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Kneller Gérald


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Publications

2016   Références trouvées : 2

Hinsen K. and Kneller G. R.  (2016)

Communication : A multiscale Bayesian inference approach to analyzing subdiffusion in particle trajectories

The Journal of chemical physics (2016) 145 (15) 151101 - doi : 10.1063/1.4965881
Anomalous diffusion is characterized by its asymptotic behavior for t —> infinity. This makes it difficult to detect and describe in particle trajectories from experiments or computer simulations, which are necessarily of finite length. We propose a new approach using Bayesian inference applied directly to the observed trajectories sampled at different time scales. We illustrate the performance of this approach using random trajectories with known statistical properties and then use it for analyzing the motion of lipid molecules in the plane of a lipid bilayer.

Anomalous diffusion is characterized by its asymptotic behavior for t —> infinity. This makes it difficult to detect and describe in particle trajectories from experiments or computer simulations, which are necessarily of finite length. We propose a new approach using Bayesian inference applied directly to the observed trajectories sampled at different time scales. We illustrate the performance of this approach using random trajectories with known statistical properties and then use it for analyzing the motion of lipid molecules in the plane of a lipid bilayer.

Kneller G.  (2016)

Asymptotic neutron scattering laws for anomalously diffusing quantum particles

The Journal of Chemical Physics (2016) 145, 044103 - doi : 10.1063/1.4959124
The paper deals with a model-free approach to the analysis of quasielastic neutron scattering intensities from anomalously diffusing quantum particles. All quantities are inferred from the asymptotic form of their time-dependent mean square displacements which grow ∝t α, with 0 ≤ α < 2. Confined diffusion (α = 0) is here explicitly included. We discuss in particular the intermediate scattering function for long times and the Fourier spectrum of the velocity autocorrelation function for small frequencies. Quantum effects enter in both cases through the general symmetry properties of quantum time correlation functions. It is shown that the fractional diffusion constant can be expressed by a Green-Kubo type relation involving the real part of the velocity autocorrelation function. The theory is exact in the diffusive regime and at moderate momentum transfers.

The paper deals with a model-free approach to the analysis of quasielastic neutron scattering intensities from anomalously diffusing quantum particles. All quantities are inferred from the asymptotic form of their time-dependent mean square displacements which grow ∝t α, with 0 ≤ α < 2. Confined diffusion (α = 0) is here explicitly included. We discuss in particular the intermediate scattering function for long times and the Fourier spectrum of the velocity autocorrelation function for small frequencies. Quantum effects enter in both cases through the general symmetry properties of quantum time correlation functions. It is shown that the fractional diffusion constant can be expressed by a Green-Kubo type relation involving the real part of the velocity autocorrelation function. The theory is exact in the diffusive regime and at moderate momentum transfers.


2015   Références trouvées : 4

Stachura S. and Kneller G. R.  (2015)

Communication : Probing anomalous diffusion in frequency space

The Journal of Chemical physics (2015) 143 (19) 191103 - doi : 10.1063/1.4936129
Anomalous diffusion processes are usually detected by analyzing the time-dependent mean square displacement of the diffusing particles. The latter evolves asymptotically as W(t) approximately 2Dalphat(alpha), where Dalpha is the fractional diffusion constant and 0 &lt; alpha &lt; 2. In this article we show that both Dalpha and alpha can also be extracted from the low-frequency Fourier spectrum of the corresponding velocity autocorrelation function. This offers a simple method for the interpretation of quasielastic neutron scattering spectra from complex (bio)molecular systems, in which subdiffusive transport is frequently encountered. The approach is illustrated and validated by analyzing molecular dynamics simulations of molecular diffusion in a lipid POPC bilayer.

Anomalous diffusion processes are usually detected by analyzing the time-dependent mean square displacement of the diffusing particles. The latter evolves asymptotically as W(t) approximately 2Dalphat(alpha), where Dalpha is the fractional diffusion constant and 0 < alpha < 2. In this article we show that both Dalpha and alpha can also be extracted from the low-frequency Fourier spectrum of the corresponding velocity autocorrelation function. This offers a simple method for the interpretation of quasielastic neutron scattering spectra from complex (bio)molecular systems, in which subdiffusive transport is frequently encountered. The approach is illustrated and validated by analyzing molecular dynamics simulations of molecular diffusion in a lipid POPC bilayer.

Kneller G. R. and Hinsen K.  (2015)

Protein secondary-structure description with a coarse-grained model

Acta crystallographica. Section D, Biological crystallography (2015) 71 (pt 7) 1411-1422 - doi : 10.1107/s1399004715007191
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(alpha) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(alpha) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(alpha) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(alpha) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data.

A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(alpha) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(alpha) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(alpha) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(alpha) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data.

Kneller G.  (2015)

Anomalous diffusion in biomolecular systems from the perspective of non-equilibrium statistical physics

Acta Physica Polonica B (2015) 46 (6) 1167-1199 - doi : 10.5506/APhysPolB.46.1167
This contribution gives a short introduction into the theory of anomalous diffusion and relaxation with illustrations from computer simulations of biomolecular systems. The theory is presented from the perspective of the non-equilibrium statistical physics, confronting stochastic models with exact results which have been recently obtained on the basis of asymptotic analysis. In this context, conditions for anomalous diffusion will be discussed and the Kubo relations for the fractional diffusion and relaxation constant will be derived.

This contribution gives a short introduction into the theory of anomalous diffusion and relaxation with illustrations from computer simulations of biomolecular systems. The theory is presented from the perspective of the non-equilibrium statistical physics, confronting stochastic models with exact results which have been recently obtained on the basis of asymptotic analysis. In this context, conditions for anomalous diffusion will be discussed and the Kubo relations for the fractional diffusion and relaxation constant will be derived.

Calligari P. A., Calandrini V., Ollivier J., Artero J.-B., Härtlein M., Johnson M., Kneller G. R.  (2015)

Adaptation of Extremophilic Proteins with Temperature and Pressure : Evidence from Initiation Factor 6

The Journal of Physical Chemistry B (2015) 119 (25) 7860-7873 - doi : 10.1021/acs.jpcb.5b02034
In this work, we study dynamical properties of an extremophilic protein, Initiation Factor 6 (IF6), produced by the archeabacterium Methanocaldococcus jannascii, which thrives close to deep-sea hydrothermal vents where temperatures reach 80 °C and the pressure is up to 750 bar. Molecular dynamics simulations (MD) and quasi-elastic neutron scattering (QENS) measurements give new insights into the dynamical properties of this protein with respect to its eukaryotic and mesophilic homologue. Results obtained by MD are supported by QENS data and are interpreted within the framework of a fractional Brownian dynamics model for the characterization of protein relaxation dynamics. IF6 from M. jannaschii at high temperature and pressure shares similar flexibility with its eukaryotic homologue from S. cerevisieae under ambient conditions. This work shows for the first time, to our knowledge, that the very common pattern of corresponding states for thermophilic protein adaptation can be extended to thermo-barophilic proteins. A detailed analysis of dynamic properties and of local structural fluctuations reveals a complex pattern for ?corresponding ? structural flexibilities. In particular, in the case of IF6, the latter seems to be strongly related to the entropic contribution given by an additional, C-terminal, 20 amino-acid tail which is evolutionary conserved in all mesophilic IF6s.

