freiburg, germany albert ludwig university imtek...

ALBERT-LUDWIGS-UNIVERSITÄT FREIBURG

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Molecular Dynafor Microsyste

IntroductioEvgenii B. Rudnyi and Jan G. K

IMTEKAlbert Ludwig Universi

Freiburg, Germany


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Preliminaries

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nyi, J.G. Korvink, Chair for Microsystem Simulation

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e Next Step for ST -> NSTearning from Nature:

Basis for cellular life processes is molecules (proteins)TranscriptionDecodingMessagingProduction

ngineering at the Nanoscale:Discovery/verification of natural molecular processes

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ck Soong, Engineering d nic/Inorganic -S evices Powered by le r Motors.

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ample: nobiotechnologyww.lifesciencesinfo.com/

ano, Nanobiotechnology, Where he Science and Applications Drive hange from Discovery through evelopment, July 16-17, 2001 -

an Diego, CAr. Rashid Bashir, Towards the se of Biological Entities to ssemble Semiconductor evices.

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ological Springs. Matsudaira, web.wi.mit.edu /

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0 µm- long acrosomal process, orseshoe crab, Limulus polyphemus


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tificial Molecular achines. Balzani, Acc. Chem. Res, 2001, 4, 445-455.

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erigna,

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directional Rotation

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Ko erin . Nature 1999, 401, 152.

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umura, N.; Zijlstra, R.W.J.; van Delden, R.A.; Harada, N.; F


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lymer Gels as olecular Motorsülch, R. W., Holdenried, J., eible, A., Wallmersperger, T.,

röplin, B.: Electrochemical timulation and control of electro-ctive polymer gels. In Smart tructures and Materials 2001. . Bar-Cohen (Ed.), Proceedings f SPIE 4329, 328-334 (2001)


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tatistical Thermodynamics and onte-Carlo (1)olecular Dynamics and

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rticle Dynamicslassical mechanics of moving articlesast computation of net forcesostprocessing and different xternal conditionstochastic particle dynamics

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ntum molecular amics.

ri e energy surfacenf tional analysis. a global optimi-

io ucture of proteins. te lding and docking.

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olecular Modelsuantum chemistryBorn-Oppenheimer approxi-mation, atomic and molecular orbitals, Hartree-Fock equation. Electron correlation, configuration interaction and DFT.olecular mechanicsEmpirical chemical bonding and non-bonding interac-tions. Determining the empirical force field. Quantum corrections and

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ical kinetics: simulating ventsc ath, transition

te, sition state theory. p rare events and

ns pathwaysnc olecular simula- P ers, mesoscale and c odeling

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olecular Dynamics d Simulationimulating phase equilibria and olecular solutionsSimulating a partition function. Particle insertion, direct simulation, Gibbs ensemble method. Molecule in solution and in the electrical field. Continuum and discrete solvation models.

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e evolution of phase partition of a Pluronic 64 and water mixtureOMACS


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Organiz

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here and whenecture: Room # 00-006, Geb. 51, Mo. 14-16xercises: Room # 00-006, Geb. 51 or in Comp. Class, Mo 16-17

cturersrof. Dr. Jan G. Korvink, [email protected], 203 7381, 03.03.033rof. Dr. Evgenii Rudnyi, [email protected], 203 7410, 03.03.017

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ional literature and online rces in each lecture

u al Chemistry List, .ccia m.info.nih.gov/lin torials.html’s , .b tes.net/leach/lo elated Sites, .k c.edu/Services/lo ks.php

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Organiz

terature. M. Haile, Molecular Dynamics imulation: Elementary Methods, ohn Wiley & Sons, Inc., New ork (1992).C. Rapaport, The Art of olecular Dynamics Simulation, ambridge University Press,

1995). R. Leach, Molecular Modelling: rinciples and Applications, ddison Wesley Longman imited, Harlow (1996)

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article Molecular ynamics (3)

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Organiz

esentation Projectresent an assignment in a 15 inute oral presentation.

resentations held are during he last two semester weeks. ach member of the team resents 7.5 minutes.

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