JOURNAL ARTICLES:

I. High Energy Physics:

    1. N. V. Dokholyan, G. V. Jikia, "Single top quark production and Vtb CKM matrix element measurement in high energy e+e- collisions." Phys. Lett. B. 336: 251-256 (1994).

II. DNA:

    2. N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distribution of base pair repeats in coding and noncoding DNA sequences." Phys. Rev. Lett. 79: 5182-5185 (1997).
    [Adobe PDF] [PostScript, gzipped]

    3. N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Model of unequal chromosomal crossing over in DNA sequences." Physica A 249: 594-599 (1998).
    [Adobe PDF] [PostScript, gzipped]

    4. S. V. Buldyrev, N. V. Dokholyan, A. L. Goldberger, S. Havlin, C.-K. Peng, H. E. Stanley, and G. M. Viswanathan, "Analysis of DNA sequences using methods of statistical physics." Physica A 249: 430-438 (1998).
    [Adobe PDF] [PostScript,gzipped]

    5. R. H. R. Stanley, N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Clumping of identical oligonucleotides in coding and noncoding DNA sequences." J. Biomol. Struct. & Dyn. 17: 79-87 (1999).
    [Adobe PDF] [PostScript,gzipped]

    6. S. V. Buldyrev, N. V. Dokholyan, S. Havlin, H. E. Stanley, and R. H. R. Stanley, "Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences." Physica A 273: 19--32 (1999).
    [Adobe PDF] [PostScript, gzipped]

    7. N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distributions of dimeric tandem repeats in noncoding and coding DNA sequences." J. Theor. Biol. 202: 273-282 (2000).
    [Adobe PDF] [PostScript,gzipped]

III. Cell motility:

    8. M. Hong, A. Jeung, N. V. Dokholyan, T. I. Smith, H. A. Schwettman, P. Huie, and S. Erramilli, "Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser." Nucl. Instr. & Methods in Phys. Res. B144: 246-255, (1998).
    [Adobe PDF] [PostScript, gzipped: approx 0.5Mb]

IV. Random systems:

    10. N. V. Dokholyan, S. V. Buldyrev, S. Havlin, P. King, Y. Lee, and H. E. Stanley, "Distribution of shortest paths in percolation." Physica A 266: 53--59 (1999).
    [Adobe PDF] [PostScript,gzipped]
    11. P. King, J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, Y. Lee, S. Havlin, and H. E. Stanley, "Percolation and Oil Recovery." Physica A 266: 107--114 (1999).
    [Adobe PDF] [PostScript,gzipped]
    12. Y. Lee, J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, G. Paul, & H. E. Stanley, "Traveling time and traveling length for flow in porous media." Phys. Rev. E 60: 3425--3428 (1999); cond-mat/9903066
    [Adobe PDF] [PostScript, gzipped]

    13. P. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, Y. Lee, and H. E. Stanley, "Application of statistical physics to the oil industry: Predicting oil recovery using percolation theory." Physica A 274: 60--66 (1999).
    [Adobe PDF] [PostScript, gzipped]

    14. G. Paul, S. V. Buldyrev, N. V. Dokholyan, P. R. King, Y. Lee, S. Havlin, & H. E. Stanley, "Dependence of conductance on percolation backbone mass." Phys. Rev. E 61: 3435-3440, (2000); cond-mat/9910236
    [Adobe PDF] [PostScript]

    15. J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, Y. Lee, G. Paul, & H. E. Stanley, "Flow in percolation clusters." Phys. Rev. E 62: 8270-8281 (2000); cond-mat/0004397
    [Adobe PDF] [PostScript]
    16. P. R. King, S. V. Buldyrev, N. V. Dokholyan, Y. Lee, S. Havlin, G. Paul, H. E. Stanley, & N. Vandesteeg "Predicting oil recovery using percolation theory." Petroleum Geoscience 7: S105-S107 (2001).
    [Adobe PDF] [PostScript]

V. Protein folding, design, and evolution:

CONFERENCE PROCEEDINGS ARTICLES:

    1. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Kinetics of the protein folding transition." AIP Proceedings of the Third Tohwa University Conference on Statistical Physics, November 8-12, 1999 419--425 (2000).
    [Adobe PDF] [PostScript,gzipped]
    2. N. V. Dokholyan and E. I. Shakhnovich, "Two models of amino acid conservation in proteins." Proceedings of the International School of Physics ``Enrico Fermi'' Course CXLV: ``Protein folding, evolution and design'', Varenna, Italy p. 227--245 (2000).

 

CONFERENCE PROCEEDINGS ABSTRACTS:

    1. N. V. Dokholyan, "Power law distribution of random repeats in DNA sequences.'' STATPHYS XIX, The 19th IUPAP International Conference on Statistical Physics, Xiamen, China, July 31 -- August 4, 1995. H. Bailin (Ed.) World Scientific, London (1995).
    2. N. V. Dokholyan, , S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Power law distribution of dimeric tandem repeats in DNA sequences.'' Proceedings of the International School of Physics "Enrico Fermi'',
    Course CXXXIV. Varenna on Lake Como, Villa Monastero, Italy, July 9 -- 19, (1996). "The Physics of Complex Systems.'' IOS Press,
    Oxford (1997).