In this work, we study dynamical properties of an extremophilic protein, Initiation Factor 6 (IF6), produced by the archeabacterium Methanocaldococcus jannascii, which thrives close to deep-sea hydrothermal vents where temperatures reach 80 °C and the pressure is up to 750 bar. Molecular dynamics simulations (MD) and quasi-elastic neutron scattering (QENS) measurements give new insights into the dynamical properties of this protein with respect to its eukaryotic and mesophilic homologue. Results obtained by MD are supported by QENS data and are interpreted within the framework of a fractional Brownian dynamics model for the characterization of protein relaxation dynamics. IF6 from M. jannaschii at high temperature and pressure shares similar flexibility with its eukaryotic homologue from S. cerevisieae under ambient conditions. This work shows for the first time, to our knowledge, that the very common pattern of corresponding states for thermophilic protein adaptation can be extended to thermo-barophilic proteins. A detailed analysis of dynamic properties and of local structural fluctuations reveals a complex pattern for ?corresponding ? structural flexibilities. In particular, in the case of IF6, the latter seems to be strongly related to the entropic contribution given by an additional, C-terminal, 20 amino-acid tail which is evolutionary conserved in all mesophilic IF6s.


2014   Références trouvées : 2

Kneller, G.R.  (2014)

Communication : A scaling approach to anomalous diffusion

The Journal of Chemical Physics (2014) 141 (4) 041105-1 - 041105-4
The paper presents a rigorous derivation of the velocity autocorrelation function for an anomalously diffusing slow solute particle in a bath of fast solvent molecules. The result is obtained within the framework of the generalized Langevin equation and uses only scaling arguments and identities which are based on asymptotic analysis. It agrees with the velocity autocorrelation function of an anomalously diffusing Rayleigh particle whose dynamics is described by a fractional Ornstein-Uhlenbeck process in velocity space. A simple semi-analytical example illustrates under which conditions the latter model is appropriate.

The paper presents a rigorous derivation of the velocity autocorrelation function for an anomalously diffusing slow solute particle in a bath of fast solvent molecules. The result is obtained within the framework of the generalized Langevin equation and uses only scaling arguments and identities which are based on asymptotic analysis. It agrees with the velocity autocorrelation function of an anomalously diffusing Rayleigh particle whose dynamics is described by a fractional Ornstein-Uhlenbeck process in velocity space. A simple semi-analytical example illustrates under which conditions the latter model is appropriate.

Stachura S. and Kneller G.R.  (2014)

Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields

Molecular Simulation (2014) 40 (1-3) 245-250 - doi : 10.1080/08927022.2013.840902
In the present article we study the lateral molecular di-usion in homogenous lipid (POPC) bilayers by molecular dynamics simulations with the all-atom OPLS and the coarse-grained MARTINI force fields. On the statistically relevant time scales the center-of-mass mean-square displacement exhibits in both cases the subdiffusive asymptotic form W (t) 2Dαtα , with α ≈ 0.67 and α ≈ 0.57 , respectively. The diffusive dynamics obtained by the MARTINI force field is, however, faster by a factor of about 3. The subdiffusive characteristics of the di-usion process is confirmed by comparing the integral of the center-of-mass velocity autocorrelation function with its analytical long-time tail. The agreement is particularly good for the MARTINI force field, which permits to extend the simulation length and the system size considerably. Our results are in agreement with experimental observations of subdi-usion in lipid bilayers on longer time scales and do not support the finding of some authors that the latter should be considered as a transient phenomenon.

In the present article we study the lateral molecular di-usion in homogenous lipid (POPC) bilayers by molecular dynamics simulations with the all-atom OPLS and the coarse-grained MARTINI force fields. On the statistically relevant time scales the center-of-mass mean-square displacement exhibits in both cases the subdiffusive asymptotic form W (t) 2Dαtα , with α ≈ 0.67 and α ≈ 0.57 , respectively. The diffusive dynamics obtained by the MARTINI force field is, however, faster by a factor of about 3. The subdiffusive characteristics of the di-usion process is confirmed by comparing the integral of the center-of-mass velocity autocorrelation function with its analytical long-time tail. The agreement is particularly good for the MARTINI force field, which permits to extend the simulation length and the system size considerably. Our results are in agreement with experimental observations of subdi-usion in lipid bilayers on longer time scales and do not support the finding of some authors that the latter should be considered as a transient phenomenon.


2013   Références trouvées : 2

Peters J. and Kneller G.R.  (2013)

Motional heterogeneity in human acetylcholinesterase revealed by a non-Gaussian model for elastic incoherent neutron scattering

The Journal of Chemical Physics (2013) 139-142 - doi : papers2 ://publication/doi/10.1063/1.4825199
We study the dynamical transition of human acetylcholinesterase by analyzing elastic neutron scat- tering data with a simulation gauged analytical model that goes beyond the standard Gaussian ap- proximation for the elastic incoherent structure factor [G. R. Kneller and K. Hinsen, J. Chem. Phys. 131, 045104 (2009)]. The model exploits the whole available momentum transfer range in the ex- perimental data and yields not only a neutron-weighted average of the atomic mean square position fluctuations, but also an estimation for their distribution. Applied to the neutron scattering data from human acetylcholinesterase, it reveals a strong increase of the motional heterogeneity at the two transition temperatures T = 150 K and T = 220 K, respectively, which can be located with less am- biguity than with the Gaussian model. We find that the first transition is essentially characterized by a change in the form of the elastic scattering profile and the second by a homogeneous increase of all motional amplitudes. These results are in agreement with previous combined experimental and simulation studies of protein dynamics, which attribute the first transition to an onset of methyl rotations and the second to more unspecific diffusion processes involving large amplitude motions.

We study the dynamical transition of human acetylcholinesterase by analyzing elastic neutron scat- tering data with a simulation gauged analytical model that goes beyond the standard Gaussian ap- proximation for the elastic incoherent structure factor [G. R. Kneller and K. Hinsen, J. Chem. Phys. 131, 045104 (2009)]. The model exploits the whole available momentum transfer range in the ex- perimental data and yields not only a neutron-weighted average of the atomic mean square position fluctuations, but also an estimation for their distribution. Applied to the neutron scattering data from human acetylcholinesterase, it reveals a strong increase of the motional heterogeneity at the two transition temperatures T = 150 K and T = 220 K, respectively, which can be located with less am- biguity than with the Gaussian model. We find that the first transition is essentially characterized by a change in the form of the elastic scattering profile and the second by a homogeneous increase of all motional amplitudes. These results are in agreement with previous combined experimental and simulation studies of protein dynamics, which attribute the first transition to an onset of methyl rotations and the second to more unspecific diffusion processes involving large amplitude motions.

