Project description

Objective O1

Monte Carlo simulation techniques for structure formation in living tissues made of many types of cells

Activities:

  • Building a discretized model for biological tissues
  • Elaboration of Monte Carlo simulation package for the self-assembly of living tissues
  • Validation for Monte Carlo simulation code by comparation with experimental results from the literature
  • Parallelization and optimization of the Monte Carlo simulations and integration into the ORCAN platform

Objective O2

Transport phenomena in micro channels using Lattice Boltzmann models

Activities:

  • Building a Lattice Boltzmann model for variable temperature systems and 2-nd order finite difference schemes
  • Lattice Boltzmann model for fluid microflow
  • Elaboration of a model for simulating the diffusion process
  • Integration of Lattice Boltzmann models into the ORCAN platform, validation of computer codes and the analysis of the results

Objective O3

Preparation of computing platform and software libraries

Activities:

  • Extension of the existing computer cluster
  • Implementation of the Web page; archive and search link (for scientific results)
  • Implementation of the ORCAN platform on the partners’ workstations
  • Administration procedure of user applications on the cluster
  • Development of a GRID portal
  • Maintenance of the web page and GRID portal

Objective O4

Independent numerical schemes for computing thermal stress in crystals

Activities:

  • Development of a computer code for thermal fields
  • Development of a computer code for thermal tension estimation
  • Integration into the ORCAN platform, theoretical validation of the new computer codes and building of the user interface
  • Comparison between numerical and experimental results for validation and optimization of ionic crystal growth

Objective O5

Monitoring the attachment of cells to porous biomatrices used in tissue engineering using aggregometry

Activities:

  • Elaboration of a principial scheme for a modified a aggregometer and the design of the devices of original conception
  • Building the modified aggregometer
  • Experimental protocol for isolation and morphological characterization of the cells which will be used in the next stages
  • Measuring the time course of the concentration of cells in suspension during the population of various types of biomatrices

Objective O6

Characterization of the aggregation or reaggregation of cells and their attachment to porous substrates used in tissue engineering

Activities:

  • Detection, characterization and statistical analysis of maxima and minima of the interference image obtained during the coherent scattering of laser radiation on biological suspensions
  • Monitorization and characterization of cell suspensions by static, small angle scattering
  • Revealing eventual attachment and reaggregation processes by dimensional description of the particles in the dispersed phase (cells of cell aggregates)
  • Investigation of the attachment and aggregation kinetics by experiments of dynamic laser scattering

Objective O7

Theoretical study of ion transport through the channels of cell membranes

Activities:

  • Structural and functional modeling of some types of biological ion channels
  • Modeling of Coulomb interactions and of periodic boundary conditions by Ewald sum techniques. Development of fast algorithms based on lattice-projected charge distributions and Fast Fourier Transform
  • Modeling of the complete force field of ion channels and preparing the thermalized initial states. Assembly of the program code and integration into the ORCAN platform.
  • Study of the ion dynamics in cellular membrane channels placed in various configurations of electrical and magnetic fields

Objective O8

Lattice Boltzmann models for the simulation of cell migration in tissue engineering

Activities:

  • Lattice Boltzmann models on distributed computing systems for mesoscopic flows in biological tissues
  • Integration into the ORCAN platform and computer code validation

Objective O9

Phase field model for micro-nano-crystallization

Activities:

  • Phase field model elaboration
  • Computer code elaboration and validation, comparison with results from the literature
  • Integration into the ORCAN platform and the study of polycrystalline materials solidification

Objective O10

The study of cell mobility in the context of tissue engineering applications

Activities:

  • Monte Carlo model for the population of porous tissue engineering scaffold with living cells
  • Lattice Boltzmann model for scaffold population dynamics
  • Comparison of numerical and experimental results obtained in objectives 5 and 6