Models for Molecular Dynamics

Meiler et al applied the model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. Ishima et aO compared the methyl rotation axis order parameters derived from the model-free analyses of the and longitudinal and transverse relaxation rates measured in the same protein sample. Best et al reported the results of molecular dynamics simulations compared with NMR relaxation experiments for maltose and isomaltose. Using the model-free formalism they could estimate reliable order parameters. Baber et used an extended model- 

It has recently become more widely appreciated that the presence of rotational diffusional anisotropy in proteins and other macromolecules can have a significant affect on the interpretation of NMR relaxation data in terms of molecular motion. Andrec et al. used a Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data. Sturz and Dolle examined the reorientational motion of toluene in neat liquid by using relaxation measurements. The relaxation rates were analyzed by rotational diffusion models. Chen et al measured self-diffusion coefficients for fluid hydrogen and fluid deuterium at pressures up to 200 MPa and in the temperature range 171-372 K by the spin echo method. The diffusion coefficients D were described by the rough sphere (RHS) model invoking the rotation translational coupling parameter A = 1. 

In the recent years there has been significant interest in the characterization of the overall hydrodynamic properties of biomacromolecules. Because the overall tumbling provides a dominant contribution to spin-relaxation rates, its accurate 

Halle and Davidovic developed a dynamic model that explicitly links protein hydrodynamics to hydration dynamics. With the aid of this model structure-based predictions of global biomolecular dynamics become possible. The validity of the model was demonstrated for a set of proteins for which accurate experimental rotational diffusion coefficients are available. Boisbouvier et al derived the rotational diffusion tensor of nucleic acid from relaxation times. 

The results were in excellent agreement with values obtained from hydro-dynamic modelling. 

Derbyshire et used a series of mathematical functions has been used to fit the proton free-induction decays of concentrated carbohydrate-water samples. For the solid protons, these functions included a sine function, as well as the Fourier transforms of single and multiple Pake functions multiplied by a Gaussian broadening. The NMR signal from the mobile protons is described by an exponential function. It is found that in most cases the sine function gives a satisfactory result and provides valuable information about the second moment 

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Juffer, A.H., Berendsen, H.J.C. Dynamic surface boundary conditions A simple boundary model for molecular dynamics simulations. Mol. Phys. 79 (1993) 623-644. 

Lu ZY, Zhang YK (2008) Interfacing ab initio quantum mechanical method with classical Drude os-illator polarizable model for molecular dynamics simulation of chemical reactions. J Chem Theory Comput 4(8) 1237-1248... 

Figure 17. An atomistic model for molecular dynamic simulation of physical diffusion of ions and mediator in Nafion clusters.138 Reprinted from Journal of Electrochemical Society, X. Zhou, Z. Chen, F. Delgado, D. Brenner, R. Srivastava, J. Electrochem. Soc. 154, B82 (2007)- reproduced by permission of the Electrochemical Society.

Ferrara P, J Apostolakis, A Caflisch (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins Struct., Funct., Genet. 46 (1) 24—33... 

Going beyond the mean-field level, several "hybrid" approaches are now being explored in MD simulations. Examples include a recent model [70] in which the immediate hydration of the solute is modeled explicitly by a layer of water molecules, and the GB model is used to treat the bulk continuum solvent outside the explicit simulation volume. A similar idea was recently found very effective in the context of replica-exchange simulations [71]. An explicit ion/implicit water (PB) solvation model for molecular dynamics of nucleic acids has recently been tested [72]. 

Chowdhary, J., et al., A Polarizable force field of dipalmitoylphos-phatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids./ Phys. Chem. B, 2013.117,9142-9160. 

Barisik M, Kim B, Beskok A (2010) Smart wall model for molecular dynamics simulations of nanoscale gas flows. Commun ComputPhys 7 977-993... 

Fenchenko studied free induction decays and transverse relaxation in entangled polymer melts. He considered both the effects of the dipolar interactions between spins in different polymer chains and within an isolated segment along s single chain. Sebastiao and co-workers presented a unifying model for molecular dynamics and NMR relaxation for chiral and non-chiral nematic liquid crystals. The model included molecular rotations/ reorientations, translational self-diffusion as well as collective motions. For the chiral nematic phase, an additional relaxation mechanism was proposed, associated with rotations induced by translational diffusion along the helical axis. The model was applied to interpret experimental data, to which we return below. 

Fiorini M, Burger K, Mark A et al (2000) A new 2,2,2-trifluoroethanol model for molecular dynamics simulatimis. J Phys Chem B 104 12347—12354... 

Sergi D, Scocchi G, Ortona A Coarse-graining MARTINI model for molecular-dynamics simulations of the wetting properties of graphitic surfaces with non-ionic, long-chain, and T-shaped surfactants, J Chem Phys 137 094904, 2012. 

Z. Y. Lu and Y. K. Zhang,/. Chem. Theory Comput., 4(8), 1237-1248 (2008). Interfacing Ab Initio Quantum Mechanical Method with Classical Drude Oscillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions. 

B. A. Bauer, G. L. Warren, and S. Patel, J. Chem. Theory Comput., 5 2), 359-373 (2009). Incorporating Phase-Dependent Polarizability in Nonadditive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface. 

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