Chevrot G., Hinsen K. and Kneller G.R.  (2013)

Model-free simulation approach to molecular diffusion tensors

The Journal of Chemical Physics (2013) 139 (15) 154110 - doi : papers2 ://publication/doi/10.1063/1.4823996
In the present work, we propose a simple model-free approach for the computation of molecular dif- fusion tensors from molecular dynamics trajectories. The method uses a rigid body trajectory of the molecule under consideration, which is constructed a posteriori by an accumulation of quaternion- based superposition fits of consecutive conformations. From the rigid body trajectory, we compute the translational and angular velocities of the molecule and by integration of the latter also the cor- responding angular trajectory. All quantities can be referred to the laboratory frame and a molecule- fixed frame. The 6 × 6 diffusion tensor is computed from the asymptotic slope of the tensorial mean square displacement and, for comparison, also from the Kubo integral of the velocity cor- relation tensor. The method is illustrated for two simple model systems – a water molecule and a lysozyme molecule in bulk water. We give estimations of the statistical accuracy of the calculations.

In the present work, we propose a simple model-free approach for the computation of molecular dif- fusion tensors from molecular dynamics trajectories. The method uses a rigid body trajectory of the molecule under consideration, which is constructed a posteriori by an accumulation of quaternion- based superposition fits of consecutive conformations. From the rigid body trajectory, we compute the translational and angular velocities of the molecule and by integration of the latter also the cor- responding angular trajectory. All quantities can be referred to the laboratory frame and a molecule- fixed frame. The 6 × 6 diffusion tensor is computed from the asymptotic slope of the tensorial mean square displacement and, for comparison, also from the Kubo integral of the velocity cor- relation tensor. The method is illustrated for two simple model systems – a water molecule and a lysozyme molecule in bulk water. We give estimations of the statistical accuracy of the calculations.


2012   Références trouvées : 5

Kneller G.R. and Chevrot G.  (2012)

Impact of anisotropic atomic motions in proteins on powder-averaged incoherent neutron scattering intensities

J Chem Phys. 137 (22) 225101
This paper addresses the question to which extent anisotropic atomic motions in proteins impact angular-averaged incoherent neutron scattering intensities, which are typically recorded for powder samples. For this purpose, the relevant correlation functions are represented as multipole series in which each term corresponds to a different degree of intrinsic motional anisotropy. The approach is illustrated by a simple analytical model and by a simulation-based example for lysozyme, considering in both cases the elastic incoherent structure factor. The second example shows that the motional anisotropy of the protein atoms is considerable and contributes significantly to the scattering intensity.

This paper addresses the question to which extent anisotropic atomic motions in proteins impact angular-averaged incoherent neutron scattering intensities, which are typically recorded for powder samples. For this purpose, the relevant correlation functions are represented as multipole series in which each term corresponds to a different degree of intrinsic motional anisotropy. The approach is illustrated by a simple analytical model and by a simulation-based example for lysozyme, considering in both cases the elastic incoherent structure factor. The second example shows that the motional anisotropy of the protein atoms is considerable and contributes significantly to the scattering intensity.

Calligari, P.A. and Kneller, G.R.  (2012)

ScrewFit : Combining localization and description of protein secondary structure

Acta Crystallogr D Biol Crystallogr. 68 (Pt 12):1690-1693
We present a new application of the ScrewFit algorithm (Acta Cryst. D 62, p.

302-11 (2006)) which adds the detection of protein secondary structure elements to

their detailed geometrical description in terms of a curve with intrinsic torsion. The

extension is based on con-dence and persistence criteria for the ScrewFit parameters

which are established by analyzing the structural 

uctuations of standard motifs in the

SCOP fold classes. The agreement with the widely used DSSP method is comparable

with the general consensus among other methods in literature. The combination of

secondary structure detection and analysis is illustrated for the enzyme Adenylate

kinase.

We present a new application of the ScrewFit algorithm (Acta Cryst. D 62, p.
302-11 (2006)) which adds the detection of protein secondary structure elements to
their detailed geometrical description in terms of a curve with intrinsic torsion. The
extension is based on con-dence and persistence criteria for the ScrewFit parameters
which are established by analyzing the structural
uctuations of standard motifs in the
SCOP fold classes. The agreement with the widely used DSSP method is comparable
with the general consensus among other methods in literature. The combination of
secondary structure detection and analysis is illustrated for the enzyme Adenylate
kinase.

Hinsen, K., Pellegrini, E., Stachura, S. and Kneller, G.R.  (2012)

nMoldyn 3 : Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations

Journal of Computational Chemistry 33 (25) 2043-2048
We present a new version of the program package nMoldyn, which has been originally developed for a neutron-scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in-depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed-memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods.

We present a new version of the program package nMoldyn, which has been originally developed for a neutron-scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in-depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed-memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods.

Kneller, G.R., Hinsen, K. and Calligari, P.  (2012)

Communication : A minimal model for the diffusion-relaxation backbone dynamics of proteins

The Journal of Chemical Physics 136 (19) 191101
We present a model for the local diffusion-relaxation dynamics of the Cα-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ⩾ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the Cα-atoms exceptionally well and reveals moreover a strong correlation between the residue's solvent-accessible surface and the fitted model parameters.

We present a model for the local diffusion-relaxation dynamics of the Cα-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ⩾ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the Cα-atoms exceptionally well and reveals moreover a strong correlation between the residue’s solvent-accessible surface and the fitted model parameters.

Smolin, N. Biehl, R. Kneller, G. R. Richter, D. and Smith, J. C.  (2012)

Functional Domain Motions in Proteins on the ∼1–100 ns Timescale : Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation

Biophysical Journal 102 (5) 1108-1117
Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ∼1–100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ∼1–100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion’s contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.


2011   Références trouvées : 7

Kneller, G. R.  (2011)

Generalized Kubo relations and conditions for anomalous diffusion : Physical insights from a mathematical theorem

J. Chem. Phys. 134 224106

Calandrini, V., Pellegrini, E., Calligari, P., Hinsen, K. and Kneller, G. R.  (2011)

nmoldyn - interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions

Collection SFN 12 201-232 ` !

Chevrot, G., Calligari, P., Hinsen, K. and Kneller, G.R.  (2011)

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

J. Chem. Phys.135 084110

Calligari, P., Calandrini, V., Kneller, G. R. and Abergel, D.  (2011)

From NMR relaxation to fractional Brownian dynamics in proteins : Results from a virtual experiment

J. Phys. Chem. B. 115 (43) 12370-12379
In a recent simulation study [J. Chem. Phys. 2010, 133, 145101], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing then. internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual (15)N R(1), R(2), and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting.

