Molecular dynamics morphology

While thin polymer films may be very smooth and homogeneous, the chain conformation may be largely distorted due to the influence of the interfaces. Since the size of the polymer molecules is comparable to the film thickness those effects may play a significant role with ultra-thin polymer films. Several recent theoretical treatments are available [136-144,127,128] based on Monte Carlo [137-141,127, 128], molecular dynamics [142], variable density [143], cooperative motion [144], and bond fluctuation [136] model calculations. The distortion of the chain conformation near the interface, the segment orientation distribution, end distribution etc. are calculated as a function of film thickness and distance from the surface. In the limit of two-dimensional systems chains segregate and specific power laws are predicted [136, 137]. In 2D-blends of polymers a particular microdomain morphology may be expected [139]. Experiments on polymers in this area are presently, however, not available on a molecular level. Indications of order on an... 

Ogata, S., Mitsuya, Y, Zhang, H. D., and Fukuzawa, K., "Molecular Dynamics Simulation for Analysis of Surface Morphology of Lubricant Films with Functional End Groups, IEEE Trans. Magn., Vol. 41,2005, pp. 3013-3015. 

Chui, Y.H., Grodiola, G., Snook, l.K. and Russo, S.P. (2007) Molecular dynamics investigation of the structural and thermodynamic properties of gold nanodusters of different morphologies. Physical Review B - Condensed Matter, 75, 033404-1-033404-4. 

At the mesoscopic scale, interactions between molecular components in membranes and catalyst layers control the self-organization into nanophase-segregated media, structural correlations, and adhesion properties of phase domains. Such complex processes can be studied by various theoretical tools and simulation techniques (e.g., by coarse-grained molecular dynamics simulations). Complex morphologies of the emerging media can be related to effective physicochemical properties that characterize transport and reaction at the macroscopic scale, using concepts from the theory of random heterogeneous media and percolation theory. 

We will briefly discuss the molecular dynamics results obtained for two systems—protein-like and random-block copolymer melts— described by a Yukawa-type potential with (i) attractive A-A interactions (saa < 0, bb = sab = 0) and with (ii) short-range repulsive interactions between unlike units (sab > 0, aa = bb = 0). The mixtures contain a large number of different components, i.e., different chemical sequences. Each system is in a randomly mixing state at the athermal condition (eap = 0). As the attractive (repulsive) interactions increase, i.e., the temperature decreases, the systems relax to new equilibrium morphologies. 

Since the headgroup of PLs contains phosphate derivatives, it is apparent that 31P NMR became the method of choice in structural studies of this class of compounds. The NMR measurements provide information about the composition of PLs mixtures, phase of samples, their morphology and molecular dynamics.86... 

In this work, we have approaehed the understanding of proton transport with two tasks. In the first task, deseribed above, we have sought to identify the moleeular-level stmeture of PFSA membranes and their relevant interfaees as a funetion of water content and polymer architecture. In the second task, described in this Section, we explain our efforts to model and quantify proton transport in these membranes and interfaces and their dependence on water content and polymer architecture. As in the task I, the tool employed is molecular dynamics (MD) simulation. A non-reactive algorithm is sufficient to generate the morphology of the membrane and its interfaces. It is also capable of providing some information about transport in the system such as diffusivities of water and the vehicular component of the proton diffusivity. Moreover, analysis of the hydration of hydronium ion provides indirect information about the structural component of proton diffusion, but a direct measure of the total proton diffusivity is beyond the capabilities of a non-reactive MD simulation. Therefore, in the task II, we develop and implement a reactive molecular dynamics algorithm that will lead to direct measurement of the total proton diffusivity. As the work is an active field, we report the work to date. 

We treat, in this chapter, mainly solid composed of water molecules such as ices and clathrate hydrates, and show recent significant contribution of simulation studies to our understanding of thermodynamic stability of those crystals in conjunction with structural morphology. Simulation technique adopted here is not limited to molecular dynamics (MD) and Monte Carlo (MC) simulations[l] but does include other method such as lattice dynamics. Electronic state as well as nucleus motion can be solved by the density functional theory[2]. Here we focus, however, our attention on the ambient condition where electronic state and character of the chemical bonds of individual molecules remain intact. Thus, we restrict ourselves to the usual simulation with intermolecular interactions given a priori. 

The ability to model the impact of impurities on the structure of a crystalline system is crucial it enables the impact of both solvents and impurities quantified. Both in terms of the overall morphology and where the interactions are likely to occur, thus providing a better understanding of the process chemistry of a system. Two principal techniques exist for simulating the effect of solvents/sorbates on the surface of a crystal Monte Carlo and Molecular Dynamics and Minimization. 

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