Publications (July 2005 - June 2008)

70) W. Nadler, J. Meinke and U.H.E. Hansmann, Folding Proteins by First-Passage-Times Optimized Replica Exchange, Phys. Rev. E 78, 061905 (2008). DOI: 10.1103/PhysRevE.78.061905

69) W. R. Bauer and W. Nadler, Dynamics and Efficiency of Brownian Rotors, J. Phys. Chem., 129, 225103 (2008). DOI: 10.1063/1.3026736

68) S. Mohanty and U.H.E. Hansmann, Caching of a Chameleon Segment facilitates Folding of a Protein with End-to-End β-sheet, J. Phys. Chem. B 112, 15134 (2008).

67) Da-Wei Li, Sandipan Mohanty, Anders Irbäck, and Shuanghong Huo, Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment, (2008) PLoS Comput. Biol. 4(12):e1000238.

66) F. Despa and R.S. Berry, Hydrophobic Interactions in a "Wetting Regime", Biophys. J. 95, 4241-4245 (2008). DOI: 10.1529/biophysj.108.137216

65) O. Zimmermann and U.H.E. Hansmann, LOCUSTRA: Accurate prediction of local protein structure using a two-layer SVM approach, J. Chem. Inf. Model., 48 (9), 1903-1908, 2008. DOI: 10.1021/ci800178a

64) F. Despa, A. Fernandez, L.R. Scott and R.S. Berry, Magnetic Relaxation Response of Water Structured by Protein Aggregation, J. Biol. Phys. 34, 577 (2008). DOI: 10.1007/s10867-008-9122-z

63) J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann and U.H.E. Hansmann, Computer Simulation of Proteins - Thermodynamics and Structure Predictions, Eur. J. Phys. D 51, 33 (2009).

62) P. Ananad, N.S. Nandel and U.H.E. Hansmann, The Alzheimer's beta amyloid (Abeta{1-39}) monomer in an implicit solvent, J. Chem. Phys., 128 (2008) 165102.

61) J.H. Meinke, S. Mohanty, W. Nadler, T. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Protein Simulations on Massively Parallel Computers, in: G. Münster, D. Wolf, M. Kremer, NIC Symposium 2008, Jülich (2008), p.9-16.

60) B. Berg and W. Wang, Numerical calculation of the combinatorial entropy of partially ordered ice, J. Chem. Phys. 127 (2007) 224502.

59) O. Zimmermann and U.H.E. Hansmann, Understanding protein folding: Small proteins in silico, Biochimica et Biophysica Acta - Proteins and Proteomics, 1784 (2008) 252.

58) Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain Ordering in a small Protein, J. Chem. Phys. 128 (2008) 025105.

57) S. Mohanty, J.H. Meinke, O. Zimmermann and U.H.E. Hansmann, Simulation of Top7-CFr: a transient helix extension guides folding, Proc. Natl. Acad. Scie (USA), 105, 8004 (2008).
doi:10.1073/pnas.0708411105

56) W. Nadler and. U.H.E. Hansmann, Optimizing Replica Exchange Moves For Molecular Dynamics, Phys. Rev. E 76 (2007) 057102.

55) J. H. Meinke, S. Mohanty, F. Eisenmenger, U. H. E. Hansmann, SMMP v. 3.0 — Simulating proteins and protein interactions in Python and Fortran, Comp. Phys. Comm., 178 (2008) 459.

54) U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007).

53) E. Arashiro, J. R. Drugowich de Felício, U. H. E. Hansmann, Global Persistence Exponent of the Helix-Coil Transition in Polypeptides, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 79-82.

52) T. Eitrich, S. Mohanty, X. Xiao, U. H. E. Hansmann, Dimensionality Reduction Techniques for Protein Folding Trajectories, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 99-102.

51) F. Fredel, J. Meinke, S. Mohanty, O. Zimmermann, U. H. E. Hansmann, Semiautomatic Workflow for Fold Recognition - Results from the CASP 2006 Competition, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 113-116.

50) P. Kar, M. Seel, U. H. E. Hansmann, S. Höfinger, Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 155-158.

49) P. Kar, M. Seel, U. H. E. Hansmann, S. Höfinger, Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 173-176.

48) J. H. Meinke, U. H. E. Hansmann, Parallelization of ECEPP/3 in SMMP, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 219-222.

