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Research done in our group primarily focuses on the investigation of all
aspects that help understand the general structural behavior of polymers, proteins, and
membranes on microscopic, mesoscopic, and macroscopic length
scales. This regards any kind of
biological and chemical process in which molecules experience
cooperative structural changes. Neither the systematic strategic approach
to counter epidemic diseases nor the design of potential nanotechnological
applications on molecular scales can be thought without
substantial background knowledge of structural transitions in
finite systems. We use and further develop methods adopted from the statistical theory of phase
transitions in large systems and employ computer simulations to
reveal and generalize system-specific characteristics of molecular
folding,
adsorption, and aggregation processes. The following list outlines
main research areas and goals of our group:
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| Computational Statistical Physics |
| Development of fundamental statistical analysis methods for extending the concept of phase transitions to finite systems |
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| Efficient simulation methods for small systems such as parallel enumeration, multicanonical and contact-density chain-growth methods |
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| Multi-core extensions for Markov-chain Monte Carlo methods in generalized ensembles: multicanonical and Wang-Landau sampling, and parallel tempering for coarse-grained and atomistic simulations |
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| Tests of alternative architectures: Simulation methodologies on graphics processing units (GPUs) |
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| Protein Folding |
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| Systematic analysis of conformational and sequence space, ground-state identification, and thermodynamics of hydrophobic-polar lattice heteropolymer models |
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| Conformational lowest-energy shapes, free-energy landscapes, and characterization of folding channels of coarse-grained off-lattice heteropolymer models |
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| All-atom model studies of folding behaviors for short synthetic peptides and bioproteins |
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| Development of a C++-based molecular mechanics package for protein folding, aggregation, and adsorption in atomistic resolution |
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| Polymer and Peptide Adsorption at Substrates |
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| Classification of structural phases for lattice and off-lattice polymers (collapse, liquid-solid, and solid-solid transitions) |
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| Substrate-specificity and conformational transitions of polymers and peptides adsorbing at flat substrates (generic coarse-grained models) |
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| Polymer alignment at nonplanar substrates such as nanowires, carbon nanotubes, and also fluctuating membranes |
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| Polyelectrolyte binding at charged soft nanoparticles and inside spherical cavities (viruses) |
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| Specific adhesion properties of semiconductor-binding peptides |
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| Aggregation of Peptides |
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| Modeling and simulation of polymeric aggregation processes |
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| Statistical analysis of first-order nucleation transitions with emphasis on finite-size effects |
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| Thermodynamics of aggregation pathways of amyloid peptides associated with neurodegenerative diseases |
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| Fluctuating Membranes |
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| Analytic strong-coupling studies of fluctuating membranes and stacks of membranes in confined geometries (path integral calculations) |
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