    3. N. V. Dokholyan, "Power law distribution of random repeats in DNA sequences.'' STATPHYS XIX, The 19th IUPAP International Conference on Statistical Physics, Xiamen, China, July 31 -- August 4, 1995. H. Bailin (Ed.) World Scientific, London (1995).

    4. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Quest for the protein folding nucleus.'' Proceedings of the American Physical Society Centennial Meeting, Atlanta, GA, USA, March
    20 -- 26, (1999).

    5. Y. Lee, S. V. Buldyrev, N. V. Dokholyan, G. Paul, H. E. Stanley, J. Andrade Jr., S. Havlin, P. King, ``Tranport in Percolation Clusters.'' Proceedings of the American Physical Society Centennial Meeting, Atlanta, GA, USA, March 20 -- 26, (1999).

    6. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Folding kinetics of the model protein from molecular dynamics'' Proceedings of the Workshop on Dynamics of Non-Equilibrium Systems,
    Trieste, Italy, August 17 -- 27, (1999).

    7. E. I. Shakhnovich, J. Shimada, E. Kussell, and N. V. Dokholyan, "Statistical mechanics of proteins: Perspective from analytical theory and simulations'' Abstracts of papers of the american chemical
    society 221: 100-COMP, (2001).

    8. P. R. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, G. Paul, and H. E. Stanley "Using percolation theory to predict oil recovery.'' STATPHYS XXI, The 21th IUPAP International Conference on Statistical
    Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez, M. Barbosa, A. Robledo (Eds.).

    9. L. R. da Silva, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, G. Paul, and H. E. Stanley "Shortest path distribution among multiple points.'' STATPHYS XXI, The 21th IUPAP International
    Conference on Statistical Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez, M. Barbosa, A. Robledo (Eds.).

    10. E. Lopez, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, G. Paul, and H. E. Stanley "Flow in percolation clusters: post-breakthrough behavior.'' STATPHYS XXI, The 21th IUPAP International Conference on Statistical Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez, M. Barbosa, A. Robledo. (Eds.).

    11. F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Direct observation of folding transition state ensemble of C-Src SH3 domain in molecular dynamics simulations.'' STATPHYS XXI, The 21th IUPAP International Conference on Statistical Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez, M. Barbosa, A. Robledo (Eds.).

    12. J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Transition State and folding nucleus of C-crk SH3 Domain from Discrete Molecular Dynamics Simulations.'' STATPHYS XXI, The 21th IUPAP International Conference on Statistical Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez, M. Barbosa, A. Robledo. (Eds.).

    13. N. V. Dokholyan, and E. I. Shakhnovich, "A model of protein evolution.'' STATPHYS XXI, The 21th IUPAP International Conference on Statistical Physics, Cancun, Mexico, July 15 -- 21, 2001. D. Lopez,
    M. Barbosa, A. Robledo (Eds.).


PREPRINTS AND SUBMITTED ARTICLES:

  I. High Energy Physics:

    P1. N. V. Dokholyan, G. V. Jikia, preprint: IHEP 93111, Protvino, Russia (1993).
    [Adobe PDF] [PostScript, gzipped]

    P2. N. V. Dokholyan, "Cabbibo - Kabayashi - Maskawa mixing matrix in the case of four generations." preprint (1994).

II. Protein folding, design, and evolution:

    P3. N. V. Dokholyan, L. A. Mirny, and E. I. Shakhnovich, "Understanding conserved amino acids in proteins." Phys. Rev. Lett. submitted (2000); cond-mat/0007084

    P4. N. V. Dokholyan, L. Li, and E. I. Shakhnovich, "Structural determinants of folding transition state in proteins." preprint (2000).

    P5. N. V. Dokholyan and E. I. Shakhnovich, "How many protein sequences correspond to a given structure?" preprint (2000).

    P6. N. V. Dokholyan, Lewyn Li, Feng Ding, and Eugene I. Shakhnovich, "Topological determinants of protein folding." Nature submitted (2001).

    P7. N. V. Dokholyan, Estelle Pitard, Sergey V. Buldyrev, and H. Eugene Stanley, "Glassy behavior of a homopolymer from molecular dynamics simulations." Phys. Rev. E submitted (2001); cond-mat/0109198

    P8. M. Vendruscolo, N. V. Dokholyan, E. Paci and M. Karplus, "A small-world view of the amino acids that play a key role in protein folding." Phys. Rev. Lett. submitted (2001).

    P9. J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Transition state of C-crk SH3 domain: Molecular dynamics simulations of simple models." J. Mol. Biol. submitted (2001).

    P10. F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Direct observation of folding transition state ensemble of C-Src SH3 domain in molecular dynamics simulations." Proc. Natl. Acad. USA submitted (2001).

III. Complex Systems:

    P11. G. Malescio, N. V. Dokholyan, S. V. Buldyrev, and H. E. Stanley, "Hierarchical organization of cities and nations."(2000); cond-mat/0005178


DISSERTATION:

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