In a recent simulation study [J. Chem. Phys. 2010, 133, 145101], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing then. internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual (15)N R(1), R(2), and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting.

Kneller, G. R., Baczynski K. and Pasenkiewicz-Gierula M.  (2011)

Consistent picture of lateral subdiffusion in lipid bilayers : molecular dynamics simulation and exact results

J. Chem. Phys. 135 (14) 141105
This communication presents a molecular dynamics simulation study of a bilayer consisting of 128 dioleoyl-sn-glycero-3-phosphocholine molecules, which focusses on the center-of-mass diffusion of the lipid molecules parallel to the membrane plane. The analysis of the simulation results is performed within the framework of the generalized Langevin equation and leads to a consistent picture of subdiffusion. The mean square displacement of the lipid molecules evolves as proportional to t(alpha), with alpha between 0.5 and 0.6, and the fractional diffusion coefficient is close to the experimental value for a similar system obtained by fluorescence correlation spectroscopy. We show that the long-time tails of the lateral velocity autocorrelation function and the associated memory function agree well with exact results which have been recently derived by asymptotic analysis [G. Kneller, J. Chem. Phys. 134, 224106 (2011)]. In this context, we define characteristic time scales for these two quantities. (C) 2011 American Institute of Physics. [doi : 10.1063/1.3651800]

This communication presents a molecular dynamics simulation study of a bilayer consisting of 128 dioleoyl-sn-glycero-3-phosphocholine molecules, which focusses on the center-of-mass diffusion of the lipid molecules parallel to the membrane plane. The analysis of the simulation results is performed within the framework of the generalized Langevin equation and leads to a consistent picture of subdiffusion. The mean square displacement of the lipid molecules evolves as proportional to t(alpha), with alpha between 0.5 and 0.6, and the fractional diffusion coefficient is close to the experimental value for a similar system obtained by fluorescence correlation spectroscopy. We show that the long-time tails of the lateral velocity autocorrelation function and the associated memory function agree well with exact results which have been recently derived by asymptotic analysis [G. Kneller, J. Chem. Phys. 134, 224106 (2011)]. In this context, we define characteristic time scales for these two quantities. (C) 2011 American Institute of Physics. [doi : 10.1063/1.3651800]

Kneller, G. R.  (2011)

Comment on “Fast Determination of the Optimal Rotational Matrix for Macromolecular Superpositions [J. Comp. Chem. 31, 1561 (2010)]

J. Comp. Chem. 32 (1) 183-184

Kneller, G.  (2011)

Dynamics of biological macromolecules

In "Dynamics of Biological Macromolecules by Neutron Scattering" Magazu, S. and Migliardo, F. (Eds.) - ISBN : 978-1-60805-219-6


2010   Références trouvées : 2

Calandrini, V., Abergel, D & Kneller, G.  (2010)

Fractional protein dynamics seen by NMR spectroscopy : relating molecular dynamics simulation and experiment.

J. Chem. Phys., 133, 145101

Kneller, G.R. & Calandrini, V.  (2010)

Self-similar dynamics of proteins under hydrostatic pressure-Computer simulations and experiments

BBA - Proteins Proteomics 1804, 56-62.


2009   Références trouvées : 5

Calligari, P.A., Kneller, G.R., Giansanti, A., Ascenzi, P., Porrello, A. & Bocedi, A.  (2009)

Group-1 and group-2 neuraminidases : Screw motion analysis reveals fine structural changes induced by binding with oseltamivir.

Biophys. Chem., 141, 117–123

Kneller, G.R. & Hinsen, K.  (2009)

Quantitative model for the heterogeneity of atomic position fluctuations in proteins : A simulation study.

J. Chem. Phys. 131, 171101.

Horvath, D. & Kneller, G.R.  (2009)

A least-constraint principle for population dynamics and reaction kinetics : Modeling entropy-controlled chemical hypercycles.

J. Chem. Phys. 131, 171101.

Fourme, R., Ascone, I. & Kneller, G.  (2009)

New trends in high-pressure molecular biophysics.

Synchrotron Radiat. News 22, 39-41.

Calandrini, V., Sutmann, G., Deriu, A. & Kneller, G.R.  (2009)

Rigid Molecule Approximation in Memory Function-based Models for Molecular Liquids : Application to Liquid Water.

Z Phys Chem. 223, 957-978.


2008   Références trouvées : 7

Kneller, G., Hinsen, K., Sutmann, G., & Calandrini, V.  (2008)

Scaling laws and memory effects in the dynamics of liquids and proteins.

Physics Particl. Nuclei Let., 5, 189–195

Wood, K., Grudinin, S., Kessler, B., Weik, M., Johnson, M., Kneller, G.R., Oesterheit, D. & Zaccai, G.  (2008)

Dynamical heterogeneity of specific amino acids in bacteriorhodopsin.

J. Mol. Biol. 380, 581-591.

Kneller, G.R.  (2008)

Eckart axis conditions, Gauss’ principle of least constraint, and the optimal superposition of molecular structures.

J. Chem. Phys. 128, 194101.

Calandrini, V. & Kneller, G.R.  (2008)

Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme : A simulation study.

J. Chem. Phys. 128, 065102.

Calandrini, V., Hamon, V., Hinsen, K., Calligari, P., Bellissent-Funel, M.C. & Kneller, G.R.  (2008)

Relaxation dynamics of lysozyme in solution under pressure : Combining molecular dynamics simulations and quasielastic neutron scattering.

Chem. Phys. 345, 289

Calandrini, V., Abergel, D. & Kneller, G.R.  (2008)

Protein dynamics from a NMR perspective : Networks of coupled rotators and fractional Brownian dynamics.

J. Chem. Phys. 128, 145102.

Hinsen, K ; Kneller, G  (2008)

Solvent effects in the slow dynamics of proteins

Proteins : Structure, Function and Genetics 70(4) 1235-1242
The influence of solvent on the slow internal dynamics of proteins is studied by comparing Molecular Dynamics simulations of solvated and unsolvated lysozyme. The dynamical trajectories are projected onto the protein's normal modes in order to obtain a separate analysis for each of the associated time scales. The results show that solvent effects are important for the slowest motions (below ï¿1/2 1/ps) but negligible for faster motions. The damping effects seen in the latter show that the principal source of friction in protein dynamics is not the solvent, but the protein itself.

The influence of solvent on the slow internal dynamics of proteins is studied by comparing Molecular Dynamics simulations of solvated and unsolvated lysozyme. The dynamical trajectories are projected onto the protein’s normal modes in order to obtain a separate analysis for each of the associated time scales. The results show that solvent effects are important for the slowest motions (below ï¿1/2 1/ps) but negligible for faster motions. The damping effects seen in the latter show that the principal source of friction in protein dynamics is not the solvent, but the protein itself.


2007   Références trouvées : 2

Kneller, G.R. & Calandrini, V.  (2007)

Estimating the influence of finite instrumental resolution on elastic neutron scattering intensities from proteins.

