1 Transport phenomena and structure formation at micro/nanometerscale in biomedicine and material...
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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 Slide 2 2 MOLECULAR LEVEL (~10 -9 m) MESOSCALE (10 -6 m) MACROSCALE (>10 -3 m) Particle Position momentum, interaction forces Distribution function Boltzmann Equation Challenge: Multiscale simulation Continuum media mechanics mass, momentum, energy equations Monte Carlo Molecular Dynamics Lattice Boltzmann Phase Field Finite Element Finite Volume Slide 3 3 MONTE CARLO SIMULATIONS The biological tissue is represented on a cubic lattice. Cell rearrangements are obtained by random sampling. Probability of acceptance Monte Carlo simulations yield energetically favourable tissue conformations by minimizing the total energy of adhesion. UNIVERSITATEA DE MEDICIN I FARMACIE VICTOR BABE TIMIOARA, CENTRUL DE MODELARE A SISTEMELOR BIOLOGICE I ANALIZA DATELOR (CMSBAD) UNIVERSITATEA DE MEDICIN I FARMACIE VICTOR BABE TIMIOARA, CENTRUL DE MODELARE A SISTEMELOR BIOLOGICE I ANALIZA DATELOR (CMSBAD) E T = effective measure of cell motility. Slide 4 4 EXAMPLEEXAMPLE 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. 20 000 MCS100 000 MCS Slide 5 5 Ion channels proteins that control the passage of ions (Na +, K + etc) across cell membranes Molecular dynamics solving Newtons law for all particles The electrolyte 1M NaCl solution: 600 H 2 O 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 Titus Beu, University Babe-Bolyai, Faculty of Physics Molecular Dynamics Simulation of biological ion channels Slide 6 6 Titus Beu, University Babe-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 Slide 7 7 SNAPSHOT Slide 8 8 Phase space discretized Boltzmann equations with BGK approximation Equilibrium distribution functions Boltzmann equation: the force term relaxation time Center for Fundamental and Advanced Technical Research Romanian Academy Timisora Branch, Center for Fundamental and Advanced Technical Research Romanian Academy Timisora Branch, Lattice Boltzmann method Slide 9 9 Approach:development of appropiate numerical schemes; implementation of diffuse reflection boundary conditions; parallel computing thermal transpiration Center for Fundamental and Advanced Technical Research Romanian Academy Timisora Branch, 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) Slide 10 10 pressure-driven Flow Rarefaction effects in micro-channels Velocity slip and temperature jump in Couette flow Center for Fundamental and Advanced Technical Research Romanian Academy Timisora Branch, Center for Fundamental and Advanced Technical Research Romanian Academy Timisora Branch, Slide 11 11 forward Process parameters e.g. geometry, heating power Crystal properties defined by application, e.g. LED, Laser diode Growth conditions e.g. temperature T and stress vm distribution T(x,y,t,t) vm Formation of crystal defects desired (doping), undesired (e.g. dislocation) inverse goal: understanding of relation between crystal properties and the conditions (parameters) of the crystal growth process Faculty of Physics, West University of Timisoara Slide 12 12 global 3D Global 3D-modeling is very expensive. 2D axi-symmetric problem: 3D-phenomena partial 3D STHAMAS3D developed in collaboration with Fraunhofer Institute, Erlangen, Germany Reduction of the complexity by using symmetry effects (e.g. axi-symmetric) simplification of geometry (partial model) Faculty of Physics, West University of Timisoara Development of Simulation Programs for Crystal Growth Slide 13 13 ASCI Earth Simulator Challenges in Computational Power 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) NANOSIM cluster at West University of Timisoara, Faculty of Physics Slide 14 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 Slide 15 15 Acknowledgements The authors would like to acknowledge the Romanian Ministry of Education and Research for the financial assistance under CEEX 11/2005