1. Andreas R. Gruber, Ronny Lorenz, Stephan H Bernhart, Richard Neubock, and Ivo L. Hofacker
    (2008). The Vienna RNA websuite. ,
    Nucl. Acids Res.,36:W70-W74.
  2. Christoph Flamm and Ivo L. Hofacker
    (2008). Beyond energy minimization: Approaches to the kinetic folding of RNA. ,
    Monatsh. f. Chemie, 139:447- 457.
  3. Muckstein, Ulrike and Tafer, Hakim and Bernhard, Stephan H. and Hernandez-Rosales, Maribel and Vogel, Jorg and Stadler, Peter F. and Hofacker, Ivo L.,
    Translational Control by {RNA-RNA} Interaction: Improved Computation of {RNA-RNA} Binding Thermodynamics,,
    BioInformatics Research and Development --- BIRD 2008,Springer, Berlin, 2008, in press,
  4. Klemm, Konstantin and Flamm, Christoph and Stadler, Peter F.,
    Funnels in Energy Landscapes,,
    2008, Eur. Phys. J. B, 63, 387-391, ECCS 2007 contribution
  5. Geis, Michael and Flamm, Christian and Wolfinger, Michael T. and Tanzer, Andrea and Hofacker, Ivo L. and Middendorf, Martin and Mandl, Christian and Stadler, Peter F. and Thurner, Caroline,
    Folding kinetics of large {RNA}s,,
    J. Mol. Biol., 379, 160-173, 2008,
  6. Geis, Michael and Middendorf, Martin,
    A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures,,
    Proceedings of the IEEE Swarm Intelligence Symposium 2007, 1-8, 2007
  7. Heine, Christian and Scheuermann, Gerik and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F.,
    Visualization of Barrier Tree Sequences,,
    IEEE Trans. Vis. Comp. Graphics, 12, 781-788, 2006, Info-Vis 2006 contribution,
  8. Flamm, Christoph and Stadler, B{\"a}rbel M. R. and Stadler, Peter F.,
    Saddles and Barrier in Landscapes of Generalized Search Operators,,
    Foundations of Genetic Algortithms IX, Stephens, C. R. and Toussaint, M. and Whitley, D. and Stadler, P. F., Springer, Berlin, Heidelberg, 2007, 194-212, Lecture Notes Comp. Sci., 4436,
  9. Kei Moritsugu and Jeremy C. Smith,
    REACH: Realistic Extension Algorithm via Covariance Hessian,,
    Biophys. J. 93, 3460-3469 (2007).
  10. Kei Moritsugu and Jeremy C. Smith,
    REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes,,
    Biophys. J. In press.
  11. B. Tarus and J. C. Smith.
    A study of the folding of the A?21-30-peptide under confining conditions.,
    in preparation
  12. Periole, X. and Mark, A. E.
    (2007) Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent,
    J. Chem. Phys. 126, 014903.
  13. Periole, X., Rampioni, A., Vendruscolo, M. and Mark, A.E.
    (2007) Molecular dynamics simulations of a cross-? filament of the GNNQQNY peptide reveal a combination of factors that determine the degree of twist of ?- sheets.,
    Biophysical Journal (submitted)
  14. Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci
    Probing the free energy landscape of the FBP28 WW domain by multiple techniques.,
    Journal Molecular Biology (submitted)
  15. Fuchslin, R. M., A. Eriksson, H. Fellermann, H.-J. Ziock,
    "Coarse-graining and scaling in dissipative particle dynamics,",
    Submitted to Journal of Chemical Physics. Preprint availabel at arXiv:cond-mat/0703.682, 2007.
  16. Eriksson, A, Nilsson Jacobi, M, Nystrom, J. and Tunstrom, K.,
    "Using force covariance to derive effective stochastic interactions in dissipative particle dynamics",,
    Physical Review E 77, 016707, 2008.
  17. Eriksson, A, Nilsson Jacobi, M, Nystrom, J. and Tunstrom, K.,
    "Effective thermostat induced by coarse-graining of SPC water",,
    to appear in Journal of Chemical Physics.
