A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavior of δ for the polymer is modeled by running molecular dynamics (MD) simulatio...

It is argued that by optimizing the orientation of a molecule in a cube can improve the efficiency of certain molecular modeling procedures.

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) si...

The state of the art of molecular modeling with particular attention to the possibilities of application to process simulation is reviewed in this paper. The basic principles of molecular modeling are presented, as well as the recent achievements in direct applications of the methods. Modeling in process engineering is discussed, showing how different models and theories must be applied for dif...

Muscle-specific kinase (MuSK) is a crucial receptor tyrosine kinase required for the development and function of neuromuscular junction. Although many domains of the protein have already been modeled with crystallographic techniques in various organisms, a single model for the whole human structure is not yet available. We have tried to predict a complete model of the protein, by using two para...

Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to th...