S V Buldyrev

Publications (126)343.61 Total impact

• Source

  Available from: Giancarlo Franzese

  Article: Nanoscale dynamics of phase flipping in water near its hypothesized liquid-liquid critical point.

  T A Kesselring, G Franzese, S V Buldyrev, H J Herrmann, H E Stanley
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  ABSTRACT: One hypothesized explanation for water's anomalies imagines the existence of a liquid-liquid (LL) phase transition line separating two liquid phases and terminating at a LL critical point. We simulate the classic ST2 model of water for times up to 1000 ns and system size up to N = 729. We find that for state points near the LL transition line, the entire system flips rapidly between liquid states of high and low density. Our finite-size scaling analysis accurately locates both the LL transition line and its associated LL critical point. We test the stability of the two liquids with respect to the crystal and find that of the 350 systems simulated, only 3 of them crystallize and these 3 for the relatively small system size N = 343 while for all other simulations the incipient crystallites vanish on a time scales smaller than ≈ 100 ns.
  Scientific Reports 01/2012; 2:474.
• Source

  Available from: Kevin Stokely

  Article: Liquid polymorphism: water in nanoconfined and biological environments.

  H E Stanley, S V Buldyrev, G Franzese, P Kumar, F Mallamace, M G Mazza, K Stokely, L Xu
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  ABSTRACT: We demonstrate some recent progress in understanding the anomalous behavior of liquid water, by combining information provided by recent experiments and simulations on water in bulk, nanoconfined, and biological environments. We interpret evidence from recent experiments designed to test the hypothesis that liquid water may display 'polymorphism' in that it can exist in two different phases--and discuss recent work on water's transport anomalies as well as the unusual behavior of water in biological environments. Finally, we will discuss how the general concept of liquid polymorphism may prove useful in understanding anomalies in other liquids, such as silicon, silica, and carbon, as well as metallic glasses which have in common that they are characterized by two characteristic length scales in their interactions.
  Journal of Physics Condensed Matter 07/2010; 22(28):284101. · 2.55 Impact Factor
• Source

  Available from: Gianpietro Malescio

  Article: Unusual phase behavior of one-component systems with two-scale isotropic interactions.

  S V Buldyrev, G Malescio, C A Angell, N Giovambattista, S Prestipino, F Saija, H E Stanley, L Xu
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  ABSTRACT: We study the phase behavior of systems of particles interacting through pair potentials with a hard core plus a soft repulsive component. We consider several different forms of soft repulsion, including a square shoulder, a linear ramp and a quasi-exponential tail. The common feature of these potentials is the presence of two repulsive length scales, which may be the origin of unusual phase behaviors such as polyamorphism both in the equilibrium liquid phase and in the glassy state, water-like anomalies in the liquid state and anomalous melting at very high pressures.
  Journal of Physics Condensed Matter 12/2009; 21(50):504106. · 2.55 Impact Factor
• Source

  Available from: Kevin Stokely

  Article: Heterogeneities in confined water and protein hydration water.

  H E Stanley, P Kumar, S Han, M G Mazza, K Stokely, S V Buldyrev, G Franzese, F Mallamace, L Xu
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  ABSTRACT: We report recent efforts to understand a broad range of experiments on confined water and protein hydration water, many initiated by a collaboration between workers at the University of Messina and MIT-the editors of this special issue. Preliminary calculations are not inconsistent with one tentative interpretation of these experiments as resulting from the system passing from the high-temperature high-pressure 'HDL' side of the Widom line (where the liquid might display non-Arrhenius behavior) to the low-temperature low-pressure 'LDL' side of the Widom line (where the liquid might display Arrhenius behavior). The Widom line-defined to be the line in the pressure-temperature plane where the correlation length has its maximum-arises if there is a critical point. Hence, interpreting the Messina-MIT experiments in terms of a Widom line is of potential relevance to testing, experimentally, the hypothesis that water displays a liquid-liquid critical point.
  Journal of Physics Condensed Matter 12/2009; 21(50):504105. · 2.55 Impact Factor
• Article: Lévy flights and random searches

