Atomic/molecular simulation

Understanding the interfacial behaviors of polymer nanomaterials at Hquid interface has received much attention due to their excellent properties and potential applications in areas such as controlled drug dehvery, biocompatible materials, Pickering emulsion, biosensing, and other fields (Shan and Tenhu, 2007). We mainly focus on the interfacial behaviors of three nanomaterials at Hquid interface, which consists of polymer, nanoparticles, and polymer brush-modified nanoparticles at liquid interface. Numerous relevant experiments and simulation works have been published however, it is stiH difficult to interpret the experimental observation at the atomistic level therefore, molecular simulation is an effective complemental approach. Due to the Hmitation at longer timescale and bi er space scale for all-atom molecular simulations, a lot of works based on coarse-grained molecular simulations have been reported. 

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

When using a switching function in a molecular simulation with a residue-based cutoff it is important that the function has the same value for all pairs of atoms in the two interacting groups. Otherwise, severe fluctuations in the energy can arise when the separation is within the cutoff region. These two contrasting situations can be formally expressed as follows ... 

Molecular Dynamics and Monte Carlo Simulations. At the heart of the method of molecular dynamics is a simulation model consisting of potential energy functions, or force fields. Molecular dynamics calculations represent a deterministic method, ie, one based on the assumption that atoms move according to laws of Newtonian mechanics. Molecular dynamics simulations can be performed for short time-periods, eg, 50—100 picoseconds, to examine localized very high frequency motions, such as bond length distortions, or, over much longer periods of time, eg, 500—2000 ps, in order to derive equiUbrium properties. It is worthwhile to summarize what properties researchers can expect to evaluate by performing molecular simulations ... 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

Ab initio methods allow the nature of active sites to be elucidated and the influence of supports or solvents on the catalytic kinetics to be predicted. Neurock and coworkers have successfully coupled theory with atomic-scale simulations and have tracked the molecular transformations that occur over different surfaces to assess their catalytic activity and selectivity [95-98]. Relevant examples are the Pt-catalyzed NO decomposition and methanol oxidation. In case of NO decomposition, density functional theory calculations and kinetic Monte Carlo simulations substantially helped to optimize the composition of the nanocatalyst by alloying Pt with Au and creating a specific structure of the PtgAu7 particles. In catalytic methanol decomposition the elementary pathways were identified... 

Most liquid phase molecular simulations with explicit atomic polarizabilities are performed with MD rather than MC techniques. This is due to the fact that, despite its general computational simplicity, MC with explicit polarization [173, 174] requires that Eq. (9-21) be solved every MC step, when even one molecule in the system is moved, and the number of configurations in an average Monte Carlo computation is orders of magnitude greater than in a MD simulation. For nonpolarizable, pairwise-additive models, MC methods can be efficient because only the... 

Advances in computational capability have raised our ability to model and simulate materials structure and properties to the level at which computer experiments can sometimes offer significant guidance to experimentation, or at least provide significant insights into experimental design and interpretation. For self-assembled macromolecular structures, these simulations can be approached from the atomic-molecular scale through the use of molecular dynamics or finite element analysis. Chapter 6 discusses opportunities in computational chemical science and computational materials science. 

Molecular calculations provide approaches to supramolecular structure and to the dynamics of self-assembly by extending atomic-molecular physics. Alternatively, the tools of finite element analysis can be used to approach the simulation of self-assembled film properties. The voxel4 size in finite element analysis needs be small compared to significant variation in structure-property relationships for self-assembled structures, this implies use of voxels of nanometer dimensions. However, the continuum constitutive relationships utilized for macroscopic-system calculations will be difficult to extend at this scale because nanostructure properties are expected to differ from microstructural properties. In addition, in structures with a high density of boundaries (such as thin multilayer films), poorly understood boundary conditions may contribute to inaccuracies. 

The sizes of the dendrimers have been determined by calculating the molecular volumes, as defined by the van der Waals radii of the atoms, and by calculating the radii of gyration for several configurations of the dendrimers, as obtained from a molecular dynamics simulation at room temperature. The solvent influence on the calculated radii was estimated by scaling the nonbonded interactions between the atoms. Molecular volumes and average radii for ensembles of 500 conformations of the BAB-dendr-(NH2)D dendrimers have been collected in Table 26.2. 

K. Kern, Institut fiir Grenzflachenforschung und Vakuumphysik, KFR Julich, P. O. Box 1913, D-5170 Julich, FDR D. S. King, Center for Atomic, Molecular and Optical Physics, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA D. P. Landau, Center for Simulational Physics, The University of Georgia, Athens, GA 30602, USA... 

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