LIST OF PUBLICATIONS

Imre Derényi

July 2014

PAPERS

  1. I. Derényi, T. Geszti, and G. Györgyi:
    Generalization in the programed teaching of a perceptron.
    Phys. Rev. E   50, 3192-3200 (1994).
    doi:10.1103/PhysRevE.50.3192
    (download PDF 778 K)

  2. I. Derényi and T. Vicsek:
    Cooperative transport of Brownian particles.
    Phys. Rev. Lett.   75, 374-377 (1995).
    doi:10.1103/PhysRevLett.75.374
    (download PDF 227 K)

  3. I. Derényi and T. Vicsek:
    The kinesin walk: a dynamic model with elastically coupled heads.
    Proc. Natl. Acad. Sci. USA   93, 6775-6779 (1996).
    doi:10.1073/pnas.93.13.6775
    (download PDF 187 K)

  4. I. Derényi and A. Ajdari:
    Collective transport of particles in a "flashing" periodic potential.
    Phys. Rev. E   54, R5-R8 (1996).
    doi:10.1103/PhysRevE.54.R5
    (download PDF 126 K)

  5. I. Derényi, C. Lee, and A.-L. Barabási:
    Ratchet effect in surface electromigration: smoothing surfaces by an ac field.
    Phys. Rev. Lett.   80, 1473-1476 (1998).
    doi:10.1103/10.1103/PhysRevLett.80.1473
    (download PDF 139 K)

  6. I. Derényi and T. Vicsek:
    Realistic models of biological motion.
    Physica A   249, 397-406 (1998).
    doi:10.1016/S0378-4371(97)00498-6
    (download PDF 438 K)

  7. I. Derényi and R. D. Astumian:
    Spontaneous onset of coherence and energy storage by membrane transporters in an RLC electric circuit.
    Phys. Rev. Lett.   80, 4602-4605 (1998).
    doi:10.1103/PhysRevLett.80.4602
    (download PDF 210 K)

  8. R. D. Astumian and I. Derényi:
    Fluctuation driven transport and models of molecular motors and pumps.
    Eur. Biophys. J.   27, 474-489 (1998).
    doi:10.1007/s002490050158
    (download PDF 1805 K)

  9. I. Derényi, P. Tegzes, and T. Vicsek:
    Collective transport in locally asymmetric periodic structures.
    Chaos   8, 657-664 (1998).
    doi:10.1063/1.166348
    (download PDF 382 K)

  10. I. Derényi and R. D. Astumian:
    ac separation of particles by biased Brownian motion in a two-dimensional sieve.
    Phys. Rev. E   58, 7781-7784 (1998).
    doi:10.1103/PhysRevE.58.7781
    (download PDF 313 K)

  11. I. Derényi and R. D. Astumian:
    Intrawell relaxation time: the limit of the adiabatic approximation.
    Phys. Rev. Lett.   82, 2623-2627 (1999).
    doi:10.1103/PhysRevLett.82.2623
    (download PDF 142 K)

  12. I. Derényi and R. D. Astumian:
    Efficiency of Brownian heat engines.
    Phys. Rev. E   59, R6219-R6222 (1999).
    doi:10.1103/PhysRevE.59.R6219
    (download PDF 100 K)

  13. M. Bier, I. Derényi, M. Kostur, and R. D. Astumian:
    Intrawell relaxation of overdamped Brownian particles.
    Phys. Rev. E   59, 6422-6432 (1999).
    doi:10.1103/PhysRevE.59.6422
    (download PDF 208 K)

  14. C.-S. Lee, B. Jankó, I. Derényi, and A.-L. Barabási:
    Reducing vortex density in superconductors using the `ratchet effect'.
    Nature   400, 337-340 (1999).
    doi:10.1038/22485
    (download PDF 808 K)

  15. I. Derényi, M. Bier, and R. D. Astumian:
    Generalized efficiency and its application to microscopic engines.
    Phys. Rev. Lett.   83, 903-906 (1999).
    doi:10.1103/PhysRevLett.83.903
    (download PDF 92 K)