  E P Raposo, S V Buldyrev, M G E da Luz, G M Viswanathan, H E Stanley
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  ABSTRACT: In this work we discuss some recent contributions to the random search problem. Our analysis includes superdiffusive Lévy processes and correlated random walks in several regimes of target site density, mobility and revisitability. We present results in the context of mean-field-like and closed-form average calculations, as well as numerical simulations. We then consider random searches performed in regular lattices and lattices with defects, and we discuss a necessary criterion for distinguishing true superdiffusion from correlated random walk processes. We invoke energy considerations in relation to critical survival states on the edge of extinction, and we analyze the emergence of Lévy behavior in deterministic search walks. Finally, we comment on the random search problem in the context of biological foraging.
  Journal of Physics A Mathematical and Theoretical 10/2009; 42(43):434003. · 1.56 Impact Factor
• Source

  Available from: Giancarlo Franzese

  Chapter: Dynamics of Water at Low Temperatures and Implications for Biomolecules

  P. Kumar, G. Franzese, S.V. Buldyrev, H.E. Stanley
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  ABSTRACT: The biological relevance of water is a puzzle that has attracted much scientific attention. Here we recall what is unusual about water and discuss the possible implications of the unusual properties of water also known as water anomalies in biological processes. We find the surprising results that some anomalous properties of water, including results of a recent experiments on hydrated biomolecules, are all consistent with the working hypothesis of the presence of a first-order phase transition between two liquids with different densities at low temperatures and high pressures, which ends in a critical point. To elucidate the relation between dynamic and thermodynamic anomalies, we investigate the presence of this liquid–liquid critical point in several models. Using molecular dynamics simulations, we find a correlation between the dynamic transition and the locus of specific heat maxima CP max (also known as Widom line) emanating from the critical point. We investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called “protein glass transition” in case of proteins, occurs at the same temperature where the dynamics of hydration water has a crossover and also coincides with the temperature of maximum of specific heat and the maximum of the temperature derivative of the orientational order parameter. Since our simulations are consistent with the possibility that the protein glass transition results from a change in the behavior of hydration water, specifically from crossing the Widom line, we explore in more details the relation between the dynamic crossover and the Widom line in a tractable model for water. We find that the dynamic crossover can be fully explained as a consequence of the thermodynamic and structural changes occurring at the Widom line of water. We, therefore, argue that the so-called “glass transition” of hydrated proteins is just a consequence of the thermodynamic and structural changes of the surrounding water.
  12/2008: pages 3-22;
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  Available from: Giancarlo Franzese

  Chapter: Liquid Polyamorphism and the Anomalous Behavior of Water

  H. E. Stanley, S. V. Buldyrev, S.-H. Chen, G. Franzese, S. Han, P. Kumar, F. Mallamace, M. G. Mazza, L. Xu, Z. Yan
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  ABSTRACT: We present evidence from experiments and computer simulations supporting the hypothesis that ∈dex{polyamorphism}water displays polyamorphism, i.e., water separates into two distinct liquid phases. This concept of a new ∈dex{liquid-liquid phase transition}liquid–liquid phase transition is finding potential application to other liquids as well as water, such as silicon and silica. Here we review the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid–liquid critical point in (i) Two models of water, TIP5P and ST2, which display a first order liquid–liquid phase transition at low temperatures; (ii) Two spherically symmetric two-scale potentials known to possess a liquid–liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions; and (iii) A Hamiltonian model of water where the idea of two length/energy scales is built in. This model also displays a first order liquid–liquid phase transition at low temperatures besides the first order liquid-gas phase transition at high temperatures. We find a correlation between the dynamic fragility crossover and the locus of specific heat maxima CP max (“Widom line”) emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesized liquid-liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between C P max and the dynamic crossover is not limited to the case of water, a hydrogen bonded network liquid, but is a more general feature of crossing the Widom line, an extension of the first-order coexistence line in the supercritical region.
  11/2008: pages 249-266;
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  Available from: Giancarlo Franzese

  Article: Liquid polyamorphism: Possible relation to the anomalous behaviour of water

