Current Diploma / PhD topics

For detailed explanations, possible other topics, and personal advice, please consult Bernd Hartke directly.

global optimization:

  • method development:
    • avoiding re-discovery of known minima (tabu search) (also allows for an estimate of search space covered)
    • merger between an extended crossover operator and “cultural algorithm” ideas, for better prediction of new candidate solutions
    • discovery of links between building block characteristics (valence, degree of directionality, range) and cluster structures, using simple model potentials
    • improvement of “numerical” evolutionary algorithms (for system-specific reparametrization of semiempirics, or for potential fitting)
  • applications:
    • large clusters of Kanamycin A molecules with physiological cations (collaboration with Prof. Schröder, Dermatology)
    • heterogeneous clusters: ligand hulls, hydration clusters, clathrate hydrates
    • solvent clusters around reacting species, and their influence on the reaction (with DFG funding)

 

quantum-mechanical reaction dynamics:

  • on-the-fly PES generation, interpolation instead of re-calculation of PES points
  • further development of an adaptive-basis representation with collocation
  • application to high-D examples, real-life applications e.g. within SFB677

 

classical-mechanical (direct) dynamics:

  • refinement of existing approaches to system-specific reparametrization of semiempirical electronic structure methods (with inclusion of analytic 1st derivative formulae)
  • surface-hopping (photo)chemical dynamics of molecular switches, without and with external forces (SFB 677)
  • design of improved molecular switches and molecular motors
  • extraction of “reaction mechanisms” from trajectory data

 

 

current and past diploma/PhD research topics:

 

 

aggregation of organic molecules: (collaboration project with Prof. Lüning): molecules interacting via multiple H-bonds

  • validation of several quantum chemical approaches, in comparison to experimental data
  • explanation of existing data on different binding strengths of several molecule pairs
  • development of design recommendations for new molecule pairs with improved binding strength and specifity

 

modeling of molecular rotors: (collaboration with Prof. Herges)

  • classical-mechanical models:
    • optimization of rotor performance with parameter tests in one-dimensional models
    • full-dimensional molecular dynamics of rotor molecules in action
  • electronic structure calculations:
    • ab-initio and semiempirical calculations of potential energy surfaces for rotor molecules
    • adjustment of simple 1D models and/or new force field terms to ab-initio calculations

 

quantum-mechanical reaction dynamics:

  • sparse wavefunction representation:
    • simplification of existing 1D proof-of-principle code, replacing numerical quadrature by collocation
    • extension from 1D to high-D
    • combination with existing high-end propagation code (Frank von Horsten)
    • application to high-D examples
  • real-life applications: Prof. Rauhut, Prof. Temps, …
  • direct collaboration with numerical mathematics (via Center for Numerical Simulations)

 

protein folding:

  • method development:
    • development of a statistical, united-atom potential of a new type
    • improvements and applications of an existing folding code
  • applications:
    • real-life proteins from the PDB data bank

 

large-scale molecular dynamics of hydrated oligosaccharides: (collaboration project with Prof. Lindhorst)

  • method development:
    • force field validation/improvement/extension
    • improvement and extension of analysis tools
  • applications:
    • influence of oligosaccharides on the surrounding water, and vice versa
    • changes of hydration properties of ions in the neighborhood of oligosaccharides
    • binding free energies between FimH and oligosaccharides, in physiological water
    • inclusion of membrane models

 

global optimization:

  • method development:
    • improvement of existing codes: extension to arbitrary mixtures of arbitrary molecules, with rigid and flexible degrees of freedom in arbitrary mixture
    • avoiding re-discovery of known minima (tabu search)
    • improvement of “numerical” evolutionary algorithms (for system-specific reparametrization of semiempirics, or for potential fitting)
    • design of new molecules for specific tasks, via global optimization of substituent patterns
  • applications:
    • benchmark functions
    • large, heterogeneous Lennard-Jones clusters
    • small Kanamycin A clusters

Last updated on Mon Aug 23, 2010