Molecular Dynamics Simulation Of The Mechanical Properties Of Collagen Molecules

Articular cartilage is a special tissue with obvious deformability.In articular cartilage,extracellular matrix is a polymeric structure consisting of collagen fibers and proteoglycan,which provides important mechanical properties for cartilage tissue.The interaction among collagen,proteoglycan,interstitial fluid and other components in the articular cartilage forms the special mechanical function of the articular cartilage.However,we don't know what mechanical properties of the various components in the cartilage are.Also,it is difficult to determine the mechanical properties of these components through experimental method.The results of the test are immensely dependent on the quality of the sample.And the dynamic motion behavior of the biological molecules cannot be observed at a micro level during the experiment.At a micro level,molecular dynamics simulation technique has become a powerful tool for analyzing the structural and dynamic information of biological molecules systems.The basic process of molecular dynamics simulation can be divided into the steps of system establishment,energy minimization,balance simulation,control simulation and result analysis.In this paper,aimed at the main component in the articular cartilage: collagen,the collagenous molecules in the cartilage were simulated by uniaxial tension and their mechanical properties were analyzed by using molecular dynamics simulation method,GROMACS molecular dynamics simulation software package based on the mechanical calculation model of collagen molecular,the collagen molecules in cartilage are simulated by uniaxial tensile simulation.The contents and results of the work are as follows:First,the installation and debugging of GROMACS software package and related software are completed on CentOS system.Second,according to the biological environment of the collagen molecules,an analog box with size of 24 nm × 3.2nm × 3.2nm is built.The interior includes a simulation system consisting of 6719 water molecules,20 sodium ions and 20 chloride ions,which is equivalent to a simple body fluid.The uniaxial tension of collagen molecules is divided into two different situations:(1)under the conditions of different temperatures and tensile rates,the collagen molecules are stretched in a single axis,and the pressure is maintained in this process;(2)under the conditions of pressure and tensile rate of different systems,collagen molecules are stretched in a single axis,and the temperature of the system is maintained in this process.In the first case,for different tensile rates,the Young's modulus of collagen molecules gradually decreased with the increase of temperature.For different temperatures,the Young's modulus of collagen molecules gradually increased with the increase of tensile rate.In the second case,for different tensile rates,the Young's modulus of collagen molecules gradually decreased with the increase of pressure of the system.For different pressures,the Young's modulus of collagen molecules increased gradually with the increase of tensile rate.The collagen molecules also showed a certain rate-dependence during the stretching process.When the tensile strain is less than 0.24,the Young's modulus of collagen molecules is small,but when the tensile strain is more than 0.32,the young's modulus of collagen molecules increases suddenly.For example,stretching the collagen molecule at the tensile rate of 0.01nm/ps,when the tensile strain is less than 0.24,the young's modulus of collagen molecule is about 7.7GPa;when the tensile strain is more than 0.29,the young's modulus of collagen molecule is about 24.7GPa.It indicates that the collagen molecule is a rate-dependence material.The ratedependence of collagen molecules is bound to have effects on the rate-dependence of cartilage to a certain extent.