Selected Publications : Biological Physics
(Dr. Sergey Buldyrev)

[Protein Folding and Aggregation] [Neuroscience] [Physics of Lungs]
[Statistical Properties of DNA sequences and Molecular Evolution] [Behavior of Complex Systems]


Protein Folding and Aggregation
  1. A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, H.E. Stanley, and E. Shakhnovich, "Parallel Folding Pathways in the SH3 Domain Protein," J. Mol. Biol. 373, 1348-1360 (2007). PDF


  2. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, "Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model" Biophys. J. 88, 147-155 (2005). PDF


  3. J. M. Borreguero, B. Urbanc, N. D. Lazo, S. V. Buldyrev, D. B. Teplow, and H. E. Stanley, "Folding events in the 21-30 region of amyloid-beta-protein (Aβ) studied in silico," Proc. Natl. Acad. Sci. 102, 6015-6020 (2005). PDF


  4. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "Multiple Folding Pathways of the SH3 Domain," Biophys. J. 87, 521-533 (2004). PDF


  5. S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, and N. V. Dokholyan, "Discrete molecular dynamics simulations of peptide aggregation," Phys. Rev. E 69, 041908, (2004). PDF


  6. B. Urbanc, L. Cruz, S. Yun, S. V. Buldyrev, G. Bitan, D. B. Teplow, and H. E. Stanley, "In Silico Study of Amyloid Beta Protein Folding and Oligomerization," Proc. Natl. Acad. Sci. 101, 17345-17350 (2004). PDF


  7. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "Molecular Dynamics Simulation of Amyloid β Dimer Formation," Biophys. J. 87, 2310-2321 (2004). PDF


  8. F. Ding, J. M. Borreguero, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "Mechanism for the α-helix to β-hairpin Transition," Proteins: Structure, Function, and Genetics 53: 220-228 (2003). PDF


  9. J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley,and E. I. Shakhnovich, "Thermodynamics and folding kinetics analysisof the SH3 domain from Discrete Molecular Dynamics."J. Mol. Biol. 318: 863-876 (2002)PDF


  10. 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." Biophys. J. 83: 3525-3532 (2002) PDF


  11. F. Ding, N. V. Dokholyan, S.V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Molecular dynamic simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism." J. Mol. Biol. 324: 851-857 (2002). PDF


  12. A. Scala, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Thermodynamically important contacts in folding of model proteins" Phys. Rev. E 63: 032901-4 (2001). PDF


  13. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Identifying the protein folding nucleus using molecular dynamics." J. Mol. Biol. 296: 1183-1188 (2000) PDF


  14. N. Dokholyan, S. V. Buldyrev, H. E. Stanley and E. I. Shakhnovich, "Discrete molecular dynamics studies of the folding of a protein-like model" Folding & Design 3: 577-587 (1998). PDF


Neuroscience
  1. L. C. Cruz, S. V. Buldyrev, S. Y. Peng, D. L. Roe, B. Urbanc, H. E. Stanley, and D. L. Rosene, "A statistically based density map method for identification and quantification of regional differences in microcolumnarity in the monkey brain" J. Neurosci. Methods 141: 321-332 (2005). PDF


  2. S. V. Buldyrev, L. Cruz, T. Gomez-Isla, S. Havlin, H. E. Stanley, B. Urbanc and B. T. Hyman "Description of Microcolumnar Ensembles in Association Cortex and their Disruption in Alzheimer and Lewy Body Dementias" Proc. Natl. Acad. Sci. 97: 5039-5043 (2000). PDF


  3. B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, B. T.Hyman, and H. E. Stanley "Dynamic Feedback in an Aggregation-Disaggregation Model" Phys. Rev. E 60: 2120-2126 (1999). PDF


  4. R. B. Knowles, C. Wyart, S. V. Buldyrev, L. Cruz, B. Urbanc, M.E. Hasselmo, S. Havlin, H. E. Stanley and B. T. Hyman, "Plaque-induced neural network disruption in Alzheimer's disease" Proc. Natl. Acad. Sci. 96: 5274-5279 (1999). PDF