J. Chem. Phys. 126, 125107.

Kneller, G.R.  (2007)

Projection formalism for constrained dynamical systems : From Newtonian to Hamiltonian mechanics.

J. Chem. Phys. 127, 164114.


2006   Références trouvées : 4

Kneller, G.R. & Calligari, P.  (2006)

Efficient characterization of protein secondary structure in terms of screw motions.

Acta Crystallogr. D 62, 302-311.

Kneller, G.R.  (2006)

Hamiltonian formalism for semiflexible molecules in Cartesian coordinates.

J. Chem. Phys. 125, 114107

Calandrini, V., Sutmann, G., Deriu, A. & Kneller, G.R.  (2006)

The role of effective atomic masses in memory function-based models for liquids : A simulation study of liquid water.

J. Chem. Phys. 125, 236102

Hamon, V ; Calligari, P ; Hinsen, K ; Kneller, GR  (2006)

Simulation studies of structural changes and relaxation processes in lysozyme under pressure

Journal of Non-Crystalline Solids 352 (42-49) 4417-4423
The paper describes preliminary results of a molecular dynamics simulation study on the influence of non-denaturing hydrostatic pressure on the structure and the relaxation dynamics of lysozyme. The overall compression and the structural changes are in agreement with results from recent nuclear magnetic resonance experiments. We find that moderate hydrostatic pressure reduces essentially the amplitudes of the atomic motions. but does not change the characteristics of the slow internal dynamics. The latter is well described by a fractional Ornstein-Uhlenbeck process, concerning both single particle and collective motions. (c) 2006 Elsevier B.V. All rights reserved.

The paper describes preliminary results of a molecular dynamics simulation study on the influence of non-denaturing hydrostatic pressure on the structure and the relaxation dynamics of lysozyme. The overall compression and the structural changes are in agreement with results from recent nuclear magnetic resonance experiments. We find that moderate hydrostatic pressure reduces essentially the amplitudes of the atomic motions. but does not change the characteristics of the slow internal dynamics. The latter is well described by a fractional Ornstein-Uhlenbeck process, concerning both single particle and collective motions. (c) 2006 Elsevier B.V. All rights reserved.


2005   Références trouvées : 4

Brutovsky, B. & G. Kneller, G.  (2005)

Linear prediction of force time series to accelerate molecular dynamics simulations

Computer Physics Communications, vol. 169, pp. 339–342

Kneller, G.  (2005)

“Comment on “Using quaternions to calculate RMSD” [J. Comp. Chem. 25, 1849 (2004)]

J. Comp. Chem., vol. 26, no. 15, pp. 1660–1662

Kneller, G.  (2005)

Quasielastic neutron scattering and relaxation processes in proteins : Analytical and simulation-based models

Physical Chemistry Chemical Physics, vol. 7, pp. 2641 – 2655

Kneller, G.  (2005)

Simulations moléculaires et leur analyse

In Neutrons et Biologie (J. Ollivier, M. Farhi, E. et Ferrand, and B. M., eds.), vol. 130, pp. 155–178, EDP Sciences


2004   Références trouvées : 2

Kneller, G. & Sutmann, G.  (2004)

Scaling of the memory function and Brownian motion

J. Chem. Phys., vol. 120, no. 4, pp. 1667–1669

Kneller, GR ; Hinsen, K  (2004)

Fractional Brownian dynamics in proteins

Journal of Chemical Physics 121 (20) 10278-10283
Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution. We show that both the dynamic structure factor and the associated memory function fit well the corresponding analytical functions calculated from the model. The numerical analysis is based on autoregressive modeling of time series. (C) 2004 American Institute of Physics.

Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution. We show that both the dynamic structure factor and the associated memory function fit well the corresponding analytical functions calculated from the model. The numerical analysis is based on autoregressive modeling of time series. (C) 2004 American Institute of Physics.


2003   Références trouvées : 3

Brutovsky, B., Mülders, T. & Kneller, G.  (2003)

Accelerating molecular dynamics sImulations by linear prediction of time series

J. Chem. Phys., vol. 118, no. 14, pp. 6971–6987

Rog, T ; Murzyn, K ; Hinsen, K ; Kneller, GR  (2003)

nMoldyn : A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations

Journal of Computational Chemistry 24 (5) 657-667
We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques.

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques.

Kneller, GR ; Hinsen, K ; Sutmann, G  (2003)

Mass and size effects on the memory function of tracer particles

Journal of Chemical Physics 118 (12) 5283-5286
Using autoregressive modeling of discrete signals, we investigate the influence of mass and size on the memory function of a tracer particle immersed in a Lennard-Jones liquid. We find that the memory function of the tracer particle scales with the inverse reduced mass of the simulated system. Increasing the particle's mass leads rapidly to a slow exponential decay of the velocity autocorrelation function, whereas the memory function changes just its amplitude. This effect is the more pronounced the smaller and the heavier the tracer particle is. (C) 2003 American Institute of Physics.

Using autoregressive modeling of discrete signals, we investigate the influence of mass and size on the memory function of a tracer particle immersed in a Lennard-Jones liquid. We find that the memory function of the tracer particle scales with the inverse reduced mass of the simulated system. Increasing the particle’s mass leads rapidly to a slow exponential decay of the velocity autocorrelation function, whereas the memory function changes just its amplitude. This effect is the more pronounced the smaller and the heavier the tracer particle is. (C) 2003 American Institute of Physics.


2002   Références trouvées : 1

Hinsen, K ; Petrescu, AJ ; Dellerue, S ; Bellissent-Funel, MC ; Kneller, GR  (2002)

Liquid-like and solid-like motions in proteins

Journal of Molecular Liquids 98-99, 381-398
Recent analyses of molecular dynamics simulations of hydrated C-phycocyanin suggest that the internal single-particle dynamics of this protein can be decomposed into four almost decoupled motion types : (1) diffusion of residues ("beads") in an effective harmonic potential, (2) corresponding vibrations in a local potential well, (3) purely rotational rigid side-chain diffusion, and (4) residue deformations, Each residue bead is represented by the corresponding C-alpha carbon atom on the main chain.

Recent analyses of molecular dynamics simulations of hydrated C-phycocyanin suggest that the internal single-particle dynamics of this protein can be decomposed into four almost decoupled motion types : (1) diffusion of residues ("beads") in an effective harmonic potential, (2) corresponding vibrations in a local potential well, (3) purely rotational rigid side-chain diffusion, and (4) residue deformations, Each residue bead is represented by the corresponding C-alpha carbon atom on the main chain.


