Transport molecular dynamics

The alternative simulation approaches are based on molecular dynamics calculations. This is conceptually simpler that the Monte Carlo method the equations of motion are solved for a system of A molecules, and periodic boundary conditions are again imposed. This method pennits both the equilibrium and transport properties of the system to be evaluated, essentially by numerically solvmg the equations of motion... 

Marrink, S.J., Jahnig, F., Berendsen, H.J.C. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys. J. 71 (1996) 632-647. 

There are basically two different computer simulation techniques known as molecular dynamics (MD) and Monte Carlo (MC) simulation. In MD molecular trajectories are computed by solving an equation of motion for equilibrium or nonequilibrium situations. Since the MD time scale is a physical one, this method permits investigations of time-dependent phenomena like, for example, transport processes [25,61-63]. In MC, on the other hand, trajectories are generated by a (biased) random walk in configuration space and, therefore, do not per se permit investigations of processes on a physical time scale (with the dynamics of spin lattices as an exception [64]). However, MC has the advantage that it can easily be applied to virtually all statistical-physical ensembles, which is of particular interest in the context of this chapter. On account of limitations of space and because excellent texts exist for the MD method [25,61-63,65], the present discussion will be restricted to the MC technique with particular emphasis on mixed stress-strain ensembles. 

In the next section we describe the basic models that have been used in simulations so far and summarize the Monte Carlo and molecular dynamics techniques that are used. Some principal results from the scaling analysis of EP are given in Sec. 3, and in Sec. 4 we focus on simulational results concerning various aspects of static properties the MWD of EP, the conformational properties of the chain molecules, and their behavior in constrained geometries. The fifth section concentrates on the specific properties of relaxation towards equilibrium in GM and LP as well as on the first numerical simulations of transport properties in such systems. The final section then concludes with summary and outlook on open problems. 

These apparent restrictions in size and length of simulation time of the fully quantum-mechanical methods or molecular-dynamics methods with continuous degrees of freedom in real space are the basic reason why the direct simulation of lattice models of the Ising type or of solid-on-solid type is still the most popular technique to simulate crystal growth processes. Consequently, a substantial part of this article will deal with scientific problems on those time and length scales which are simultaneously accessible by the experimental STM methods on one hand and by Monte Carlo lattice simulations on the other hand. Even these methods, however, are too microscopic to incorporate the boundary conditions from the laboratory set-up into the models in a reahstic way. Therefore one uses phenomenological models of the phase-field or sharp-interface type, and finally even finite-element methods, to treat the diffusion transport and hydrodynamic convections which control a reahstic crystal growth process from the melt on an industrial scale. 

Whenever the polymer crystal assumes a loosely packed hexagonal structure at high pressure, the ECC structure is found to be realized. Hikosaka [165] then proposed the sliding diffusion of a polymer chain as dominant transport process. Molecular dynamics simulations will be helpful for the understanding of this shding diffusion. Folding phenomena of chains are also studied intensively by Monte Carlo methods and generalizations [166,167]. 

The theories of structure and transport outlined above will be compared with molecular dynamics In what follows. 

Chapter 15 gives an extensive and detailed review of theoretical and practical aspects of macromolecular transport in nanostructured media. Chapter 16 examines the change in transport properties of electrolytes confmed in nanostructures, such as pores of membranes. The confinment effect is also analyzed by molecular dynamic simulation. 

There is difficulty in defining the absolute mobilities of the constituent ions in a molten salt, since it does not contain fixed particles that could serve as a coordinate reference. Experimental means for measuring external transport numbers or external mobilities are scarce, although the zone electromigration method (layer method) and the improved Hittorf method may be used. In addition, external mobilities in molten salts cannot be easily calculated, even from molecular dynamics simulation. 

Besides these generalities, little is known about proton transfer towards an electrode surface. Based on classical molecular dynamics, it has been suggested that the ratedetermining step is the orientation of the HsO with one proton towards the surface [Pecina and Schmickler, 1998] this would be in line with proton transport in bulk water, where the proton transfer itself occurs without a barrier, once the participating molecules have a suitable orientation. This is also supported by a recent quantum chemical study of hydrogen evolution on a Pt(lll) surface [Skulason et al., 2007], in which the barrier for proton transfer to the surface was found to be lower than 0.15 eV. This extensive study used a highly idealized model for the solution—a bilayer of water with a few protons added—and it is not clear how this simplification affects the result. However, a fully quantum chemical model must necessarily limit the number of particles, and this study is probably among the best that one can do at present. 

