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Simulation and visualization of complex bio-molecules are gaining importance; this is because of the fact that functional properties of such molecules are more dependent on their 3D structures. One of the challenges of computational biology is prediction of structures of protein from amino sequence. Three dimensional visualization of molecular structure is also an important research goal in nano engineering. Such visualization, simulation and animation of reaction dynamics are essential for modern chemistry. Force field simulation of large number of atoms in complex molecular structure is computationally challenging. To find equilibrium of force fields and resultant dynamic structure of large atomic clusters which assembles to predictable molecules is one of the major goals of computational biology. In this paper we describe a simple but efficient algorithm (MoliSim3D) to simulate and dynamically visualize in 3D the assembly of atoms in presence of internal and external forces. It helps monitoring and measuring different bond angles, dimensions and displacements of selected portions from thousands of atoms forming target molecule. Pattern recognition, pattern error detection and reaction control are advance tools of virtual molecular assembly. The proposed system is basically intended as educational tool and to help researchers in understanding complex molecular dynamics and functionality with high degree of confidence in simulated environment.

SIMULATION AND 3D VISUALIZATION OF COMPLEX MOLECULAR STRUCTURE FOR STUDY OF PROTEIN AND NANO MATERIALS