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
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
J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley,
and E. I. Shakhnovich, "Thermodynamics and folding kinetics analysis
of the SH3 domain from Discrete Molecular Dynamics."
J. Mol. Biol. 318: 863-876 (2002)
PDF
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
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
F. Ding, J. M. Borreguero, S. V. Buldyrev, { H. E. Stanley}, and
N. V. Dokholyan, "Mechanism for the alpha-helix to beta-hairpin
Transition," Proteins: Structure, Function, and Genetics 53:
220-228 (2003).PDF
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).
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
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. National Acad. Sci. 94: 7612-7616 (1997).
PDF
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
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. National Acad. Sci. 96: 5274-5279 (1999).
PDF
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
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. National Academy of Sciences 97:
5039-5043 (2000).
PDF
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 beta Dimer Formation,"
Biophys. J.87: 2310-2321 (2004).
S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. C. Cruz, H. E. Stanley,
and N. V. Dokholyan, "Discrete Molecular Dynamics Simulations of
Peptide Aggregation" Phys. Rev. E69: 041908 (2004).
B. Urbanc, L. C. Cruz, Yun S. S. V. Buldyrev, G. Bitan, D. B. Teplow,
and H. E. Stanley, "In silico study of amyloid beta-protein folding and
oligomerization" Proc. Nat. Acad. Sci.101:
17345-17350 (2004).
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. Methods141:
321-332 (2005).
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 (A beta) studied in silico"
Proc. Nat. Acad. Sci.102: 6015-6020 (2005).
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
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
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
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
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
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
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
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
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 Letters3, R1-R25 (2003).
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).
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
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
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
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).
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
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
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).
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
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
N. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Model
of unequal chromosomal crossing over" Physica A 249: 594-599 (1998).
PDF
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
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
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
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
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).
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
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
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 Around
Chernobyl" Phys. Rev. E 62: 4389-4392 (2000).
PDF
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
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
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).
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).
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