2001   Références trouvées : 2

Mülders, T., Toxvaerd, S. & Kneller, G.  (2001)

“Reply to "Comment on "Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes""

Phys. Rve. E, vol. 63

Kneller, GR ; Hinsen, K  (2001)

Computing memory functions from molecular dynamics simulations

Journal of Chemical Physics 115 (24) 11097-11105
We propose a new method to compute reliable estimates for memory functions of dynamical variables from molecular dynamics simulations. The key point is that the dynamical variable under consideration, which we take to be the velocity of a fluid particle, is modeled as an autoregressive stochastic process. The parameters of this stochastic process can be determined from molecular dynamics trajectories using efficient algorithms that are well established in signal processing. The procedure is also referred to as the maximum entropy method. From the autoregressive model of the velocity autocorrelation function we compute the one-sided z transform of the discretized memory function and the memory function itself. Using liquid argon as a simple model system, we demonstrate that the autocorrelation function and its power spectrum can be approximated to almost arbitrary precision. The same is therefore true for the memory function, which is calculated within the same stochastic model. (C) 2001 American Institute of Physics.

We propose a new method to compute reliable estimates for memory functions of dynamical variables from molecular dynamics simulations. The key point is that the dynamical variable under consideration, which we take to be the velocity of a fluid particle, is modeled as an autoregressive stochastic process. The parameters of this stochastic process can be determined from molecular dynamics trajectories using efficient algorithms that are well established in signal processing. The procedure is also referred to as the maximum entropy method. From the autoregressive model of the velocity autocorrelation function we compute the one-sided z transform of the discretized memory function and the memory function itself. Using liquid argon as a simple model system, we demonstrate that the autocorrelation function and its power spectrum can be approximated to almost arbitrary precision. The same is therefore true for the memory function, which is calculated within the same stochastic model. (C) 2001 American Institute of Physics.


2000   Références trouvées : 6

Jardat, M. J., Bernard, O., Treiner, C., Kneller, G. & Turq, P.  (2000)

Dynamical properties of electrolyte solutions from Brownian Dynamics simulations

J. Phys. IV (France), vol. 10, pp. Pr5–113

Jardat, M., Durand-Vidal, S., Turq, P. & Kneller, G.  (2000)

Brownian dynamics simulations of electrolyte mixtures : Computation of transport coefficients and comparison with analytical theory

J. Mol. Liquids, vol. 85, pp. 45–55

Kneller, G.  (2000)

Inelastic neutron scattering from damped collective vibrations of macromolecules

Chem. Phys., vol. 261, no. 1+2, pp. 1–24, 2000. Special volume "Condensed Phase Structure and Dynamics : A combined neutron scattering and molecular modelling approach

Hinsen, K ; Kneller, GR  (2000)

Projection methods for the analysis of complex motions in macromolecules

Molecular Simulation 23 (4-5) 275-292
In studies of macromolecular dynamics it is often desirable to analyze complex motions in terms of a small number of coordinates. Only for simple types of motion, e.g., rigid-body motions, these coordinates can be easily constructed from the Cartesian atomic coordinates. This article presents an approach that is applicable to infinitesimal or approximately infinitesimal motions, e.g., Cartesian velocities, normal modes, or atomic fluctuations. The basic idea is to characterize the subspace of interesting motions by a set of (possibly linearly dependent) vectors describing elementary displacements, and then project the dynamics onto this subspace. Often the elementary displacements can be found by physical intuition. The restriction to small displacements facilitates the study of complicated coupled motions and permits the construction of collective-motion subspaces that do not correspond to any set of generalized coordinates. As an example for this technique, we analyze the low-frequency normal modes of proteins up to approximate to 20 THz (600 cm(-1)) in order to see what kinds of motions occupy which frequency range. This kind of analysis is useful for the interpretation of spectroscopic measurements on proteins, e.g., inelastic neutron scattering experiments.

In studies of macromolecular dynamics it is often desirable to analyze complex motions in terms of a small number of coordinates. Only for simple types of motion, e.g., rigid-body motions, these coordinates can be easily constructed from the Cartesian atomic coordinates. This article presents an approach that is applicable to infinitesimal or approximately infinitesimal motions, e.g., Cartesian velocities, normal modes, or atomic fluctuations. The basic idea is to characterize the subspace of interesting motions by a set of (possibly linearly dependent) vectors describing elementary displacements, and then project the dynamics onto this subspace. Often the elementary displacements can be found by physical intuition. The restriction to small displacements facilitates the study of complicated coupled motions and permits the construction of collective-motion subspaces that do not correspond to any set of generalized coordinates. As an example for this technique, we analyze the low-frequency normal modes of proteins up to approximate to 20 THz (600 cm(-1)) in order to see what kinds of motions occupy which frequency range. This kind of analysis is useful for the interpretation of spectroscopic measurements on proteins, e.g., inelastic neutron scattering experiments.

Viduna, D ; Hinsen, K ; Kneller, G  (2000)

The influence of molecular flexibility on DNA radiosensitivity : A simulation study

Physical Review E 62 (3) 3986-3990 Part B
Radiation damage in DNA is caused mainly by hydroxyl radicals which are generated by ionizing radiation in water and removing hydrogen atoms from the DNA chain. This damage affects certain nucleotide sequences more than others due to differences in the local structure of the DNA chains. This sequence dependence has been analyzed experimentally and calculated theoretically for a rigid DNA model. In this paper we take into account the flexibility of the DNA chain and show how it modifies the strand breakage probabilities. We use a simple harmonic model for DNA flexibility which permits the study of a long (68 base pair) fragment with modest computational effort. The essential influence of flexibility is an increased breakage probability towards the ends of the fragment, which can also be identified in the experimental data.

Radiation damage in DNA is caused mainly by hydroxyl radicals which are generated by ionizing radiation in water and removing hydrogen atoms from the DNA chain. This damage affects certain nucleotide sequences more than others due to differences in the local structure of the DNA chains. This sequence dependence has been analyzed experimentally and calculated theoretically for a rigid DNA model. In this paper we take into account the flexibility of the DNA chain and show how it modifies the strand breakage probabilities. We use a simple harmonic model for DNA flexibility which permits the study of a long (68 base pair) fragment with modest computational effort. The essential influence of flexibility is an increased breakage probability towards the ends of the fragment, which can also be identified in the experimental data.

Hinsen, K ; Petrescu, AJ ; Dellerue, S ; Bellissent-Funel, MC ; Kneller, GR  (2000)

Harmonicity in slow protein dynamics

Chemical Physics 261 (1-2) 25-37
The slow dynamics of proteins around its native folded state is usually described by diffusion in a strongly anharmonic potential. In this paper, we try to understand the form and origin of the anharmonicities, with the principal aim of gaining a better understanding of the principal motion types, but also in order to develop more efficient numerical methods for simulating neutron scattering spectra of large proteins.

The slow dynamics of proteins around its native folded state is usually described by diffusion in a strongly anharmonic potential. In this paper, we try to understand the form and origin of the anharmonicities, with the principal aim of gaining a better understanding of the principal motion types, but also in order to develop more efficient numerical methods for simulating neutron scattering spectra of large proteins.