    10.1016/S0006-3495(99)76950-X

  16. R. D. Astumian and I. Derényi:
    A chemically reversible Brownian motor: application to kinesin and Ncd.
    Biophys. J.   77, 993-1002 (1999).
    doi:10.1016/S0006-3495(99)76950-X
    (download PDF 103 K)

  17. M. Bier, M. Kostur, I. Derényi, and R. D. Astumian:
    Nonlinearly coupled flows.
    Phys. Rev. E   61, 7184-7187 (2000).
    doi:10.1103/PhysRevE.61.7184
    (download PDF 364 K)

  18. R. D. Astumian and I. Derényi:
    Towards a chemically driven molecular electron pump.
    Phys. Rev. Lett.   86, 3859-3862 (2001).
    doi:10.1103/PhysRevLett.86.3859
    (download PDF 90 K)

  19. I. J. Farkas, I. Derényi, A.-L. Barabási, and T. Vicsek:
    Spectra of "real-world" graphs: Beyond the semicircle law.
    Phys. Rev. E   64, 026704 (2001).
    doi:10.1103/PhysRevE.64.026704
    (download PDF 164 K)

  20. D. Bartolo, I. Derényi, and A. Ajdari:
    Dynamic response of adhesion complexes: Beyond the single-path picture.
    Phys. Rev. E   65, 051910 (2002).
    doi:10.1103/PhysRevE.65.051910
    (download PDF 437 K)

  21. I. Derényi:
    Application of the ratchet effect to improve material quality (reducing vortex density in superconductors and smoothing surfaces).
    Appl. Phys. A   75, 217-222 (2002).
    doi:10.1007/s003390201323
    (download PDF 797 K)

  22. I. Derényi, F. Jülicher, and J. Prost:
    Formation and interaction of membrane tubes.
    Phys. Rev. Lett.   88, 238101 (2002).
    doi:10.1103/PhysRevLett.88.238101
    (download PDF 120 K)

  23. I. Farkas, I. Derényi, H. Jeong, Z. Néda, Z. N. Oltvai, E. Ravasz, A. Schubert, A.-L. Barabási, and T. Vicsek:
    Networks in life: scaling properties and eigenvalue spectra.
    Physica A   314, 25-34 (2002).
    doi:10.1016/S0378-4371(02)01181-0
    (download PDF 301 K)

  24. O. Rossier, D. Cuvelier, N. Borghi, P. H. Puech, I. Derényi, A. Buguin, P. Nassoy, and F. Brochard-Wyart:
    Giant Vesicles under Flows: Extrusion and Retraction of Tubes.
    Langmuir   19, 575-584 (2003).
    doi:10.1021/la026236t
    (download PDF 238 K)

  25. Z. Farkas, I. Derényi, and T. Vicsek:
    DNA uptake into nuclei: numerical and analytical results.
    J. Phys.: Condens. Matter   15, S1767-S1777 (2003).
    doi:10.1088/0953-8984/15/18/310
    (download PDF 368 K)

  26. I. Derényi, I. Farkas, G. Palla, and T. Vicsek:
    Topological phase transitions of random networks.
    Physica A   334, 583-590 (2004).
    doi:10.1016/j.physa.2003.10.083
    (download PDF 224 K)

  27. I. Derényi, D. Bartolo, and A. Ajdari:
    Effects of intermediate bound states in dynamic force spectroscopy.
    Biophys. J.   86, 1263-1269 (2004).
    doi:10.1016/S0006-3495(04)74200-9
    (download PDF 174 K)

  28. G. Palla, I. Derényi, I. Farkas, and T. Vicsek:
    Statistical mechanics of topological phase transitions in networks.
    Phys. Rev. E   69, 046117 (2004).
    doi:10.1103/PhysRevE.69.046117
    (download PDF 218 K)

