Urs Zimmerli
Est. 1977
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PhD Thesis

Link: Computational nanofluidics for the study of biomolecular flows

Main topics:

  • Molecular interaction potentials within density functional theory
  • Generalized steering for molecular dynamics
  • Polarizability effects in the water-carbon interaction
  • The curvature induced static dipole moment of carbon nanotubes: influence on transport, wetting and water structure
  • RNA Transport through transmembrane carbon nanotubes

Refereed journal articles and book chapters

  • U. Zimmerli, M. Parrinello and P. Koumoutsakos. Dispersion corrections to density functionals for water aromatic interactions. J. Chem. Phys., 120 (6):2693--2699, 2004
  • U. Zimmerli, M. Parrinello and P. Koumoutsakos. Dispersion corrected density functionals applied to the water naphthalene cluster. Lect. Notes Comput. Sc., 39:205--214, 2004
  • J. H. Walther, T. Werder, R. L. Jaffe, P. Gonnet, M. Berdorf, U. Zimmerli and P. Koumoutsakos. Water-carbon interactions 3: the influence of surface and fluid impurities. Phys. Chem. Chem. Phys., 6:1988--1995, 2004
  • P. Koumoutsakos, U. Zimmerli, T. Werder and J. H. Walther. Nanoscale fluid mechanics. In Akhlesh Lakhtakia, editor, The Handbook of Nanotechnology. Nanometer Structures: Theory, Modeling and Simulation, chapter 8, pages 319--393, SPIE/ASME, 2004
  • U. Zimmerli, P. G. Gonnet, J. H. Walther and P. Koumoutsakos. Curvature induced L-defects in water conduction in carbon nanotubes. Nano Letters, 5 (6):1017--1022, 2005
  • U. Zimmerli and P. Koumoutsakos. Simulations of Electrophoretic RNA Transport Through Transmembrane Carbon Nanotubes. Biophys. J., 94:2546--2557, 2005

Reports

  • R. L. Jaffe, U. Zimmerli, J. H. Walther, P. Koumoutsakos, Interaction of Alkanamines and Other Small Molecules with Carbon Nanotubes, ETH CoLab Annual Research Briefs, 19-24, 2004
  • J. H. Walther, U. Zimmerli, P. Gonnet, P. Koumoutsakos, Carbon nanotubes as nanopores -- influence of the static dipole moment, ETH CoLab Annual Research Briefs, 137-148, 2004
  • R. L. Jaffe, J. H. Walther, U. Zimmerli, P. Koumoutsakos, Modeling the interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube, NASA technical report, NASA Ames Research Center, 2004

Talks and Conference Proceedings

  • U. Zimmerli, P. Koumoutsakos, Nanofluidics of Carbon Nanotubes: Towards the Development of Nanoscale Biosensors, Proceedings of the Fifth World Congress on Computational Mechanics, (WCCM V), July 7 - 12, 2002, Vienna, Austria
  • P. Gonnet, U. Zimmerli, J. H. Walther, T. Werder, P. Koumoutsakos, Wetting and Hydrophobicity of Nanoscale Systems with Impurities, Nanotech, 3, 69-72, 2004
  • U. Zimmerli, P. Koumoutsakos, M. Parrinello, Bounds for water graphite interaction from DFT, Program of the CPMD 2003 conference, page 66
  • P. Koumoutsakos, J. H. Walther, T. Werder, U. Zimmerli, R. L. Jaffe, Potential energy calibration for molecular dynamics simulations using experiments and quantum system calculations, 225th ACS National Meeting, Meeting Abstract 023-COMP (Computational Nanotechnology), 23-27 March 2003, New Orleans, USA.
  • J. H. Walther, T. Werder, U. Zimmerli, P. Koumoutsakos, Molecular fluid mechanics of carbon nanotubes, New Horizons in Molecular Sciences and Systems: An Integrated Approach, 16-18 October 2003, Nago City, Okinawa, Japan, page 20
  • P. Koumoutsakos, U. Zimmerli, J. H. Walther, Simulations of carbon nanotubes in aqueous environments, ASME International Mechanical Engineering Congress, 15-21 November 2003, Washington, D.C., USA
  • U. Zimmerli, M. Parinello and P. Koumoutsakos, Dispersion corrections for density functionals, at the Theoretical Chemistry Seminar, University of Zürich, April 28, 2004, Zürich, Switzerland.
  • R. Jaffe, J. H. Walther, U. Zimmerli, P. Koumoutsakos, Modeling the Interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube, 206th Joint International Meeting of the Electrochemical Society, 3 - 8 October 2004, Honolulu, Hawaii.
  • U. Zimmerli, J. H. Walther, Thermophoresis between Solids: A Molecular Dynamics Study of Gold Nanoparticles Confined and Thermally Driven through Carbon Nanotubes, eChemInfo InterAction Meeting, November 10, 2005, Basel, Switzerland
  • U. Zimmerli and P. Koumoutsakos, RNA Transport through Carbon Nanotube Transmembrane Nanopores. Micro and Nano Science Platform, Industry Day, September 04, 2006, Zurich, Switzerland
  • U. Zimmerli and P. Koumoutsakos, RNA Transport through Carbon Nanotube Transmembrane Nanopores. MRC Symposium, June 29, 2006, Zurich, Switzerland

Master Thesis

Semester Projects

  • "Simulation of a batch reactor" in Dynamic behaviour of process systems, 4th year chemical engineering at Imperial College, upon request.
  • Gestaltung von Anreizsystemen zur Optimierung der Zulieferer-Abnehmer-Beziehung Seminar "Kostenmanagement in der Supply Chain", FernUniversität Hagen: Text, Vortrag.

Other Stuff

Physics lecture notes:

A Java class to convert a gregorian date into its modified julian counterpart and to calculate the difference in days between two dates: