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:

Computational Statistical Physics
Development of fundamental statistical analysis methods for extending the concept of phase transitions to finite systems
Efficient simulation methods for small systems such as parallel enumeration, multicanonical and contact-density chain-growth methods
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
Tests of alternative architectures: Simulation methodologies on graphics processing units (GPUs)

Protein Folding
Systematic analysis of conformational and sequence space, ground-state identification, and thermodynamics of hydrophobic-polar lattice heteropolymer models
Conformational lowest-energy shapes, free-energy landscapes, and characterization of folding channels of coarse-grained off-lattice heteropolymer models
All-atom model studies of folding behaviors for short synthetic peptides and bioproteins
The BONSAI Project: Development of a C++-based molecular mechanics package for protein folding, aggregation, and adsorption in atomistic resolution

Polymer and Peptide Adsorption at Substrates
Classification of structural phases for lattice and off-lattice polymers (collapse, liquid-solid, and solid-solid transitions)
Substrate-specificity and conformational transitions of polymers and peptides adsorbing at flat substrates (generic coarse-grained models)
Polymer alignment at nonplanar substrates such as nanowires, carbon nanotubes, and also fluctuating membranes
Polyelectrolyte binding at charged soft nanoparticles and inside spherical cavities (viruses)
Specific adhesion properties of semiconductor-binding peptides (using bonsai)

Aggregation of Peptides
Modeling and simulation of polymeric aggregation processes
Statistical analysis of first-order nucleation transitions with emphasis on finite-size effects
Thermodynamics of aggregation pathways of amyloid peptides associated with neurodegenerative diseases (bonsai simulations)

Fluctuating Membranes
Analytic strong-coupling studies of fluctuating membranes and stacks of membranes in confined geometries (path integral calculations)




Contact:
E-mail: bachmann[at]smsyslab.org