In addition to enhancing surface reactions, water can also facilitate surface transport processes. First-principles ab initio molecular dynamics simulations of the aqueous/ metal interface for Rh(l 11) [Vassilev et al., 2002] and PtRu(OOOl) alloy [Desai et al., 2003b] surfaces showed that the aqueous interface enhanced the apparent transport or diffusion of OH intermediates across the metal surface. Adsorbed OH and H2O molecules engage in fast proton transfer, such that OH appears to diffuse across the surface. The oxygen atoms, however, remained fixed at the same positions, and it is only the proton that transfers. Transport occurs via the symmetric reaction... 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

The sensitivity of Magnetic Resonance (MR) to the local concentration, molecular dynamics and molecular environment of these nuclei make it well suited for the study of deterioration processes in concrete materials. Hydrogen (water), lithium, sodium, chlorine and potassium are all MR sensitive nuclei and play an important role in cement chemistry. The ability of MRI to spatially resolve and non-destructively examine test samples as a function of treatment or exposure has the potential to provide new insight to better understand deterioration mechanisms and mass transport properties of concrete materials. 

There are several attractive features of such a mesoscopic description. Because the dynamics is simple, it is both easy and efficient to simulate. The equations of motion are easily written and the techniques of nonequilibriun statistical mechanics can be used to derive macroscopic laws and correlation function expressions for the transport properties. Accurate analytical expressions for the transport coefficient can be derived. The mesoscopic description can be combined with full molecular dynamics in order to describe the properties of solute species, such as polymers or colloids, in solution. Because all of the conservation laws are satisfied, hydrodynamic interactions, which play an important role in the dynamical properties of such systems, are automatically taken into account. 

The set of rotations used in MPC dynamics can be chosen in various ways and the specific choice will determine the values of the transport properties of the system, just as the choice of the intermolecular potential will determine the transport properties in a system evolving by full molecular dynamics through Newton s equations of motion. It is often convenient to use rotations about a randomly chosen direction, n, by an angle a chosen from a set of angles. The... 

Most descriptions of the dynamics of molecular or particle motion in solution require a knowledge of the frictional properties of the system. This is especially true for polymer solutions, colloidal suspensions, molecular transport processes, and biomolecular conformational changes. Particle friction also plays an important role in the calculation of diffusion-influenced reaction rates, which will be discussed later. Solvent multiparticle collision dynamics, in conjunction with molecular dynamics of solute particles, provides a means to study such systems. In this section we show how the frictional properties and hydrodynamic interactions among solute or colloidal particles can be studied using hybrid MPC-MD schemes. 

Multiparticle collision dynamics describes the interactions in a many-body system in terms of effective collisions that occur at discrete time intervals. Although the dynamics is a simplified representation of real dynamics, it conserves mass, momentum, and energy and preserves phase space volumes. Consequently, it retains many of the basic characteristics of classical Newtonian dynamics. The statistical mechanical basis of multiparticle collision dynamics is well established. Starting with the specification of the dynamics and the collision model, one may verify its dynamical properties, derive macroscopic laws, and, perhaps most importantly, obtain expressions for the transport coefficients. These features distinguish MPC dynamics from a number of other mesoscopic schemes. In order to describe solute motion in solution, MPC dynamics may be combined with molecular dynamics to construct hybrid schemes that can be used to explore a variety of phenomena. The fact that hydrodynamic interactions are properly accounted for in hybrid MPC-MD dynamics makes it a useful tool for the investigation of polymer and colloid dynamics. Since it is a particle-based scheme it incorporates fluctuations so that the reactive and nonreactive dynamics in small systems where such effects are important can be studied. 

Monte Carlo heat flow simulation, nonequilibrium molecular dynamics, 73-74, 77-81 multiparticle collision dynamics hydrodynamic equations, 105-107 macroscopic laws and transport coefficients, 102-104 single-particle friction and diffusion, 114-118... 

The favourable properties which mark out vesicles as protocell models were confirmed by computer simulation (Pohorill and Wilson, 1995). These researchers studied the molecular dynamics of simple membrane/water boundary layers the bilayer surface fluctuated in time and space. The model membrane consisted of glycerine-1-monooleate defects were present which allowed ion transport to occur, whereby negative ions passed through the bilayer more easily than positive ions. The membrane-water boundary layer should be particularly suited to reactions which are accelerated by heterogeneous catalysis. Thus, the authors believe that these vesicles fulfil almost all the conditions required for the first protocells on earth ... 

Tuckerman, M., K. Laasonen, M. Sprik, and M. Parrinello. 1995. Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J. Chem. Phys. 103, 150. 

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