  18. Gornerup, O., and J. P. Crutchfield,
    Primordial Evolution in the Finitary Process Soup,,
    Electronic Journal of Theoretical Physics Special Issue 2007: Physics of Emergence and Organization, 4:16 I (2007). In press.
  19. Gornerup, O. and Nilsson Jacobi, M.
    "A Method for Inferring Hierarchical Dynamics in Stochastic Processes",,
    in Advances in Complex Systems, 11 (1), p. 1-16, 2008.
  20. Helvik, T., K. Lindgren, and M. G. Nordahl,
    "Continuity of information transport in surjective cellular automata,",
    Communications in Mathematical Physics 272, 53-74 (2007).
  21. Lindgren, K.,
    Information Theory for Complex Systems - Lecture Notes.,
    Chalmers University of Technology, 2008. (To be revised and exteneded for a book publication.)
  22. Nilsson Jacobi, M.,
    "Quotient Manifold Projections and Hierarchical Dynamics",,
    in proceeding of ECCS, 2006.
  23. Nilsson Jacobi, M.,
    "Hierarchical Dynamics",,
    to appear in Springer's encyclopedia on complex systems,
  24. Nilsson Jacobi, M. and Gornerup, O.
    "A dual eigenvector condition for strong lumpability in Markov chains",,
    submitted to Journal of Linear algebra and its applications, arXiv:0710.1986
  25. Nilsson Jacobi, M. and Gornerup, O.
    "Aggregation of variables in linear dynamical systems",,
    submitted for publication in Advances in complex systems.
  26. Nilsson Jacobi, M. and Gornerup, O.
    "An algorithm for aggregating variables in linear dynamical systems",,
    submitted for publication in Advances in complex systems.
  27. Christian H. Jensen, Dmitry Nerukh, and Robert C. Glen,
    Controlling protein molecular dynamics: how to accelerate folding while preserving the native state,
    accepted for publication in J. Chem. Phys.
  28. Dmitry Nerukh,
    Computational Mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems,
    Chem. Phys. Lett., 457(4-6), 439-443 (2008) Erratum to "Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems" [Chem. Phys. Lett. 457 (2008) 439], Chem. Phys. Lett., 459(1-6), 203 (2008)
  29. Dmitry Nerukh,
    Dynamical frustration of protein's environment at the nanoseconds time scale,
    accepted for publication in J. Mol. Liq.
  30. V.A. Buts, A.G. Nerukh, N.N. Ruzhytska, and D.A. Nerukh,
    Wave Chaotic Behaviour Generated by Linear Systems,
    accepted for publication in Optical and Quantum Electronics
  31. Dmitry Nerukh, Vladimir Ryabov, and Robert C. Glen,
    Complex temporal patterns in molecular dynamics: a direct measure of the phase space exploration by the trajectory at macroscopic time scales,
    Phys. Rev. E, 77, 036225 (2008) (reproduced in Virtual Journal of Biological Physics Research, 15(7), (2008))
  32. Christian H. Jensen, Dmitry Nerukh, and Robert C. Glen,
    Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory,
    J. Chem. Phys., 128, 115107 (2008) (reproduced in Virtual Journal of Biological Physics Research, 15(7), (2008))
  33. F. Cecconi, C. Guardiani, and R. Livi,
    "Stability and kinetic properties of C5-domain of Myosin binding protein C and its mutants",
    Biophysical Journal, 94, 1403-1411, (2007).
  34. C. Guardiani, F. Cecconi, and R. Livi,
    "Computational analysis of folding and mutation properties of C5 domain of Myosin binding protein C",
    Proteins: Structure, Function, and Bioinformatics 70, 1313-1322, (2008).
  35. F. Cecconi, C. Guardiani and R. Livi,
    "Analyzing pathogenic mutations of C5 domain from cardiac myosin binding protein C through MD simulations",
    European Biophysics Journal (2008, to appear).
  36. M. Baiesi, E. Orlandini, and A. L. Stella,
    "Ranking knots of random, globular polymer rings",
    Physical Review Letters 99, 058301 (2007).
  37. M. Baiesi and R. Livi,
    "Multiple time scales in a model for DNA denaturation dynamics" ,
    submitted for publication (2007).