  5. B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, H. E. Stanley and B. T. Hyman, "Dynamics of Plaque Formation in Alzheimer Disease" Biophys. J. 76: 1330-1334 (1999). PDF


  6. L. Cruz, B. Kutnjac-Urbanc, S. V. Buldyrev, R. Christie, T. Gomez-Isla, S. Havlin, M. McNamara, H. E. Stanley, and B. T. Hyman, "Aggregation and Disaggregation of Senile Plaques in Alzheimer Disease" Proc. Natl. Acad. Sci. 94: 7612-7616 (1997). PDF


  7. B. T. Hyman, H.L. West, G. W. Rebeck, S. V. Buldyrev, R. N. Mantegna, M. Ukleja, S. Havlin, and H. E. Stanley, "Quantitative analysis of senile plaques in Alzheimer disease: Observation of log-normal size distribution and of differences associated with apolipoprotein E genotype and trisomy 21 (Down syndrome)," Proc. Natl. Acad. Sci. 92: 3586-3590 (1995). PDF


Physics of The Lungs
  1. A. B. Almeida, S. V. Buldyrev and A. M. Alencar, "Crackling Sound Generation During the Formation of Liquid Bridges: A Lattice Gas Model," Physica A 392, 3409-3416 (2013). PDF


  2. A. M. Alencar, E. Wolfe, and S. V. Buldyrev, "Monte Carlo simulation of liquid bridge rupture: Application to lung physiology," Phys. Rev. E 74, 026311 (2006). PDF


  3. A. Majumdar, A. M. Alencar, S. V. Buldyrev, Z. Hantos, K.R. Lutchen, H. E. Stanley, and B. Suki, "Relating airway diameter distributions and branching asymmetry in the lung," Phys. Rev. Lett. 95, 168101 (2005). PDF


  4. B. Suki, A. M. Alencar, U. Frey, P. Ch. Ivanov, S. V. Buldyrev, A. Majumdar, H. E. Stanley, C. A. Dawson, G. S. Krenz, and M. Mishima, "Fluctuations, Noise, and Scaling in the Cardio-Pulmonary System," Fluctuations and Noise Letters 3, R1-R25 (2003). PDF


  5. A. M. Alencar, S. V. Buldyrev, A. Majumdar, H. E. Stanley,and B. Suki, "Perimeter Growth of a Branched Structure: Application to Crackle Sounds in the Lung" Phys. Rev. E 68: 11909 (2003). PDF


  6. A. Majumdar, A. M. Alencar, S. V. Buldyrev, Z. Hantos, H. E. Stanley,and B. Suki, "Fluid transport in branched structures with temporary closures: A model for quasistatic lung inflation" Phys. Rev. E 67: 031912 (2003). PDF


  7. A. M. Alencar, S. Arold, S. V. Buldyrev, A. Majumdar, D. Stamenovic, H. E. Stanley, and B. Suki, "Dynamic Instabilities in the Inflating Lung," Nature 417: 809--811 (2002). PDF


  8. A. Majumdar, A. M. Alencar, S. V. Buldyrev, Z. Hantos, H. E. Stanley and B. Suki, "Characterization of the Branching Structure of the Lung from Macroscopic Pressure-Volume Measurements" Phys. Rev. Letters 87: 058102-4 (2001). PDF


  9. A. M. Alencar, S. V. Buldyrev, A. Majumdar, H. E. Stanley, and B. Suki, "Avalanche Dynamics of Crackle Sound in the Lung" Phys. Rev. Lett. 87: 088101-4 (2001). PDF


  10. M. P. Almeida, J. S. Andrade Jr., S. V. Buldyrev, F. S. A. Cavalcante, H. E. Stanley, and B. Suki, "Fluid Flow through Ramified Structures" Phys. Rev. E 60: 5486-5494 (1999). PDF


  11. A. M. Alencar, Z. Hantos, F. Hantos, F. Petak, J. Tolnai, T. Asztalos, S. Zapperi, J. S. Andrade, S. V. Buldyrev, H. E. Stanley, and B. Suki, "Scaling Behavior in Crackle Sound during Lung Inflation" Phys. Rev E 60: 4659-4663 (1999). PDF