47) S. Mohanty, U. H. E. Hansmann, Folding and Aggregation of Proteins with Monte Carlo Simulations, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 227-229.

46) M. Magiera, T. Neuhaus, U. H. E. Hansmann, Efficient Parallel Tempering with Multiple Gaussian Modified Ensembles, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 243-245.

45) Y. Wei, W. Nadler, U. H. E. Hansmann, Side-Chain Ordering in Homopolymers, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 297-300.

44) O. Zimmermann, U. H. E. Hansmann, Dihedral Angle Patterns in Coil Regions of Protein Structures, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 301-303.

43) W. Nadler and U.H.E. Hansmann, Dynamics and optimal number of replicas in parallel tempering simulations, Phys. Rev. E 76 (2007) 065701.

42) T. Neuhaus, M.P. Magiera, and U.H.E. Hansmann, Efficient Parallel Tempering for First Order Phase Transitions Phys. Rev. E 76 (2007) 045701.

41) S. Trebst and U.H.E. Hansmann, Optimized Folding Simulations of Protein A, Eur. Phys. J. E., 24 (2007) 311.

40) S. Mohanty and U.H.E. Hansmann, Folding of a Miniprotein with mixed Fold, J. Chem. Phys., 127 (2007) 035102.

39) P. Kar, M. Seel, U.H.E. Hansmann and S. Höfinger, Dispersion Terms and Analysis of Size- and Charge Dependence in an Enhanced Poisson-Boltzmann Approach , J. Phys. Chem. B, 111 (2007) 8910 .

38) O. Zimmermann, L. Wang and U.H.E. Hansmann, BETTY: Prediction of beta-strand type from sequence, In Silico Biology, 7 (2007) 0037.

37) A. Nussbaumer, E. Bittner, T. Neuhaus and W. Janke, Universality of the Evaporation/Condensation Transition, to appear in the proceedings of the 20th annual workshop on "Recent Developments in Computer Simulation Studies in Condensed Matter Physics", Athens (GA), USA, Feb. 19-23, 2007.

36) S. Mohanty, A. Irbaeck, S. Mitternacht, G. Favrin and U.H.E. Hansmann, Protein folding, aggregation and unfolding in Monte Carlo Simulations, to appear in the proceedings of the 20th annual workshop on "Recent Developments in Computer Simulation Studies in Condensed Matter Physics", Athens (GA), USA, Feb. 19-23, 2007.

35) M. Magiera, T. Neuhaus and U.H.E. Hansmann, Aspects of Efficient Parallel Tempering for First Order Phase Transitions, to appear in the proceedings of the 20th annual workshop on "Recent Developments in Computer Simulation Studies in Condensed Matter Physics", Athens (GA), USA, Feb. 19-23, 2007.

34) S. Mohanty and U.H.E. Hansmann, Improving an all-atom force field , Phys. Rev. E, 76 (2007) 012901.

33) Y. Wei, W. Nadler and U.H.E. Hansmann, On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase, J. Chem. Phys.,126 (2007) 204307.

32) M. Cheon, I. Chang, S. Mohanty, L.M. Luheshi, C.M. Dobson, M. Vendruscolo and G. Favrin, Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrilss, PLoS Computational Biology, 3 (2007) e173..

31) P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, Systematic Study of the Boundary Composition in Poisson Boltzmann Calculations, J. Comp. Chem., 28 (2007) 2538..

30) E. Arashiro, J.R. Drugowich de Felicio and U.H.E. Hansmann, Short-Time Dynamics of Polypeptides, J. Chem. Phys., 126 (2007) 045107.

29) Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in Homopolymers, J. Phys. Chem. B, 111 (2007) 4244.

28) J. Meinke and U.H.E. Hansmann, Protein Simulations combining an All-Atom Force Field with a Go-Term, J. Phys.: Cond. Mat. 19 (2007) 285215.

27) A. Nussbaumer, E. Bittner, T. Neuhaus and W. Janke, Monte Carlo study of the evaporation/condensation transition of Ising droplets, Europhys. Lett., 75 (5), pp. 716-722 (2006)

26) T. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Ring Polymer Simulations with Global Radius of Curvature, Phys. Rev. E, 75 (2007) 051803.

25) J. Meinke and U.H.E. Hansmann, Aggregation of beta-Amyloid Fragments, J. Chem. Phys.,126 (2006) 014706

24) J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006).

