Optimized Algorithm For The Calculation Of Potentials In Molecular Simulation Of Protein Adsorption

Protein adsorption on interfaces is a kind of complicated and fascinating phenomenon, which can be applied to a broad range of areas like biological engineering, biological pharmacy, etc. In terms of strong relationships between protein structure and its functions, in-depth research in biological field can hardly be achieved before we can obtain a deep understanding of protein structural changes. Fortunately, molecular simulation brings hope for the study of protein adsorption, which can help us study mechanism of adsorption and adsorption dynamics at molecular level.In most molecular simulation, calculation of short-range potential is the most time-consuming part, thus optimization of algorithm for calculation of potential is always a critical subject. Based on the Verlet neighbor list and cell link list methods, the author put forward a new efficient algorithm for potential calculation which has the following characteristics: (1)based on Bekker method, atoms in the system are divided into several sections according to their positions, decreasing the number of Verlet neighbor lists for each atom from 9 to 4 at most; (2) direction vector matrix is proposed to speed up the search of the cell link lists for each atom, accelerating the generation of Verlet neighbor list; (3)a particular and efficient data structure is introduced, bringing more convenience to data manipulation. According to the comparison of simulation time between new algorithm and conventional algorithm, the former is only 30%~40% of the latter.Using the new algorithm, we performed MD simulation of poly-10-lysine adsorption on solid/liquid interface. Here are the conditions and simplified models we adopted: NVT system, periodic boundary condition, rigid-body model, spherical cutoff model. The results show that: as the adsorption went on, dihedral angles of main chain tend to deviate from its initial helix conformation. Compared with its initial conformation, internal energy of poly-10-lysine increased, accompanied by its conformation transition from a low energy state to a higher one. The results of this offer a theoretical basis for explanation of protein degeneration in adsorption process.