Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations

Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes can be simulated, including the initial steps of misfolding. By introducing mutations in silico, the effect of pathogenic mutations on PrP conformation and dynamics can be assessed. Here, we briefly introduce molecular dynamics methods and review the application of molecular dynamics simulations to obtain insight into various aspects of the PrP, including the mechanism of misfolding, the response to changes in the environment, and the influence of disease-related mutations

The Dynamics of Silica Melts under High Pressure: Mode-Coupling Theory Results

The high-pressure dynamics of a computer-modeled silica melt is studied in the framework of the mode-coupling theory of the glass transition (MCT) using static-structure input from molecular-dynamics (MD) computer simulation. The theory reproduces the experimentally known viscosity minimum (diffusivity maximum) as a function of density or pressure and explains it in terms of a corresponding minimum in its critical temperature. This minimum arises from a gradual change in the equilibrium static structure which shifts from being dominated by tetrahedral ordering to showing the cageing known from high-density liquids. The theory is in qualitative agreement with computer simulation results.Comment: Presented at ESF EW Glassy Liquids under Pressure, to be published in Journal of Physic

The Structure and Dynamics of Sodium Disilicate

We investigate the structure and dynamics of sodium disilicate by means of molecular dynamics computer simulation. We show that the structure is described by a partially destroyed tetrahedral SiO_4 network and a spherical super structure formed by the silicon and sodium atoms. The static structure factor of our simulation is in very good agreement with one from a neutron scattering experiment. For 1008 particles we find strong finite size effects in the dynamics which are due to the missing of modes contributing to the boson peak.Comment: 7 pages of Latex, 3 figure

Computer simulation of liquid crystals

A review is presented of molecular and mesoscopic computer simulations of liquid crystalline systems. Molecular simulation approaches applied to such systems are described and the key findings for bulk phase behaviour are reported. Following this, recently developed lattice Boltzmann (LB) approaches to the mesoscale modelling of nemato-dynamics are reviewed. The article concludes with a discussion of possible areas for future development in this field.</p

Molecular Dynamics Computer Simulation of the Dynamics of Supercooled Silica

We present the results of a large scale computer simulation of supercooled silica. We find that at high temperatures the diffusion constants show a non-Arrhenius temperature dependence whereas at low temperature this dependence is also compatible with an Arrhenius law. We demonstrate that at low temperatures the intermediate scattering function shows a two-step relaxation behavior and that it obeys the time temperature superposition principle. We also discuss the wave-vector dependence of the nonergodicity parameter and the time and temperature dependence of the non-Gaussian parameter.Comment: 5 pages, Latex, 6 postscript figure

A quantitative test of the mode-coupling theory of the ideal glass transition for a binary Lennard-Jones system

Using a molecular dynamics computer simulation we determine the temperature dependence of the partial structure factors for a binary Lennard-Jones system. These structure factors are used as input data to solve numerically the wave-vector dependent mode-coupling equations in the long time limit. Using the so determined solutions, we compare the predictions of mode-coupling theory (MCT) with the results of a previously done molecular dynamics computer simulation [Phys. Rev. E 51, 4626 (1995), ibid. 52, 4134 (1995)]. From this comparison we conclude that MCT gives a fair estimate of the critical coupling constant, a good estimate of the exponent parameter, predicts the wave-vector dependence of the various nonergodicity parameters very well, except for very large wave-vectors, and gives also a very good description of the space dependence of the various critical amplitudes. In an attempt to correct for some of the remaining discrepancies between the theory and the results of the simulation, we investigate two small (ad hoc) modifications of the theory. We find that one modification gives a worse agreement between theory and simulation, whereas the second one leads to an improved agreement.Comment: Figures available from W. Ko

Molecular Dynamics Computer Simulation of Crystal Growth and Melting in Al50Ni50

The melting and crystallization of Al50Ni50} are studied by means of molecular dynamics computer simulations, using a potential of the embedded atom type to model the interactions between the particles. Systems in a slab geometry are simulated where the B2 phase of AlNi in the middle of an elongated simulation box is separated by two planar interfaces from the liquid phase, thereby considering the (100) crystal orientation. By determining the temperature dependence of the interface velocity, an accurate estimate of the melting temperature is provided. The value k=0.0025 m/s/K for the kinetic growth coefficient is found. This value is about two orders of magnitude smaller than that found in recent simulation studies of one-component metals. The classical Wilson-Frenkel model is not able to describe the crystal growth kinetics on a quantitative level. We argue that this is due to the neglect of diffusion processes in the liquid-crystal interface.Comment: 6 pages, 6 figure

Systematic coarse graining: "Four lessons and a caveat" from nonequilibrium statistical mechanics

With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained information for dynamic systems. We sketch the role and potential of Monte Carlo, molecular dynamics and Brownian dynamics simulations in the thermodynamic approach to coarse graining. A melt of entangled linear polyethylene molecules serves us as an illustrative example.Comment: 15 pages, 4 figure

Ab-Initio Molecular Dynamics

Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method and the recently devised efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics, which unifies best of both schemes are discussed. The predictive power of this novel second-generation Car-Parrinello approach is demonstrated by a series of applications ranging from liquid metals, to semiconductors and water. This development allows for ab-initio molecular dynamics simulations on much larger length and time scales than previously thought feasible.Comment: 13 pages, 3 figure