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Transport phenomena and structure formation at micro/nanometerscale in biomedicine and material science. Daniel Vizman , West University of Timisoara, Faculty of Physics Victor Sofonea , Center for Fundamental and Advanced Technical Research, Romanian Academy – Timisoara Branch

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Daniel vizman west university of timisoara faculty of physics
Transport phenomena and structure formation at micro/nanometerscale in biomedicine and material science

  • Daniel Vizman, West University of Timisoara, Faculty of Physics

  • Victor Sofonea, Center for Fundamental and Advanced Technical Research, Romanian Academy – Timisoara Branch

  • Titus Beu, Babes-Bolyai University, Faculty of Physics, Cluj- Napoca

  • Adrian Neagu, “Victor Babes” University of Medicine and Pharmacy, Timisoara


Daniel vizman west university of timisoara faculty of physics

Challenge: Multiscale simulation micro/nanometerscale in biomedicine and material science

Continuum media mechanics

mass, momentum, energy

equations

Particle

Position momentum,

interaction forces

Distribution function

Boltzmann Equation

MESOSCALE

(10-6m)

MACROSCALE

(>10-3m)

MOLECULAR

LEVEL (~10-9m)

  • Finite Element

  • Finite Volume

  • Monte Carlo

  • Molecular Dynamics

  • Lattice Boltzmann

  • Phase Field


Daniel vizman west university of timisoara faculty of physics

UNIVERSITATEA DE MEDICIN micro/nanometerscale in biomedicine and material scienceĂŞI FARMACIE

“VICTOR BABEŞ” TIMIŞOARA,

CENTRUL DEMODELARE A SISTEMELOR

BIOLOGICE ŞI ANALIZA DATELOR

(CMSBAD)

MONTE CARLO SIMULATIONS

  • The biological tissue is represented on a cubic lattice.

  • Cell rearrangements are obtained by random sampling.

  • Probability of acceptance

ET = effective measure of cell motility.

Monte Carlo simulations yield energetically favourable tissue conformations by minimizing the total energy of adhesion.


Daniel vizman west university of timisoara faculty of physics

20 000 MCS micro/nanometerscale in biomedicine and material science

100 000 MCS

EXAMPLE

  • Spontaneous emergence of tubular structures:

  • Aggregate:

  • 200 m diameter

  • Rint/Rext = 0.8

  • 2060 cells

  • 2109 nodes occupied by gel

Neagu A. et al. Phys. Rev. Lett. 95:178104-1– 4.


Daniel vizman west university of timisoara faculty of physics

Titus Beu, University ”Babeş-Bolyai”, Faculty of Physics

  • Ion channels – proteins that control the passage of ions (Na+, K+ etc) across cell membranes

  • Molecular dynamics – solving Newton’s law for all particles

  • The electrolyte – 1M NaCl solution: 600 H2O molecules, 8 Na+ and 8 Cl-

  • Water – rigid molecules:

    • Site-site intermolecular potential TIP4P

    • Rigid-body dynamics – rotation about CM – quaternions

  • Periodic boundary conditions

  • Coulomb interactions – Ewald sum technique with lattice-based charge distribution and Fast Fourier Transform – increases speed substantially

Molecular Dynamics Simulation of biological ion channels


Daniel vizman west university of timisoara faculty of physics

Titus Beu, University ”Babeş-Bolyai”, Faculty of Physics

The model membrane channel

  • similar to nicotine acetycloline receptor

  • 388 interaction sites: charges (-0.5e, -0.35e, +0.35e, +0.5e, neutral)+ Lennard-Jones interactions

11 20-atom rings

relative rotation 9°


Daniel vizman west university of timisoara faculty of physics

SNAPSHOT Physics


Daniel vizman west university of timisoara faculty of physics

Center for Fundamental and Advanced Technical Research Physics

Romanian Academy – Timisora Branch,

Lattice Boltzmann method

Boltzmann equation:

Phase space discretized Boltzmann equations with BGK approximation

relaxation time

the force term

Equilibrium distribution functions


Daniel vizman west university of timisoara faculty of physics

Center for Fundamental and Advanced Technical Research Physics

Romanian Academy – Timisora Branch,

Objective: investigation of two - dimensional, non - isothermal fluid flow phenomena in micro – electro – mechanical systems (MEMS)

thermal transpiration


Daniel vizman west university of timisoara faculty of physics

Center for Fundamental and Advanced Technical Research Physics

Romanian Academy – Timisora Branch,

Rarefaction effects in micro-channels

Velocity slip and temperature jump in Couette flow


Daniel vizman west university of timisoara faculty of physics

Process parameters Physics

Growth

conditions

Formation of crystal defects

Crystal

properties

svm

T(x,y,t,t)

e.g. geometry, heating power

e.g. temperature T and stress svm distribution

desired (doping), undesired (e.g. dislocation)

defined by application, e.g. LED, Laser diode

forward

inverse

Faculty of Physics, West University of Timisoara

goal: understanding of relation between crystal properties and

the conditions (parameters) of the crystal growth process


Daniel vizman west university of timisoara faculty of physics

Reduction of the complexity Physics

  • by using symmetry effects (e.g. axi-symmetric)

  • simplification of geometry (partial model)

2D axi-symmetric

problem: 3D-phenomena

partial 3D

STHAMAS3D – developed in collaboration with Fraunhofer Institute, Erlangen, Germany

Faculty of Physics, West University of Timisoara

Development of Simulation Programs for Crystal Growth

Global 3D-modeling is very expensive.

global 3D


Daniel vizman west university of timisoara faculty of physics

ASCI Physics

EarthSimulator

Challenges in Computational Power

NANOSIM – cluster at West University of Timisoara, Faculty of Physics

  • Computing speeds advances (uni- and multi-processor systems), Grid Computing

  • Systems Software

  • Applications Advances (parallel & grid computing)

  • Algorithms advances (parallel &grid computing, numeric and non-numeric techniques: dynamic meshing, data assimilation)


Daniel vizman west university of timisoara faculty of physics

Conclusions Physics

  • Challenge is to integrate what is happening on the atomic level with the mesoscopic and macroscopic classical level. Collaboration between scientists ‘working at every level’ is strongly necessary

  • Theoretical and computational skills can be learned by training, meaningful applications is achieved only with experience. User friendly software should be developed.

  • Grids and Service Oriented Architectures are necessary (worldwide networks of interconnected computers that behave as a single entity) to increase computational power

  • Local hardware infrastructure development necessary

  • While computational experiment is much less expensive than real experiment it is necessary to develop an application oriented computational culture and community


Daniel vizman west university of timisoara faculty of physics

Acknowledgements Physics

  • The authors would like to acknowledge the Romanian Ministry of Education and Research for the financial assistance under CEEX 11/2005