  12. M. K. Sujeer, S. V. Buldyrev, S. Zapperi, J. Andrade, H. E. Stanley, and B. Suki, "Volume Distributions of Avalanches in Lung Inflation: A Statistical Mechanical Approach" Phys. Rev. E 56: 3385-3394 (1997). PDF


  13. A.-L. Barabasi, S. V. Buldyrev, H. E. Stanley, and B. Suki, "Avalanches in the Lung: A Statistical Mechanical Approach," Phys.Rev. Lett. 76: 2192-2195 (1996). PDF


Statistical Properties of DNA Sequences and Molecular Evolution
  1. I. Grosse, H. Herzel, S. V. Buldyrev, and H. E. Stanley, "Species Independence of Mutual Information in Coding and Noncoding DNA," Phys. Rev. E 61: 5624-5629 (2000). PDF


  2. N. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences," J. Theor. Biol. 202: 273-282 (2000). PDF


  3. 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). PDF


  4. 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. Structure and Dynamics 17: 79-87 PDF


  5. N. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Model of unequal chromosomal crossing over" Physica A 249: 594-599 (1998). PDF


  6. 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). PDF


  7. 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). PDF


  8. G. M. Viswanathan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Quantification of DNA Patchiness using Correlation Measures," Biophys. J. 72: 866-875 (1997). PDF, Correction


  9. R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons, and H. E. Stanley, "Systematic Analysis of Coding and Noncoding DNA Sequences Using Methods of Statistical Linguistics," Phys. Rev. E 52: 2939-2950 (1995). PDF


  10. S. V. Buldyrev, A. L. Goldberger, S. Havlin, R. N. Mantegna, M. E. Matsa, C.-K. Peng, M. Simons, and H. E. Stanley, "Long-Range Correlation Properties of Coding and Noncoding DNA Sequences: GenBank Analysis," Phys. Rev. E 51: 5084-5091 (1995). PDF


  11. S. M. Ossadnik, S. V. Buldyrev, A. L. Goldberger, S. Havlin, R.N. Mantegna, C.-K. Peng, M. Simons, and H. E. Stanley, "Correlation Approach to Identify Coding Regions in DNA Sequences" Biophys. J. 67: 64-70 (1994). PDF


  12. R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons, and H. E. Stanley, "Linguistic Features of Noncoding DNA-Sequences," Phys. Rev. Lett. 73, 3169-3172 (1994). PDF


  13. C. K. Peng, S. V. Buldyrev, S. Havlin, M. Simons, H. E. Stanley and A. L. Goldberger, "Mosaic Organization of DNA Sequences," Phys. Rev. E 49: 1685-1689 (1994). PDF


  14. C. K. Peng, S. V. Buldyrev, A. L. Goldberger, S. Havlin, M. Simons, and H. E. Stanley, "Finite Size Effects on Long-Range Correlations: Implications for Analyzing DNA Sequences," Phys. Rev. E 47:, 3730-3733 (1993). PDF


  15. S. V. Buldyrev, A. Goldberger, S. Havlin, C.-K. Peng, F. Sciortino, M. Simons and H. E. Stanley, "On Long-Range Power Law Correlations in DNA", Phys. Rev. Lett. 71: 1776 (1993). PDF


  16. S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, H. E. Stanley and M. Simons, "Fractal Landscapes and Molecular Evolution: Modeling the Myosin Heavy Chain Gene Family" Biophys. J. 65: 2675-2681 (1993). PDF


  17. S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons, and H. E. Stanley, "Generalized Lévy Walk Model for DNA Nucleotide Sequences," Phys. Rev. E 47: 4514-4523 (1993). PDF


  18. C. K. Peng, S. V. Buldyrev, A. Goldberger, S. Havlin, F. Sciortino, M. Simons and H. E. Stanley, "Long-Range Correlations in Nucleotide Sequences," Nature 356: 168--171 (1992). PDF


Behavior of Complex Systems

Peer-Reviewed Publications
  1. D. Rybski, S. V. Buldyrev, S. Havlin, F. Liljeros, H.A. Makse, "Communication activity in a social network: relation between long-term correlations and inter-event clustering," Sci. Rep. 2, 560 (2012). PDF


