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Daniel Vizman , West University of Timisoara, Faculty of Physics

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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

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 MEDICINĂŞI 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.

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°

Center for Fundamental and Advanced Technical Research

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

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

Romanian Academy – Timisora Branch,

Rarefaction effects in micro-channels

Velocity slip and temperature jump in Couette flow

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

- 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

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)

- 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

- 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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