  38. L. N. Mazzoni and L. Casetti,
    "Geometry of the energy landscape and folding in a simple model of a protein",
    Physical Review E 77, 051917 (2008).
    [selected for the Virtual Journal of Biological Physics Research]
  39. A. Imparato, S. Luccioli, and A. Torcini,
    "Reconstructing the free energy landscape of a mechanically unfolded model protein",,
    Physical Review Letters 99, 168101 (2007).
    [selected for the Virtual Journal of Biological Physics Research]
  40. A. Imparato, S. Luccioli, and A. Torcini,
    "Erratum: Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein",
    Physical Review Letters 100, 159903(E) (2008).
  41. S. Luccioli, A. Imparato, and A. Torcini,
    "Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction",
    submitted for publication (2008).
  42. S. Mitternacht, S. Luccioli, A. Torcini, A. Imparato, and A. Irbaeck,
    "Changing the mechanical unfolding pathway of FnIII_10 by tuning the pulling strength",
    submitted for publication (2008).
  43. S. Marchetti, F. Sbrana, R. Raccis, L. Lanzi, C.M.C. Gambi, M. Vassalli, B.Tiribilli, A. Pacini, and A. Toscano,
    "Dynamic light scattering and atomic force microscopy imaging on fragments of beta-connectin from human cardiac muscle",,
    Physical Review E 77, 021910 (2008).
    [selected for the Virtual Journal of Biological Physics Research]
  44. A. Imparato, F. Sbrana, and M. Vassalli,
    "Reconstructing the free energy landscape of a polyprotein by single molecule experiments",,
    Europhysics Letters 82, 58006 (2008).
  45. F. Sbrana, C. Sassoli, D. Nosi, R. Squecco, F. Paternostro, B. Tiribilli, S. Zecchi Orlandini, F. Francini, and L. Formigli,
    "Role for stress fiber contraction on membrane tension and stretch activated channel activation",
    submitted for publication (2008).
  46. Martin Mann, Sebastian Will, and Rolf Backofen,
    The energy landscape library - a platform for generic algorithms,
    In BIRD'07 volume 217, pages 83-86. Oesterreichische Computer Gesellschaft, 2007
  47. Martin Mann, Sebastian Will, and Rolf Backofen,
    CPSP-tools - exact and complete algorithms for high-throughput 3D lattice protein studies,
    BMC Bioinformatics 9 pp. 230, 2008. doi:10.1186/1471-2105-9-230
  48. Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC,
    Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding,
    Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15230-5
  49. T. Thalheim, D. Merkle, M. Middendorf,
    A Hybrid Population based ACO Algorithm for Protein Folding,
    Proc. 2008 IAENG International Conference on Bioinformatics 6 pp. (2008)
  50. A. Imparato, S. Luccioli, and A. Torcini,
    Reconstructing the free energy landscape of a mechanically unfolded model protein,
    Phys. Rev. Lett. to appear (2007)
  51. Christoph Flamm, Barbel M. R. Stadler, and Peter F. Stadler,
    Saddles and Barrier in Landscapes of Generalized Search Operators,
    in Foundations of Genetic Algortithms IX, C. Stephens et al., (2007)
  52. Peter F. Stadler and Barbel M. R. Stadler,
    Genotype Phenotype Maps,
    Biological Theory 3, 268-279 (2006)
  53. Matthias Kruspe and Peter F. Stadler,
    Progressive Multiple Sequence Alignments from Triplets,
    BMC Bioinformatics in press (2007)
  54. S. Janson, D. Merkle,
    A New Multi-Objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking,
    in Proc. Second Int. Workshop on Hybrid Metaheuristics (HM 2005), Springer, LNCS 3636, 128-140, (2005)
  55. S. Janson, D. Merkle, M. Middendorf,
    Solving molecular docking with particle swarm optimization,
    in Abstracts of 5th Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig, 77, (2006)
  56. S. Janson, M. Middendorf,
    A Hierarchical Particle Swarm Optimizer for Noisy and Dynamic Environments,
    Accepted for Genetic Programming and Evolvable Machines
  57. Kei Moritsugu and Jeremy C. Smith,