  2. D. Rybski, S. V. Buldyrev, S. Havlin, F. Liljeros, and H.A. Makse, "Communication activity in social networks: growth and correlations," Europ. Phys J. B 84, 147-159 (2011). PDF


  3. D. Rybski, S. V. Buldyrev, S. Havlin, F. Liljeros, and H.A. Makse, "Scaling laws of human interaction activity," Proc. Natl. Acad. Sci. 106, 12640-12645 (2009). PDF


  4. A. M. Edwards, R. A. Phillips, N. W. Watkins, M. P. Freeman, E. J. Murphy, V. Afanasyev, S. V. Buldyrev, M. G. E. da Luz, E. P. Raposo, H. E. Stanley, G. M. Viswanathan, "Revisiting Levy flight search patterns of wandering albatrosses, bumblebees and deer," Nature 449, 1044-U5 (2007). PDF


  5. S. V. Buldyrev, J. Ferrante, F. R. Zypman, "Dry friction avalanches: Experiment and theory," Phys. Rev. E 74, 066110 (2006). PDF


  6. E. Raposo, S. V. Buldyrev, M. G. da Luz, M. C. Santos, H. E. Stanley, G. M. Viswanathan, "Dynamical robustness of Levy search strategies" Phys. Rev. Lett.91: 240601-4 (2003). PDF


  7. S. V. Buldyrev, S. Havlin, A. Ya. Kazakov, M. G. E. da Luz, E. P. Raposo, H. E. Stanley, and G. M. Viswanathan, "Average Time Spent by Levy Flights and Walks on an Interval with Absorbing Boundaries" Phys. Rev. E 64: 041108-11 (2001). PDF


  8. S. V. Buldyrev, M. Gitterman, S. Havlin, A. Ya. Kazakov, M. G. E. da Luz, E. P. Raposo, H. E. Stanley, and G. M. Viswanathan, "Properties of Levy fights on an interval with absorbing boundaries" Physica A 302: 148-161 (2001). PDF


  9. G. M. Viswanathan, S. V. Buldyrev, E. Garger, V. A. Kashpur,L. S. Lucena, A. Shlyakhter, J.Tschiersch, and H. E. Stanley,"Log-Normal Behavior of 137Cs Concentration Fluctuations AroundChernobyl" Phys. Rev. E 62: 4389-4392 (2000). PDF


  10. G. M. Viswanathan, S. V. Buldyrev, S. Havlin, M. G. da Luz, E. Raposo, and H. E. Stanley, "Optimizing the Success of Random Searches" Nature 401: 911-914 (1999). PDF


  11. G. M. Viswanathan, V. Afanasyev, S. V. Buldyrev, E. J. Murphy, P. A. Prince, and H. E. Stanley, "Levy Flight Search Patterns of Wandering Albatrosses" Nature 381: 413-415 (1996). PDF


  12. S. Rabinovich, G. Berkolaiko, S. V. Buldyrev, and A. Shekhter, "Logistic Map — An Analytical Solution," Physica A 218, 457-460 (1995). PDF


  13. B. Jovanovic, S. V. Buldyrev, S. Havlin, H. E. Stanley, "Punctuated Equilibrium and `History Dependent' Percolation," Phys. Rev. E 50: R2403-R2406 (1994). PDF


Reviews and Conference Proceedings
  1. T. H. Keitt, L. A. N. Amaral, S. V. Buldyrev, and H. E. Stanley, "Scaling in the Growth of Geogrpahically Subdivided Populations: Scale-Invariant Patterns from a Continent-Wide Biological Survey" Phil. Trans. Royal Soc. B Biological Sciences 357: 627-633 (2002).


  2. H. E. Stanley, V. Afanasyev, L. A. N. Amaral, S. V. Buldyrev, A. L. Goldberger, S. Havlin, H. Leschhorn, P. Maass, R. N. Mantegna, C.-K. Peng, P. A. Prince, M. A. Salinger, M. H. R. Stanley, and G. M. Viswanathan, "Anomalous Fluctuations in the Dynamics of Complex Systems: From DNA and Physiology to Econophysics" Physica A 224: 302-321 (1996). PDF