1999   Références trouvées : 4

Jardat, M., Bernard, O.,Turq, P. & Kneller, G.  (1999)

Transport coefficients of electrolyte solutions from smart Brownian Dynamics simulations

J. Chem. Phys., vol. 110, no. 16, p. 7993

Spotheim-Maurizot, M., Sy, D., Begusova, M., Hinsen, K., Savoye, C., Tartier, L., Viduna, D., Kneller, G. & M. Charlier, M.  (1999)

Conformational effects on DNA radiation damage. Influence of structure on the accessibility to OH radicals

In Radiation Research. Vol. 2. Congress Proceedings, Intenational Association for Radiation Research, Allen Press

Hinsen, K ; Kneller, GR  (1999)

A simplified force field for describing vibrational protein dynamics over the whole frequency range

Journal of Chemical Physics 111 (24) 10766-10769
The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution. (C) 1999 American Institute of Physics. [S0021-9606(99)52348-9].

The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution. (C) 1999 American Institute of Physics. [S0021-9606(99)52348-9].

Kneller, GR ; Hinsen, K   (1999)

Analysis of low-frequency motions in proteins by computer simulation and neutron scattering experiment

Neutrons and Numerical Methods 147 - Editor(s) : D. Kearley and M. Johnson


1998   Références trouvées : 3

Mülders, T., Toxvaerd, S. & Kneller, G.  (1998)

Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes

Phys. Rev. E 58, (5) 6766–6780

Kneller, G. & Mülders, T.   (1998)

Comment on "atomic stress isobaric scaling for systems subjected to holonomic constraints" [J. Chem. Phys. 106, 195 (1997)]

J. Chem. Phys., vol. 109, no. 7, pp. 6508–6509, 1998

Morélon, N.-D., Kneller, G., Ferrand, M., Grand, A., Smith, J. & Bée, M.  (1998)

Dynamics of alkane chains included in an organic matrix : Molecular dynamics simulation and comparison with neutron scattering experiment

J. Chem. Phys. 109, (7) 2883


1996   Références trouvées : 3

Kneller, G. & T. Mülders, T.  (1996)

Nosé-andersen molecular dynamics for partially rigid molecules : Coupling all atoms to heat and pressure baths

Phys. Rev.E, vol. 54, no. 6, pp. 6825–6837

Kneller, GR ; Hinsen, K  (1996)

Sedimentation of clusters of spheres 2. Constrained systems

Journal of Molecular Modeling 2 (9) 239-250
Starting from the N-body friction matrix of an unconstrained system of N rigid particles immersed in a viscous liquid, we derive rigorous expressions for the corresponding friction and mobility matrices of a geometrically constrained dynamical system. Our method is based on the fact that geometrical constraints in a dynamical system can be cast in the form of linear constraints for the Cartesian translational and angular velocities of its constituents. Corresponding equations of motion for Molecular Dynamics simulations have been derived recently [1].

Starting from the N-body friction matrix of an unconstrained system of N rigid particles immersed in a viscous liquid, we derive rigorous expressions for the corresponding friction and mobility matrices of a geometrically constrained dynamical system. Our method is based on the fact that geometrical constraints in a dynamical system can be cast in the form of linear constraints for the Cartesian translational and angular velocities of its constituents. Corresponding equations of motion for Molecular Dynamics simulations have been derived recently [1].

Hinsen, K ; Kneller, GR  (1996)

Sedimentation of clusters of spheres 1. Unconstrained systems

Journal of Molecular Modeling 2 (9) 227-238
We describe a numerical method for calculating hydrodynamic interactions between spherical particles efficiently and accurately, both for particles immersed in an infinite liquid and for systems with periodic boundary conditions. Our method is based on a multipole expansion in Cartesian tensors. We then show how to solve the equations of motion for translational and rotational motion of suspended particles at large Peclet numbers. As an example we study the sedimentation of an array of spheres with and without periodic boundary conditions. We also study the effect of perturbations on the stability of the trajectories.

We describe a numerical method for calculating hydrodynamic interactions between spherical particles efficiently and accurately, both for particles immersed in an infinite liquid and for systems with periodic boundary conditions. Our method is based on a multipole expansion in Cartesian tensors. We then show how to solve the equations of motion for translational and rotational motion of suspended particles at large Peclet numbers. As an example we study the sedimentation of an array of spheres with and without periodic boundary conditions. We also study the effect of perturbations on the stability of the trajectories.


1995   Références trouvées : 3

Kneller, G., Keiner, V., Kneller, M. & Schiller, M.  (1995)

Nmoldyn, a program package for the calculation and analysis of neutron scattering spectra from MD simulations

Comp. Phys. Comm., vol. 91, pp. 191–214, 1995. Full description in report ILL95KN02T, Institut Laue-Langevin, 156 X, F-38042 Grenoble Cedex, France

Dianoux, A. Sauvajol, J. Kneller, G. & Smith, J.  (1995)

Inelastic neutron scattering and molecular dynamics simulations of pristine and doped polyacetylene

in Proceedings of the 4th Meeting on Disorder in Molecular Solids, Garchy, France

Hinsen, K ; Kneller, GR  (1995)

Influence of geometrical constraints on the dynamics of polypeptide-chains

Physical Review E 52 (6) 6868-6874 Part B
Based on the equations of motion for linked rigid bodies that we derived recently [G. Kneller and K. Hinsen, Phys Rev. E 50, 1559 (1994)], we develop a technique for the simulation of molecular systems with constraints. We apply it to analyze the importance of the-various degrees of freedom of a polypeptide chain for its dynamics. We find that keeping the peptide planes rigid does not change the dynamics much, but that the bending degrees of freedom of the alpha-carbon bond geometry are essential for large-amplitude backbone motions. This means that the phi and psi angles commonly used to characterize protein conformations and protein backbone dynamics do not constitute a sufficient set of variables to perform dynamical simulations.

Based on the equations of motion for linked rigid bodies that we derived recently [G. Kneller and K. Hinsen, Phys Rev. E 50, 1559 (1994)], we develop a technique for the simulation of molecular systems with constraints. We apply it to analyze the importance of the-various degrees of freedom of a polypeptide chain for its dynamics. We find that keeping the peptide planes rigid does not change the dynamics much, but that the bending degrees of freedom of the alpha-carbon bond geometry are essential for large-amplitude backbone motions. This means that the phi and psi angles commonly used to characterize protein conformations and protein backbone dynamics do not constitute a sufficient set of variables to perform dynamical simulations.