  H. E. Stanley, P. Kumar, G. Franzese, L. Xu, Z. Yan, M. G. Mazza, S. V. Buldyrev, S.-H. Chen, F. Mallamace
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  ABSTRACT: We present evidence from experiments and computer simulations supporting the hypothesis that water displays polyamorphism, i.e., water separates into two distinct liquid phases. This concept of a new liquid-liquid phase transition is finding application to other liquids as well as water, such as silicon and silica. Specifically, we investigate, the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid-liquid critical point in(i)Two models of water, TIP5P and ST2, which display a first order liquid-liquid phase transition at low temperatures;(ii)the Jagla model, a spherically symmetric two-scale potential known to possess a liquid-liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions; and(iii)A Hamiltonian model of water where the idea of two length/energy scales is built in. This model also displays a first order liquid-liquid phase transition at low temperatures besides the first order liquid-gas phase transition at high temperatures. We find a correlation between the dynamic fragility crossover and the locus of specific heat maxima CPmax (“Widom line”) emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesised liquid-liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between CPmax and the dynamic crossover is not limited to the case of water, a hydrogen bonded network liquid, but is a more general feature of crossing the Widom line, an extension of the first-order coexistence line in the supercritical region. Dedicated to Armin Bunde on the occasion of his 60th birthday.
  The European Physical Journal Special Topics 01/2008; 161(1):1-17. · 1.56 Impact Factor
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  Available from: Feng Ding

  Article: Parallel folding pathways in the SH3 domain protein.

  A R Lam, J M Borreguero, F Ding, N V Dokholyan, S V Buldyrev, H E Stanley, E Shakhnovich
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  ABSTRACT: The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive molecular dynamics simulations of the Go model and computing the folding probability of a generated set of TSE candidate conformations. We found that the TSE possesses a well-defined hydrophobic core with variable enveloping structures resulting from the superposition of three parallel folding pathways. The most preferred pathway agrees with the experimentally determined TSE, while the two least preferred pathways differ significantly. The knowledge of the different pathways allows us to design the interactions between amino acids that guide the protein to fold through the least preferred pathway. This particular design is akin to a circular permutation of the protein. The finding motivates the hypothesis that the different experimentally observed TSEs in homologous proteins and circular permutants may represent potentially available pathways to the wild-type protein.
  Journal of Molecular Biology 12/2007; 373(5):1348-60. · 4.00 Impact Factor
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  Available from: arxiv.org

  Article: A generalized preferential attachment model for business firms growth rates

  Massimo Riccaboni, S. V. Buldyrev, F. Pammolli, K. Yamasaki, D.-F. Fu, K. Matia, H. E. Stanley
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  ABSTRACT: We present a preferential attachment growth model to obtain the distribution P(K) of number of units K in the classes which may represent business firms or other socio-economic entities. We found that P(K) is described in its central part by a power law with an exponent ϕ=2+b/(1-b) which depends on the probability of entry of new classes, b. In a particular problem of city population this distribution is equivalent to the well known Zipf law. In the absence of the new classes entry, the distribution P(K) is exponential. Using analytical form of P(K) and assuming proportional growth for units, we derive P(g), the distribution of business firm growth rates. The model predicts that P(g) has a Laplacian cusp in the central part and asymptotic power-law tails with an exponent ζ=3. We test the analytical expressions derived using heuristic arguments by simulations. The model might also explain the size-variance relationship of the firm growth rates. Copyright EDP Sciences/Società Italiana di Fisica/Springer-Verlag 2007
  Physics of Condensed Matter 04/2007; 57(2):131-138. · 1.53 Impact Factor
• Article: Parallel foldng pathways in the SH3 domain protein

  A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, E. Shakhnovich
  [show abstract] [hide abstract]
  ABSTRACT: The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive molecular dynamics simulations of the G (o) over bar model and computing the folding probability of a generated set of TSE candidate conformations. We found that the TSE possesses a well-defined hydrophobic core with variable enveloping structures resulting from the superposition of three parallel folding pathways. The most preferred pathway agrees with the experimentally determined TSE, while the two least preferred pathways differ significantly. The knowledge of the different pathways allows us to design the interactions between amino acids that guide the protein to fold through the least preferred pathway. This particular design is akin to a circular permutation of the protein. The finding motivates the hypothesis that the different experimentally observed TSEs in homologous proteins and circular permutants may represent potentially available pathways to the wild-type protein. (C) 2007 Elsevier Ltd. All rights reserved.
  Journal of Molecular Biology. 01/2007; 373(5):1348-1360.
• Source