  29. I. Farkas, I. Derényi, G. Palla, and T. Vicsek:
    Equilibrium statistical mechanics of network structures.
    Lect. Notes Phys.   650, 163-187 (Springer-Verlag, Berlin Heidelberg, 2004).
    doi:10.1007/b98716
    (download PDF 544 K)

  30. G. J. Szöllősi, I. Derényi, and J. Vörös:
    Reversible mesoscopic model of protein adsorption: From equilibrium to dynamics.
    Physica A   343, 359-375 (2004).
    doi:10.1016/j.physa.2004.06.062
    (download PDF 479 K)

  31. G. Palla, I. Farkas, I. Derényi, A.-L. Barabási, and T. Vicsek:
    Reverse engineering of linking preferences from network restructuring.
    Phys. Rev. E   70, 046115 (2004).
    doi:10.1103/PhysRevE.70.046115
    (download PDF 99 K)

  32. M. A. Makeev, I. Derényi, and A.-L. Barabási:
    Emergence of large-scale vorticity during diffusion in a random potential under an alternating bias.
    Phys. Rev. E   71, 026112 (2005).
    doi:10.1103/PhysRevE.71.026112
    (download PDF 99 K)

  33. G. Koster, A. Cacciuto, I. Derényi, D. Frenkel, and M. Dogterom:
    Force barriers for membrane tube formation.
    Phys. Rev. Lett.   94, 068101 (2005).
    doi:10.1103/PhysRevLett.94.068101
    (download PDF 710 K)

  34. D. Cuvelier, I. Derényi, P. Bassereau, and P. Nassoy:
    Coalescence of membrane tethers: Experiments, theory, and applications.
    Biophys. J.   88, 2714-2726 (2005).
    doi:10.1529/biophysj.104.056473
    (download PDF 350 K)

  35. I. Derényi, G. Palla, and T. Vicsek:
    Clique percolation in random networks.
    Phys. Rev. Lett.   94, 160202 (2005).
    doi:10.1103/PhysRevLett.94.160202
    (download PDF 418 K)

  36. G. Palla, I. Derényi, I. Farkas, and T. Vicsek:
    Uncovering the overlapping community structure of complex networks in nature and society.
    Nature   435, 814-818 (2005).
    doi:10.1038/nature03607
    (download PDF 496 K)   (download supplementary material 286 K)
    Go to the clustering and community finding software page.

  37. B. Adamcsek, G. Palla, I. J. Farkas, I. Derényi, and T. Vicsek:
    CFinder: locating cliques and overlapping modules in biological networks.
    Bioinformatics   22, 1021-1023 (2006).
    doi:10.1093/bioinformatics/btl039
    (download PDF 264 K)
    Go to the clustering and community finding software page.

  38. G. J. Szöllősi, I. Derényi, and T. Vellai:
    The maintenance of sex in bacteria is ensured by its potential to reload genes.
    Genetics   174, 2173-2180 (2006).
    doi:10.1534/genetics.106.063412
    (download PDF 1142 K)

  39. I. Derényi, G. Koster, M. M. van Duijn, A. Czövek, M. Dogterom, and J. Prost:
    Membrane nanotubes.
    Lect. Notes Phys.   711, 141-159 (Springer-Verlag, Berlin Heidelberg, 2007).
    doi:10.1007/3-540-49522-3_7
    (download PDF 1041 K)

  40. G. Palla, I. Derényi, and T. Vicsek:
    The critical point of k-clique percolation in the Erdős-Rényi graph.
    J. Stat. Phys.   128, 219-227 (2007).
    doi:10.1007/s10955-006-9184-x
    (download PDF 210 K)

  41. G. Palla, I. J. Farkas, I. Derényi, P. Pollner, and T. Vicsek:
    Directed network modules.
    New J. Phys.   9, 186 (2007).
    doi:10.1088/1367-2630/9/6/186
    (download PDF 2144 K)

