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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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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


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


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.


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.


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


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°


SNAPSHOT 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


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


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


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


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


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)


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


Acknowledgements Physics

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


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