A Molecular Dynamics on the Thermally Developing Flow of Alanine in Nano-Channel

The flow of the body fluid in the bio-chip and local metabolism require general solutions for the thermally developing flow model in bio-tissue. An algorithm based on the molecular dynamics (MD) and the GROMACS protein data bank is developed to solve the thermally developing bio-flow problem. The flow of the Alanine in the nano-channel driven by a constant external force and applied the thermal boundary are studied. Both global effect (effective channel width) and local effect (thermal boundary) are examined to demonstrate the features of the distributions of velocity in the system. This algorithm can be applied in the design of bio-chip's channel and the building of fundamental phenomena of the burn or frostbite.