Loading...

Multi-Scale Simulation of the Viscoelastic Behavior of the Cell Membrane

Ali Khourshaei Shargh | 2017

671 Viewed
  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 49508 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): NaghdAbadi, Reza; Sohrabpour, Saeed
  7. Abstract:
  8. Due to the limitations on experiments in the field of cell mechanics, computational modeling of biological cells have attracted attention within two recent decades. In general, some models have been developed in two different scales, known as microstructure and continuum, both of which have their own pros and cons. Nevertheless, viscoelastic behavior of cell membrane has attracted less attention of scientists up to now. Therefore, multi-scale simulation of the viscoelastic behavior of the cell membrane has been chosen as the main goal of this thesis. Toward this goal, at first the energy of the simulation box, consisting of 128 Dipalmitoylphosphatidylcholine and 3655 water molecules, was minimized by the use of stteepest descent algorithm. Then, the system experienced a 5ns equilibration in an NPT ensemble, and the relaxation test under two different boundary condition was implemented on the system in a Non-Equilibrum molecular dynamics simulation. Afterwards, by fitting the results on maxwell-wirchet rheologic model, parameters pertinent to the three different components of relxation modulus in the time domain were obtained. Utilizing concept of laplace transformation, parameters of relxation modulus were calculated in frequency domain. For instance, M_I^' in frequncy of 1 GHz was obtained about 18.748 kbar which is in good aggreement with available experimental data. Moreover, in order to verify calculated parameters, doubling the dimensions of the system, normal to lipid bilayers, no significant changes in pre-calculated parameters were noticed. Finally, to decrease computational costs, the possibility of making use of coarse-grained multiscale simulation in obtaining the viscoelastic properties of the cell membrane was investigated
  9. Keywords:
  10. Cell Membrane ; Molecular Dynamics ; Coarse Grained Model ; Multi-Scale Simulation ; Viscoelastic Behavior

 Digital Object List

 Bookmark

No TOC