat and O. Bernard and P. Turq and G. R. Kneller, J. Chem. Phys.  110  7993  (1999)

• Comment on "Atomic stress isobaric scaling for systems subjected to holonomic constraints" [J. Chem. Phys. 106, 195 (1997)]
  G. R. Kneller and T. Mülders, J. Chem. Phys.  109  6508-6509  (1998)

• Dynamics of alkane chains included in an organic matrix: {M}olecular dynamics simulation and comparison with neutron scattering experiment
  N.-D. Morélon and G. R. Kneller and M. Ferrand and A. Grand and J. C. Smith and M. Bée, J. Chem. Phys.  109  2883  (1998)

• Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes
  T. Mülders and S. Toxvaerd and G. R. Kneller, Phys. Rev. E  58  6766-6780  (1998)

• Nosé-Andersen molecular dynamics for partially rigid molecules: {C}oupling all atoms to heat and pressure baths
  G. R. Kneller and T. Mülders, Phys. Rev.E  54  6825-6837  (1996)

• The influence of geometrical constraints on the dynamics of polypeptide chains
  K. Hinsen and G. R. Kneller, Phys. Rev. E  52  6868-6874  (1995)

• nMoldyn, a program package for the calculation and analysis of neutron scattering spectra from {MD} simulations
  G. R. Kneller and V. Keiner and M. Kneller and M. Schiller, Comp. Phys. Comm.  91  191-214  (1995)

• Dynamics of pristine and doped polyacetylene: {A} combined neutron scattering and computer simulation analysis
  A. J. Dianoux and G. R. Kneller and J. L. Sauvajol and J. C. Smith, J. Non-Cryst. Solids  172-174  472-480  (1994)

• Dynamics of sodium-doped polyacetylene
  A. J. Dianoux and G. R. Kneller and J. L. Sauvajol and J. C. Smith, J. Chem. Phys.  101  634-644  (1994)

• Liquid-like Side-Chain Motions in Myoglobin
  G. R. Kneller and J. C. Smith, J. Mol. Biol.  242  181-185  (1994)

• Neutron scattering from classical systems: Stationary phase approximation of the scattering law
  G. R. Kneller, Mol. Phys.  83  63-87  (1994)

• Generalized {E}uler equations for linked rigid bodies
  G. R. Kneller and K. Hinsen, Phys. Rev. E  50  1559-1564  (1994)

• The polarized density of states of crystalline polyacetylene: {M}olecular dynamics {A}nalysis and comparison with neutron scattering results
  A. J. Dianoux and G. R. Kneller and J. L. Sauvajol and J. C. Smith, J. Chem. Phys.  99  5586-5596  (1993)

• Picosecond Timescale Rigid-Helix and Side-Chain Motions in Deoxymyoglobin
  S. Furois-Corbin and J. C. Smith and G. R. Kneller, Proteins: Structure, Function, and Genetics  16  141-154  (1993)

• Methyl group dynamics in the crystalline alanine dipeptide: {A} molecular dynamics and incoherent neutron scattering analysis
  G. R. Kneller and J. C. Smith and S. Cusack and W. Doster, J. Chem. Phys.  97  8864-8879  (1992)

• Superposition of Molecular Structures using Quaternions
  G. R. Kneller, Mol. Sim.  7  113-119  (1991)

• Molecular dynamics of liquid water using the NCC ab initio potential
  U. Niesar, G. Corongiu, E. Clementi, G. R. Kneller and D. K. Bhattacharya, J. Phys. Chem.  94  7949-7956  (1990)

• Molecular dynamics studies and neutron scattering experiments on methylen chloride. II. Dynamics
  G. R. Kneller and A. Geiger, Mol. Phys.  70  465-483  (1990)

• Molecular dynamics studies and neutron scattering experiments on methylen chloride. I. Structure
  G. R. Kneller and A. Geiger, Mol. Phys.  68  487-498  (1989)

• A method to calculate the g-coefficients of the molecular pair correlation function from MD-simulations
  G. R. Kneller and A. Geiger, Mol. Sim.  3  283-300  (1989)

• Boundary Layer Effects on the Rate of Diffusion Controlled Reactions
  G. R. Kneller and U. M. Titulaer, Physica  129A  514-534  (1985)

• The covariant form of the Klein-Kramers-equation and the associated moment equations
  G. R. Kneller and U. M. Titulaer, Physica  129A  81-94  (1984)

• Coupling of a BAF2-szintillator to a TMAE-photocathode in a low pressure wire chamber
  D. Anderson and G. Charpak and R. Bouclier and S. Majewski and G. R. Kneller, Nuclear Instruments and Methods  217  217-223  (1983)