Structure simulation models using methods

Simulation methods have been proved to be useful in the study of many different molecular systems, in particular in the case of flexible polymers chains [ 14]. According to the variety of structures and the theoretical difficulties inherent to branched structures, simulation work is a very powerful tool in the study of this type of polymer, and can be applied to the general problems outHned above. Sometimes, this utility is manifested even for behaviors which can be explained with simple theoretical treatments in the case of linear chains. Thus, the description of the theta state of a star chain cannot be performed through the use of the simple Gaussian model. The adequate simulation model and method depend strongly on the particular problem investigated. Some cases require a realistic representation of the atoms in the molecular models [10]. Other cases, however, only require simplified coarse-grained models, where some real mon-... 

Having previously introduced the key methods to determine the important variables with respect to stress and strength distributions, the most acceptable way to predict mechanical component reliability is by applying SSI theory (Dhillon, 1980). SSI analysis is one of the oldest methods to assess structural reliability, and is the most commonly used method because of its simplicity, ease and economy (Murty and Naikan, 1997 Sundararajan and Witt, 1995). It is a practical engineering tool used for quantitatively predicting the reliability of mechanical components subjected to mechanical loading (Sadlon, 1993) and has been described as a simulative model of failure (Dasgupta and Pecht, 1991). 

Unlike the simulations which only consider particle-cluster interactions discussed earlier, hierarchical cluster-cluster aggregation (HCCA) allows for the formation of clusters from two clusters of the same size. Clusters formed by this method are not as dense as clusters formed by particle-cluster simulations, because a cluster cannot penetrate into another cluster as far as a single particle can (Fig. 37). The fractal dimension of HCCA clusters varies from 2.0 to 2.3 depending on the model used to generate the structure DLA, RLA, or LTA. For additional details, the reader may consult Meakin (1988). 

This chapter is concerned with the application of liquid state methods to the behavior of polymers at surfaces. The focus is on computer simulation and liquid state theories for the structure of continuous-space or off-lattice models of polymers near surfaces. The first computer simulations of off-lattice models of polymers at surfaces appeared in the late 1980s, and the first theory was reported in 1991. Since then there have been many theoretical and simulation studies on a number of polymer models using a variety of techniques. This chapter does not address or discuss the considerable body of literature on the adsorption of a single chain to a surface, the scaling behavior of polymers confined to narrow spaces, or self-consistent field theories and simulations of lattice models of polymers. The interested reader is instead guided to review articles [9-11] and books [12-15] that cover these topics. 

Molecular simulations are used most often for modeling proteins and nucleic acids. We mention the methods here only because they are methods for computing a free energy directly. However, they are rather complex calculations, so we will keep our comments brief. Molecular dynamics simulations give information about the variation in structure and energy of a molecule over an interval of time (78,79). In MD, each atom moves according to Newton s equations of motion for classical particles ... 

To establish the molecular thermodynamic model for uniform systems based on concepts from statistical mechanics, an effective method by combining statistical mechanics and molecular simulation has been recommended (Hu and Liu, 2006). Here, the role of molecular simulation is not limited to be a standard to test the reliability of models. More directly, a few simulation results are used to determine the analytical form and the corresponding coefficients of the models. It retains the rigor of statistical mechanics, while mathematical difficulties are avoided by using simulation results. The method is characterized by two steps (1) based on a statistical-mechanical derivation, an analytical expression is obtained first. The expression may contain unknown functions or coefficients because of mathematical difficulty or sometimes because of the introduced simplifications. (2) The form of the unknown functions or unknown coefficients is then determined by simulation results. For the adsorption of polymers at interfaces, simulation was used to test the validity of the weighting function of the WDA in DFT. For the meso-structure of a diblock copolymer melt confined in curved surfaces, we found from MC simulation that some more complex structures exist. From the information provided by simulation, these complex structures were approximated as a combination of simple structures. Then, the Helmholtz energy of these complex structures can be calculated by summing those of the different simple structures. 

Molecular modelling is not strictly an analytical tool that can be used directly. It is, however, a valuable way of visualizing supramolecular systems and predicting structures. The most sophisticated methods are able to predict properties associated with the model that can usefully be compared to data gathered on the real system. This is useful when several different interpretations of an experiment arise as one model may be shown to fit the data best and so be the most probable explanation. The main limitations of molecular modelling, and computational techniques in general, are the accuracy of the output and the the size of simulation that can usefully be attempted without recourse to a supercomputer or massively parallel facility. 

---