  Available from: buphy.bu.edu

  Chapter: Dynamic crossover and liquid-liquid critical point in the TIP5P model of water

  Pradeep Kumar, S. V. Buldyrev, H. Eugene Stanley
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  ABSTRACT: Water is hypothesized to have a low temperature phase transition line which separates a high density water at high temperatures from a low density water at low temperatures. This negatively sloped first order liquid-liquid phase coexistence line terminates at a critical point known as the liquid-liquid critical point. This critical point is hypothesized to exist in a deeply supercooled region of the phase diagram of water. Recent experiments have given an indirect indication of this phase transition. Neutron scattering and NMR experiments on water confined in hydrophilic nanopores revealed that the dynamics of water changes from the dynamics of a high density liquid (non-Arrhenius) at high temperatures to that of a low density liquid (Arrhenius) at low temperatures. Motivated Motivated by these experiments we investigated the TIP5P model of w ater. We find that the dynamic transition appears to be related to crossing the specific heat maxima line (Widom line) which emanates from the liquidliquid critical point. Moreover, we find that water not only undergoes dynamical change but also structural changes on crossing the Widom line. The structure of the liquid changes from a high density liquid to a low density liquid. Keywordsliquid-liquid critical point-fragile-to-strong transition-supercooled water-TIP5P-Widom line
  12/2006: pages 23-33;
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  Available from: Marco G. Mazza

  Article: Glass transition in biomolecules and the liquid-liquid critical point of water.

  Pradeep Kumar, Z Yan, L Xu, M G Mazza, S V Buldyrev, S-H Chen, S Sastry, H E Stanley
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  ABSTRACT: Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.
  Physical Review Letters 11/2006; 97(17):177802. · 7.37 Impact Factor
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  Available from: ArXiv

  Article: A Generalized Preferential Attachment Model for Business Firms Growth Rates: II. Mathematical Treatment

  S V Buldyrev, F. Pammolli, M. Riccaboni, K. Yamasaki, D. Fu, K. Matia, H E Stanley
  [show abstract] [hide abstract]
  ABSTRACT: We present a preferential attachment growth model to obtain the distribution $P(K)$ of number of units $K$ in the classes which may represent business firms or other socio-economic entities. We found that $P(K)$ is described in its central part by a power law with an exponent $\phi=2+b/(1-b)$ which depends on the probability of entry of new classes, $b$. In a particular problem of city population this distribution is equivalent to the well known Zipf law. In the absence of the new classes entry, the distribution $P(K)$ is exponential. Using analytical form of $P(K)$ and assuming proportional growth for units, we derive $P(g)$, the distribution of business firm growth rates. The model predicts that $P(g)$ has a Laplacian cusp in the central part and asymptotic power-law tails with an exponent $\zeta=3$. We test the analytical expressions derived using heuristic arguments by simulations. The model might also explain the size-variance relationship of the firm growth rates. Comment: 19 pages 6 figures Applications of Physics in Financial Analysis, APFA5
  09/2006;
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  Available from: ArXiv

  Article: A Generalized Preferential Attachment Model for Business Firms Growth Rates: I. Empirical Evidence

  Fabio Pammolli, Dongfeng Fu, S V Buldyrev, Massimo Riccaboni, Kaushik Matia, Kazuko Yamasaki, H E Stanley
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  ABSTRACT: We introduce a model of proportional growth to explain the distribution $P(g)$ of business firm growth rates. The model predicts that $P(g)$ is Laplace in the central part and depicts an asymptotic power-law behavior in the tails with an exponent $\zeta=3$. Because of data limitations, previous studies in this field have been focusing exclusively on the Laplace shape of the body of the distribution. We test the model at different levels of aggregation in the economy, from products, to firms, to countries, and we find that the its predictions are in good agreement with empirical evidence on both growth distributions and size-variance relationships. Comment: 8 pages, 4 figures
  09/2006;
• Chapter: Fractals in biology and medicine

  H. E. Stanley, S. V. Buldyrev, A. L. Goldberger, S. Havlin, R. N. Mantegna, S. M. Ossadnik, C. -K. Peng, F. Sciortino, M. Simons
  04/2006: pages 147-178;
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  Available from: ArXiv

  Article: The growth of business firms: theoretical framework and empirical evidence.