  42. P. Pollner, G. Palla, D. Ábel, A. Vicsek, I. J. Farkas, I. Derényi, and T. Vicsek:
    Centrality properties of directed module members in social networks.
    Physica A   387, 4959-4966 (2008).
    doi:10.1016/j.physa.2008.04.025
    (download PDF 687 K)

  43. G. J. Szöllősi and I. Derényi:
    The effect of recombination on the neutral evolution of genetic robustness.
    Math. Biosci.   214, 58-62 (2008).
    doi:10.1016/j.mbs.2008.03.010
    (download PDF 258 K)

  44. A. Czövek, G. J. Szöllősi, and I. Derényi:
    The relevance of neck linker docking in the motility of kinesin.
    BioSystems   93, 29-33 (2008).
    doi:10.1016/j.biosystems.2008.04.006
    (download PDF 383 K)

  45. G. J. Szöllősi and I. Derényi:
    Evolutionary games on minimally structured populations.
    Phys. Rev. E   78, 031919 (2008).
    doi:10.1103/PhysRevE.78.031919
    (download PDF 835 K)

  46. G. Palla, I. J. Farkas, I. Derényi, P. Pollner, and T. Vicsek:
    Fundamental statistical features and self-similar properties of tagged networks.
    New J. Phys.   10, 123026 (2008).
    doi:10.1088/1367-2630/10/12/123026
    (download PDF 1741 K)

  47. G. J. Szöllősi and I. Derényi:
    Congruent evolution of genetic and environmental robustness in micro-RNA.
    Mol. Biol. Evol. 26, 867-874 (2009).
    doi:10.1093/molbev/msp008
    (download PDF 524 K)

  48. M. Gyimesi, K. Sarlós, I. Derényi, and M. Kovács:
    Streamlined determination of processive run length and mechanochemical coupling of nucleic acid motor activities.
    Nucl. Acids Res. 38, e102 (2010).
    doi:10.1093/nar/gkq014
    (download PDF 2103 K)

  49. A. Czövek, G. J. Szöllősi, and I. Derényi:
    Neck linker docking coordinates the kinetics of kinesin's heads.
    Biophys. J. 100, 1729-1736 (2011).
    doi:10.1016/j.bpj.2011.01.039
    (download PDF 344 K)
    (download Supporting Material 1 (PDF 437 K), 2 (MOV 406 K), 3 (MOV 394 K))

  50. A. Á. Rauscher, Z. Simon, G. J. Szöllősi, L. Gráf, I. Derényi, and A. Málnási-Csizmadia:
    Temperature dependence of internal friction in enzyme reactions.
    FASEB J. 25, 2804-2813 (2011).
    doi:10.1096/fj.11-180794
    (download PDF 363 K)
    (download Supporting Material 1 (DOC 32 K), 2 (DOC 1271 K))

  51. K. Sugihara, M. Chami, I. Derényi, J. Vörös, and T. Zambelli:
    Directed self-assembly of lipid nanotubes from inverted hexagonal structures.
    ACS Nano 6, 6626-6632 (2012).
    doi:10.1021/nn300557s
    (download PDF 1298 K)
    (download Supporting Material 1 (PDF 843 K), 2 (AVI 4671 K))

  52. A. Rauscher, I. Derényi, L. Gráf, and A. Málnási-Csizmadia:
    Internal Friction in Enzyme Reactions.
    IUBMB Life 65, 35-42 (2013).
    doi:10.1002/iub.1101
    (download PDF 440 K)

  53. I. Derényi and I. Lagzi:
    Fatty acid droplet self-division driven by a chemical reaction.
    Phys. Chem. Chem. Phys. 16, 4639-4641 (2014).
    doi:10.1039/C3CP54676D
    (download PDF 1246 K)

  54. A. Takáts-Nyeste and I. Derényi:
    The rupture of lipid vesicles near solid surfaces.
    Phys. Rev. E   (submitted).
    (download PDF 276 K)

  55. N. Orgován, A. Rauscher, A. Málnási-Csizmadia and I. Derényi:
    The viscosity dependence of passage through a fluctuating bottleneck.
    J. Chem. Phys.   (submitted).
    (download PDF 151 K)

