شبيه سازي غشاء دو لايه اي سلول زنده و محاسبه ضريب ديفيوژن آب از غشاء به روش ديناميك استهلاكي ذره

چكيده انگليسي :

Isfahan University of Technology Simulation of Biological Cell Bilayer Membranes and Calculation of Diffusion Coefficient for water through the membrane by Dissipative Particle Dynamics Method Somaye Yaghubi Kupaye s yaghubi@me iut ac ir March 15 2010 Department of Mechanical Engineering Isfahan University of Technology Isfahan 84156 83111 Iran Degree M Sc Language English Supervisors Dr Ahmad Reza Pishevar apishe@cc iut ac ir Prof mohammad S Saidi mssaidi@sharif edu Abstract The dependence of the material properties of lipid bilayer membranes on the structure of their component molecules is important biologically The plasma membrane that surrounds all living cells must be strong enough to prevent the permeation of unwanted ions and molecules but also flexible enough so that for example red blood cells can squeeze through capillaries whose width is only one third of the cell s diameter Solutions of amphiphilic molecules such as lipids in water are characterized by a wide range of length scales These molecules usually resemble semiflexible rods with a length of the order of 1 2 nm which is already large compared to the atomic size 0 1 nm In solution these rodlike molecules form supramolecular aggregates such as spherical and cylindrical micelles or bilayers For this purpose we perfect to use Dissipative Particle Dynamics DPD method to simulate biological membranes In this method several atoms are united into a single simulation particle The elementary units in a DPD simulation are fluid elements or soft beads A soft bead represents a volume of fluid that is large on a molecular scale and hence contains at least several molecules or molecular groups but still macroscopically small In this simulation we use three atoms as one DPD particle Beads interact via effective forces chosen so as to reproduce the hydrodynamic behavior of the fluid without reference to its molecular structure DPD differs in this respect from Molecular Dynamics MD simulations in which the forces are chosen to model the intermolecular interactions of a system as accurately as possible Forces in DPD are pairwise additive conserve momentum have no hard core and are short ranged Our bilayer membranes are composed of surfactants which consist of hydrophilic head groups and hydorophobic tail groups These surfactants are modeled by single chains or even double chains of particles interconnected by a harmonic bond potential Double chain surfactants have symmetric chains or maybe asymmetric chains In addition we incorporate the bending stiffness of these chains Unsaturated carbon bonds can change the stiffness of a membrane lipid We model the stiffness of the chain by introducing this bond bending potential Using DPD simulations we observe the self assembly of the surfactant molecules into bilayer membranes We also calculate the surface tension of the bilayers The stress profile is gained and is similar to that found in coarse grained Molecular Dynamics simulations but requires a fraction of the computational cost The effect of changes in the chain length and stiffness of the surfactants on the properties of the model membranes are studied We observe that changes of the stiffness have significant effects if these changes are made close to the head group of the surfactant If on the other hand changes are made at the end of the tail of the surfactant the properties of the bilayer are similar to the properties of a bilayer consisting of flexible chains We observed as the tail length increases the area per surfactant increases then we compare these results with the theoretical calculations of Cantor on a lattice model We were able to give to our surfactants a special chemistry structure and do this membrane simulation more actual It becomes our work quite distinct from most of studies Another goal in this work is to calculate the diffusion coefficient of the water through the modeled membrane Then we compare this coefficient with theoretical results and other simula

يعقوبي كوپايي، سميه

شبيه سازي غشاء دو لايه اي سلول زنده و محاسبه ضريب ديفيوژن آب از غشاء به روش ديناميك استهلاكي ذره

غشاء بيولوژيكي , دولايه ي ليپيدي , ديفيوژن