Daniel Vizman , West University of Timisoara, Faculty of Physics

1. 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

2. 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

3. 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.

4. 20 000 MCS 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.

5. 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

6. 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°

7. SNAPSHOT

8. 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

9. 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

10. Center for Fundamental and Advanced Technical Research Romanian Academy – Timisora Branch, Rarefaction effects in micro-channels Velocity slip and temperature jump in Couette flow

11. Process parameters 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

12. Reduction of the complexity • 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

13. ASCI 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)

14. Conclusions • 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

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