  56. N. Orgován, A. Rauscher, A. Málnási-Csizmadia and I. Derényi:
    A minimal model of the internal friction of proteins based on two elastically coupled reaction coordinates.
    Phys. Rev. Lett.   (submitted).
    (download PDF 219 K)

  57. I. Derényi and G. J. Szöllősi:
    The effective temperature of mutations.
    Phys. Rev. Lett.   (submitted).
    (download PDF 1987 K)

  58. A. Takáts-Nyeste and I. Derényi:
    The formation hat-shaped liposomes on solid support.
    Langmuir   (submitted).

  59. N. Orgován and I. Derényi:
    The stepping mechanism of one-head-loaded kinesin.
    PLOS Comp. Biol.   (submitted).
    (download PDF 350 K)

  60. R. Deák and I. Derényi:
    The internal friction and anomalous conformational diffusion of proteins.
    Proc. Natl. Acad. Sci. USA   (to be submitted).

PAPERS IN HUNGARIAN

  1. Czirók A., Csahók Z., Derényi I. és Vicsek T.:
    Biológiai mozgások statisztikus fizikai modelljei.
    Fizikai Szemle   1996/6, 189-195 (1996).

  2. Derényi I., Farkas I., Palla G. és Vicsek T.:
    Csoportosulások szociológiai, technológiai és biológiai hálózatokban.
    Magyar Tudomány   2006/11, 1319-1324 (2006).
    (view HTML)

  3. Derényi I.:
    Membrán nanocsövek.
    Fizikai Szemle   2006/12, B3-B4 (2006).
    (view HTML)

  4. Palla G., Derényi I., Farkas I., Pollner P. és Vicsek T.:
    A természet és a társadalom komplex hálózataiban található átfedő csoportosulások feltárása.
    Műszaki Szemle   42, 9-18 (2008).
    (download PDF 976 K)

BOOK CHAPTERS

  1. I. Derényi and T. Vicsek:
    Microscopic mechanisms of biological motion.
    In Fluctuations and Scaling in Biology,
    edited by T. Vicsek
    (Oxford University Press, New York, 2001) pp. 117-176.

PROCEEDINGS

  1. I. Derényi and R. D. Astumian:
    Brownian ratchets and their application to biological transport processes and macromolecular separation.
    In Structure and Dynamics of Confined Polymers. NATO Science Series 87,
    edited by J. J. Kasianowicz, M. S. Z. Kellermayer, and D. W. Deamer
    (Kluwer Academic Publishers, 2002) pp. 281-294.

  2. Z. Farkas, I. Derényi, and T. Vicsek:
    Dynamics of actin filaments in motility assays: A microscopic model and its numerical simulation.
    In Structure and Dynamics of Confined Polymers. NATO Science Series 87,
    edited by J. J. Kasianowicz, M. S. Z. Kellermayer, and D. W. Deamer
    (Kluwer Academic Publishers, 2002) pp. 327-332.

  3. N. Borghi, F. Brochard-Wyart, E. Karatekin, and I. Derényi:
    Giant vesicles: Transient pores and tube extraction.
    In Proceedings of the International School of Physics "Enrico Fermi", Course CLV,
    edited by F. Mallamace and H. E. Stanley
    (IOS Press, Amsterdam, 2004) pp. 313-333.

  4. G. Palla, D. Ábel, I. J. Farkas, P. Pollner, I. Derényi, and T. Vicsek:
    k-clique percolation and clustering.
    In Handbook of Large-Scale Random Networks. Bolyai Society Mathematical Studies 18,
    edited by B. Bollobás, R. Kozma, and D. Miklós
    (Springer, 2008) pp. 1-40.

PATENTS

  1. A.-L. Barabási, B. Jankó, C.-S. Lee, and I. Derényi:
    Reducing vortex densities and transporting vortices in superconductors.
    U.S. Patent   No. 6,469,880 (October 22, 2002).