    Langevin Model of the Temperature and Hydration Dependence of Protein Vibrational Dynamics,
    J. Phys. Chem. B, 109, 12182-12194 (2005)
  58. Kei Moritsugu and Jeremy C. Smith,
    Temperature Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description,
    J. Phys. Chem. B, 110, 5807-5816 (2006)
  59. F. Noe', D. Krachtus, J. C. Smith and S. Fischer,
    Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins,
    J. Chem. Theory and Comput., 2, 840-857 (2006)
  60. F. Noe', M. Oswald, G. Reinelt, S. Fischer and J. C. Smith,
    Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the L - R Transitions in Octaalanine,
    Multiscale Model. Sim., 5, 393-419 (2006)
  61. C. Heine, G. Scheuermann, Ch. Flamm, I.L. Hofacker, P.F.Stadler,
    Visualization of Barrier Tree Sequences,
    IEEE Transactions on Visualization and Computer Graphics, 12 (5), (2006)
  62. O. Gornerup and J. P. Crutchfield,
    Hierarchical Self-Organization in the Finitary Process Soup,
    To appear in Proceedings of ALife X, 2006
  63. M. Nilsson,
    Hierarchical Structures in Smooth Dynamical Systems,
    Artificial Life 11, 493-512 (2005)
  64. Sebastian Will and Martin Mann,
    Counting protein structures by dfs with dynamic decomposition,
    in Proc. of the Workshop on Constraint Based Methods for Bioinformatics, page 6, 2006
  65. L. Bongini, R. Livi, A. Politi, and A. Torcini,
    Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity,
    Physical Review E 72, 051929 (2005).
    [selected for the the December 1, 2005 issue of Virtual Journal of Biological Physics Research (http://www.vjbio.org)]
  66. L. N. Mazzoni and L. Casetti,
    Curvature of the energy landscape and folding of model proteins,
    Physical Review Letters 97, 218104 (2006).
    [Featured in Physics News Update] [selected for the Virtual Journal of Biological Physics Research]
  67. C. Guardiani and F. Bagnoli,
    A toy model of polymer stretching,
    Journal of Chemical Physics 125, 084908 (2006).
  68. Dmitry Nerukh, George Karvounis, and Robert C. Glen,
    Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding,
    accepted for publication in Lecture Notes in Bioinformatics (LNBI)
  69. S. Potzsch, G. Scheuermann, M. T. Wolfinger, C. Flamm, P. F. Stadler,
    Visualization of Lattice-Based Protein Folding Simulations,
    10th International Conference on Information Visualization London, July 2006
  70. Konstantin Klemm, Peter F. Stadler,
    Statistics of cycles in large networks,
    Phys. Rev. E 73, 025101(R) (2006)
  71. Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler,
    Exploring the Lower Part of Discrete Polymer Model Energy Landscapes,
    Europhysics Letters 74(4), 726-732 (2006)
  72. Dmitry Nerukh, Anatoliy V. Luzanov,
    Simple One-Electron Invariants of Molecular Chirality,
    accepted for publication in J. Math. Chem.
  73. Soto, P., Cladera, J., Mark, A.E. and Daura, X.
    Stability of SIV gp32 Fusion Peptide Single Layer Protofibrils as Monitored by Molecular Dynamics Simulations,
    Angewandte Chemie 17, 1089-1091 (2005).
  74. Fan H, Mark A.E., Zhu J, Honig, B
    Comparative study of generalized Born models: Protein dynamics,
    Proceedings of the National Academy of Sciences of the United States of America, 102, 19, 6760-6764 (2005)
  75. Marrink S.J., Risselada J, Mark A.E.
    Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model,
    Chem and Phys of Lipids, 135, 2, 223-244 (2005)
  76. de Vries A.H., Yefimov S, Mark A.E., Marrink S.J.
    Molecular structure of the lecithin ripple phase,
    Proceedings of the National Academy of Sciences of the United States of America, 102, 15, 5392-5396 (2005)
  77. Knecht, V., Mueller, M., Bonn, M., Marrink, S.J. and Mark, A.E.
    Simulation studies of pore and domain formation in a phospholipid monolayer,
    J.Chem.Phys. 122, 024704 1-9 (2005)
back
Modified:
27 Jun 2008		 Dmitry Nerukh [dn232@cam.ac.uk]