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  1. No Access

    Chapter and Conference Paper

    Ensemble Optimization Techniques for the Simulation of Slowly Equilibrating Systems

    Competing phases or interactions in complex many-particle systems can result in free energy barriers that strongly suppress thermal equilibration. Here we discuss how extended ensemble Monte Carlo simulations ...

    S. Trebst, D. A. Huse, E. Gull… in Computer Simulation Studies in Condensed-M… (2009)

  2. No Access

    Article

    Computer simulation of proteins: thermodynamics and structure prediction

    Over the last decade, computer simulations have become an increasingly important tool to study proteins. They now regularly complement experimental investigations and often are the only instrument to probe pro...

    J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann… in The European Physical Journal D (2009)

  3. No Access

    Article

    A method of faster in silico folding of proteins

    The successful deciphering of the human genome has highlighted an old challenge in protein science: for most of the resolved protein sequences, we do not know the corresponding structures and functions. Neithe...

    U. H. E. Hansmann, Ja. Skřivánek in Physics of Particles and Nuclei Letters (2008)

  4. No Access

    Article

    Optimized folding simulations of protein A

    We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of ≈ 3 Å to the experimentally determined structure ...

    S. Trebst, U. H. E. Hansmann in The European Physical Journal E (2007)

  5. No Access

    Chapter and Conference Paper

    Generalized-Ensemble Simulations of Small Proteins

    U. H. E. Hansmann in Computer Simulation Studies in Condensed-Matter Physics XVI (2006)

  6. No Access

    Chapter

    VIII. Protein Folding Simulations by a Generalized-Ensemble Algorithm Based on Tsallis Statistics

    We review uses of Tsallis statistical mechanics as a generalized-ensemble simulation algorithm in the protein folding problem. A simulation based on this algorithm performs a random walk in energy space, and ...

    Y. Okamoto, U.H.E. Hansmann in Nonextensive Statistical Mechanics and Its Applications (2001)

  7. No Access

    Article

    Is there a universality of the helix-coil transition in protein models?

    The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-al...

    J.P. Kemp, U.H.E. Hansmann, Zheng Yu Chen in The European Physical Journal B - Condense… (2000)

  8. No Access

    Article

    Protein folding simulations in a deformed energy landscape

    A modified version of stochastic tunneling, a recently introduced global optimization technique, is introduced as a new generalized-ensemble technique and tested for a benchmark peptide, Met-enkephalin. It is ...

    U.H.E. Hansmann in The European Physical Journal B - Condensed Matter and Complex Systems (1999)

  9. No Access

    Article

    Configuration space for random walk dynamics

    Applied to statistical physics models, the random cost algorithm enforces a Random Walk (RW) in energy (or possibly other thermodynamic quantities). The dynamics of this procedure is distinct from fixed weight...

    B.A. Berg, U.H.E. Hansmann in The European Physical Journal B - Condense… (1998)

  10. No Access

    Chapter and Conference Paper

    Generalized Ensemble Simulation of Peptides and Proteins

    We discuss the generalized ensemble approach for simulation of peptides and proteins. The simulated molecules are frustrated systems with a complicated energy landscape. The resulting slowing down is alleviate...

    U. H. E. Hansmann, Y. Okamoto in Computer Simulation Studies in Condensed-Matter Physics X (1998)

  11. No Access

    Chapter and Conference Paper

    A Multicanonical Study of Non-Polar Amino Acids

    We perform a multicanonical simulation of non polar amino acids and study their α-helix propensities. Starting simulations from completely random initial conformations, we have calculated various quantities li...

    U. H. E. Hansmann… in Computer Simulation Studies in Condensed-Matter Physics VII (1994)

  12. No Access

    Article

    The van Hemmen spin glass revisited

    We simulated the van Hemmen spin glass model by multicanonical algorithm. The exact results for this mean-field model are reproduced. Physical quantities such as energy density, specific heat, susceptibility a...

    T. Celik, U. H. E. Hansmann, M. Katoot in Journal of Statistical Physics (1993)

  13. No Access

    Chapter and Conference Paper

    Prediction of Peptide Conformation by the Multicanonical Algorithm

    We test the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. As a simple example we study Metenkephalin. The lowest-energy conformation obtained agr...

    U. H. E. Hansmann, Y. Okamoto in Computer Simulation Studies in Condensed-Matter Physics VI (1993)

  14. No Access

    Chapter and Conference Paper

    Study of ± J Ising Spin Glasses via Multicanonical Ensemble

    We performed numerical simulations of 2D and 3D Edwards-Anderson spin glass models by using the recently developed multicanonical ensemble. Our ergodicity times increase with the lattice size approximately as V ...

    T. Celik, U. H. E. Hansmann, B. Berg in Computer Simulation Studies in Condensed-M… (1993)