1994   Références trouvées : 10

Dianoux, A., Kneller, G., Sauvajol, J. & Smith, J.  (1994)

Dynamics of pure and doped polyacetylene

in Proceedings of the First European Conference on Computational Chemistry, Nancy, France (F. Bernardi and J.L. Rivail, eds.), vol. 330 of AIP Conference Proceedings, pp. 362–366, American Institure of Physics

Dianoux, A., Kneller, G., Sauvajol, J. & Smith, J.  (1994)

Dynamics of pristine and doped polyacetylene : A combined neutron scattering and computer simulation analysis

vol. 172-174, pp. 472–480, 1994. Conference Proceedings 2nd International Discussion Meeting on Relaxations in Complex Systems

Dianoux, A., Kneller, G., Sauvajol, J. & Smith, J.  (1994)

Dynamics of sodium-doped polyacetylene

J. Chem. Phys., vol. 101, no. 1, pp. 634–644

Kneller, G. & Smith, J.  (1994)

Liquid-like side-chain motions in myoglobin

J. Mol. Biol., vol. 242, pp. 181–185

G. Kneller, G.  (1994)

Neutron scattering from classical systems : Stationary phase approximation of the scattering law

Mol. Phys., vol. 83, no. 1, pp. 63–87

Rittger, E., Kneller, G., Micu, A., Souaille, M. & Smith, J.  (1994)

Dynamics of proteins : Simulations versus scattering and spectroscopy experiments

in Proceedings of the First European Conference on Computational Chemistry, Nancy, France (F. Bernardi and J.L. Rivail, eds.), vol. 330 of AIP Conference Proceedings, American Institure of Physics

Smith, J., Calmettes, P., Durand, D., Desmadril, M., Furois-Corbin, S., Kneller, G. & Roux, B.  (1994)

On the configurations accessible to folded and to denatured proteins

in Statistical Mechanics, Protein Structure and Substrate Interactions (S. Doniach, ed.), (New York), pp. 135–145, Plenum Press

Smith, J., Durand, D., Field, M., Furois-Corbin, S., Kneller, G., Nina, M. & Roux, B.  (1994)

Supramolecular interactions and atomic dynamics in proteins and peptide cystals. Jumps, lattice waves and liquid-like diffusion

in Computational Approaches in Supramolecular Chemistry (G. Wipf, ed.), pp. 457–475, Kluwer Academic Publishers

Smith, J., Durand, D., Field, M., Furois-Corbin, S. Kneller, G. & Roux, B.  (1994)

Structure dynamics and function of hydrogen-bonded networks in proteins and related systems

in Hydrogen Bond Networks (M. Belissent-Funel and J. Dore, eds.), pp. 489–508, Kluwer Academic Publishers

Kneller, GR ; Hinsen, K  (1994)

Generalized euler equations for linked rigid bodies

Physical Review E 50 (2) 1559-1564 Part B
We derive the equations of motion for linked rigid bodies from Lagrange mechanics and from Gauss's principle of least constraint. The rotational motion of the subunits is described in terms of quaternion parameters and angular velocities. Different types of joints can be incorporated via axis constraints for the angular velocities. The resulting equations of motion are generalizations of the Euler equations of motion for a single rotor.

We derive the equations of motion for linked rigid bodies from Lagrange mechanics and from Gauss’s principle of least constraint. The rotational motion of the subunits is described in terms of quaternion parameters and angular velocities. Different types of joints can be incorporated via axis constraints for the angular velocities. The resulting equations of motion are generalizations of the Euler equations of motion for a single rotor.


1993   Références trouvées : 3

Dianoux, A., Kneller, G., Sauvajol, J. & Smith, J.  (1993)

The polarized density of states of crystalline polyacetylene : Molecular dynamics Analysis and comparison with neutron scattering results

J. Chem. Phys., vol. 99, no. 7, pp. 5586–5596

Furois-Corbin, S., Smith, J. & Kneller, G.  (1993)

Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin

Proteins : Structure, Function, and Genetics, vol. 16, pp. 141–154

Smith, J. & Kneller, G.  (1993)

Combination of neutron scattering and molecular dynamics to determine internal motions in biomolecules

Mol. Sim., vol. 10, no. 2-6, pp. 363–375


1992   Références trouvées : 2

Kneller, G.  (1992)

Quaternions as a tool for the analysis of molecular systems

Journal de Chimie Physique, vol. 88, pp. 2709–2715

Kneller, G., Smith, J., Cusack, S. & Doster, W.  (1992)

Methyl group dynamics in the crystalline alanine dipeptide : A molecular dynamics and incoherent neutron scattering analysis

J. Chem. Phys., vol. 97, no. 12, pp. 8864–8879


1991   Références trouvées : 2

Garen, J., Field, M., Kneller, G., Karplus, M. & Smith, J.  (1991)

Torsional motions of methyl and ammonium groups in the l-alanine crystal : A comparison of molecular dynamics and normal mode calculations

Journal de Chimie Physique, vol. 88, pp. 2587–2596

Kneller, G.  (1991)

Superposition of molecular structures using quaternions

Mol. Sim., vol. 7, pp. 113–119


1990   Références trouvées : 3

Clementi, E., Corongiu, G., Aida, M., Niesar, U. & Kneller, G.  (1990)

MOTECC 1990 - Modern techniques in computational chemistry

ch. Monte Carlo and Molecular Dynamics Simulations, p. 805. Leiden, The Netherlands : Escom

Kneller, G. & Geiger, A.  (1990)

Molecular dynamics studies and neutron scattering experiments on methylen chloride. II, Dynamics

Mol. Phys., vol. 70, no. 3, pp. 465–483

Niesar, U., Corongiu, G., Clementi, E., Kneller, G. & Bhattacharya, D.  (1990)

Molecular dynamics of liquid water using the NCC ab initio potential

J. Phys. Chem., vol. 94, pp. 7949–7956


1989   Références trouvées : 3

Kneller, G. & Titulaer, U.  (1989)

Boundary layer effects on the rate of diffusion controlled reactions

Physica, vol. 129A, pp. 514–534

Kneller, G. & Geiger, A.  (1989)

Molecular dynamics studies and neutron scattering experiments on methylen chloride. I. Structure

Mol. Phys., vol. 68, no. 2, pp. 487–498

Kneller, G. & Geiger, A.  (1989)

A method to calculate the g-coefficients of the molecular pair correlation function from MD-simulations

Mol. Sim., vol. 3, pp. 283–300


1985   Références trouvées : 1

Anderson, D., Bouclier, R., Charpak, G., Majewski, S. & Kneller, G.  (1985)

Coupling of a BAF2-szintillator to a TMAE-photocathode in a low pressure wire chamber

Atomnya Tekhnia za Ruhbezhom, vol. 5, pp. 18–23, 1985. Translation into Russian


1984   Références trouvées : 1

Kneller, G. & Titulaer, U.  (1984)

The covariant form of the Klein-Kramers-equation and the associated moment equations

Physica, vol. 129A, pp. 81–94


1983   Références trouvées : 1

Anderson, D., Charpak, G., Bouclier, R., Majewski, S. & Kneller, G.  (1983)

Coupling of a BAF2-szintillator to a TMAE-photocathode in a low pressure wire chamber

Nuclear Instruments and Methods, vol. 217, pp. 217–223


Mots-clés

Professeur , Responsable de groupe thématique , Biophysique théorique, simulation moléculaire et calcul scientifique