23) Ch. Junghans and U.H.E. Hansmann, Cross-Check Methods in Protein Simulations, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 157 - 160.

22) Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain Ordering in PolyGlutamic Acid, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 205 - 209.

21) Th. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Simulations of thick polymers, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 177 - 180.

20) L. Wang, O. Zimmermann and U.H.E. Hansmann, Prediction of Parallel and Antiparallel Beta Sheets Based on Sequence Profiles Using Support Vector Machines, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 201 - 204.

19) Parimal Kar, Yanjie Wei, Ulrich H.E. Hansmann, Siegfried Höfinger The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 161 - 164.

18) Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in a Polypeptide, J. Chem. Phys. 125 (2006) 164902.

17) J. Busa, Sh. Hayryan, C-K. Hu, J. Skrivanek and M-C. Wu, Enveloping Triangulation Method for Detecting Internal Cavities in Proteins and Algorithm for Computing Their Surface Areas and Volumes, Journal of Computational Chemistry 30 (2009), p. 346-357.

16) J. Skrivanek and U.H.E. Hansmann, Equations of Motion for Polymers Fully Described in Internal Coordinates, Particles and Nuclei, Letters, 5 (2008) 236.

15) R. Mahajan, D. Krazmüller, J. Volkert, U.H.E. Hansmann and S. Höfinger, Detecting Secondary Bottlenecks in Scientific MPI-Applications, Int. J. Mod. Phys. C 19 (2008) 1-13.

14) T. Neuhaus and J. Hager, Free Energy Calculations with Multiple Gaussian Modified Ensembles, Phys. Rev. E., 74 (2006) 036702.

13) S. Höfinger, B. Almeida and U.H.E. Hansmann, Parallel Tempering Molecular Dynamics Folding Simulation of a Signal Peptide in Explicit Water , Proteins: Structure, Function and Bioinformatics, 68 (2007) 662.

12) U.H.E. Hansmann, All-Atom Simulation of Proteins,in: W. Janke (Ed.) Rugged Free Energy Landscapes, Lect. Notes Phys. 736 (2008) 293.

11) W. Nadler and U.H.E. Hansmann, Generalized Ensemble and Tempering Simulations: A Unified View, Phys.Rev. E, 75 (2007) 026109.

10) S. Mohanty and U.H.E. Hansmann, Folding of Proteins with diverse folds, Biophysical Journal, 92 (2006) 3573.

9) A. Irbaeck and S. Mohanty, PROFASI: a Monte Carlo simulation package for protein folding and aggregation, J. Comp. Chem. 27 (2006) 1548.

8) O. Zimmermann and U.H.E. Hansmann, Support Vector Machines for Prediction of Dihedral Angle Regions, Bioinformatics 22 (2006) 3009.

7) U.H.E. Hansmann, Protein Folding in Silico, inSide 3 (2005) 12-13

6) U.H.E. Hansmann, Computational Biology and Biophysics at NIC, in: G. Münster, D. Wolf, M. Kremer, NIC Symposium 2006, Jülich (2006), p.13-20.

5) U.H.E. Hansmann, How to fold proteins on a computer? in: S. Blügel,G. Gompper, H. Müller-Krumbhaar, E. Koch, R.G. Winkler and R. Spatschek, 37th IFF Spring School "Computational Condensed Matter Physics, Jülich (2006), B11.1-14.

4) S. Trebst, D.A. Huse, E. Gull, H.G. Katzgraber, U.H.E. Hansmanns and M. Troyer, Ensemble optimization techniques for the simulation of slowly equilibrating systems, to appear in the proceedings of the 19th annual workshop "Recent Developments in Computer Simulation Studies in Condensed Matter Physics", Athens, GA, Feb 20-24, 2006.

3) R. Mahajan, D. Krazmüller, U.H.E. Hansmann, J. Volkert and S. Höfinger, Computational assesment of the entropy of solvation of small-sized hydrophobic entities, Physical Chemistry Chemical Physics, 8 (2006) 5515.

2) C. Junghans and U.H.E. Hansmann, Numerical Comparison of Wang-Landau Sampling and Parallel Tempering for Met-enkephalin, Int. J. Mod. Phys. C, 17 (2006) 817.

1) S. Trebst, M. Troyer and U.H.E. Hansmann, Optimized parallel tempering simulations of Proteins, J. Chem. Phys. 124 (2006) 174903.