  Dongfeng Fu, Fabio Pammolli, S V Buldyrev, Massimo Riccaboni, Kaushik Matia, Kazuko Yamasaki, H Eugene Stanley
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  ABSTRACT: We introduce a model of proportional growth to explain the distribution P(g)(g) of business-firm growth rates. The model predicts that P(g)(g) is exponential in the central part and depicts an asymptotic power-law behavior in the tails with an exponent zeta = 3. Because of data limitations, previous studies in this field have been focusing exclusively on the Laplace shape of the body of the distribution. In this article, we test the model at different levels of aggregation in the economy, from products to firms to countries, and we find that the predictions of the model agree with empirical growth distributions and size-variance relationships.
  Proceedings of the National Academy of Sciences 01/2006; 102(52):18801-6. · 9.68 Impact Factor
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  Available from: ArXiv

  Article: Relation between the Widom line and the dynamic crossover in systems with a liquid-liquid phase transition.

  Limei Xu, Pradeep Kumar, S V Buldyrev, S-H Chen, P H Poole, F Sciortino, H E Stanley
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  ABSTRACT: We investigate, for two water models displaying a liquid-liquid critical point, the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid-liquid critical point. We find a correlation between the dynamic crossover and the locus of specific heat maxima C(P)(max) ("Widom line") emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesized liquid-liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between C(P)(max) and dynamic crossover is not limited to the case of water, a hydrogen bond network-forming liquid, but is a more general feature of crossing the Widom line. Specifically, we also study the Jagla potential, a spherically symmetric two-scale potential known to possess a liquid-liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions.
  Proceedings of the National Academy of Sciences 12/2005; 102(46):16558-62. · 9.68 Impact Factor
• Source

  Available from: Brigita Urbanc

  Article: Discrete Molecular Dynamics Study of Aβ16-22 Folding and Aggregation

  S Peng, B Urbanc, S V Buldyrev, L Cruz, S Yun, D B Teplow, H E Stanley
  10/2005;
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  Available from: David Teplow

  Article: In silico study of amyloid beta-protein folding and oligomerization.

  B Urbanc, L Cruz, S Yun, S V Buldyrev, G Bitan, D B Teplow, H E Stanley
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  ABSTRACT: Experimental findings suggest that oligomeric forms of the amyloid beta protein (Abeta) play a critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of their formation is critical for developing therapeutic agents. We use discrete molecular dynamics simulations and a four-bead protein model to study oligomerization of two predominant alloforms, Abeta40 and Abeta42, at the atomic level. The four-bead model incorporates backbone hydrogen-bond interactions and amino acid-specific interactions mediated through hydrophobic and hydrophilic elements of the side chains. During the simulations we observe monomer folding and aggregation of monomers into oligomers of variable sizes. Abeta40 forms significantly more dimers than Abeta42, whereas pentamers are significantly more abundant in Abeta42 relative to Abeta40. Structure analysis reveals a turn centered at Gly-37-Gly-38 that is present in a folded Abeta42 monomer but not in a folded Abeta40 monomer and is associated with the first contacts that form during monomer folding. Our results suggest that this turn plays an important role in Abeta42 pentamer formation. Abeta pentamers have a globular structure comprising hydrophobic residues within the pentamer's core and hydrophilic N-terminal residues at the surface of the pentamer. The N termini of Abeta40 pentamers are more spatially restricted than Abeta42 pentamers. Abeta40 pentamers form a beta-strand structure involving Ala-2-Phe-4, which is absent in Abeta42 pentamers. These structural differences imply a different degree of hydrophobic core exposure between pentamers of the two alloforms, with the hydrophobic core of the Abeta42 pentamer being more exposed and thus more prone to form larger oligomers.
  Proceedings of the National Academy of Sciences 01/2005; 101(50):17345-50. · 9.68 Impact Factor