Papers by Sergey Buldyrev
PloS one, 2015
A fully automated weighbridge using a new algorithm and mechanics integrated with a Radio Frequen... more A fully automated weighbridge using a new algorithm and mechanics integrated with a Radio Frequency Identification System is described. It is currently in use collecting data on Macaroni penguins (Eudyptes chrysolophus) at Bird Island, South Georgia. The technology allows researchers to collect very large, highly accurate datasets of both penguin weight and direction of their travel into or out of a breeding colony, providing important contributory information to help understand penguin breeding success, reproductive output and availability of prey. Reliable discrimination between single and multiple penguin crossings is demonstrated. Passive radio frequency tags implanted into penguins allow researchers to match weight and trip direction to individual birds. Low unit and operation costs, low maintenance needs, simple operator requirements and accurate time stamping of every record are all important features of this type of weighbridge, as is its proven ability to operate 24 hours a...
The slope of the coexistence line of the liquid-liquid phase transition (LLPT) can be positive, n... more The slope of the coexistence line of the liquid-liquid phase transition (LLPT) can be positive, negative, or zero. All three possibilities have been found in Monte-Carlo simulations of a modified spherically symmetric two-scale Jagla model. Since the liquid-liquid critical point (LLCP) frequently lies in a region of the phase diagram that is difficult to access experimentally, it is of great interest to study critical phenomena in the supercritical region. We therefore study the properties of the Widom line, which is defined in the one-phase region above the critical point as the locus of maximum correlation length as function of the ordering field at constant thermal field. Asymptotically close to the critical point, the Widom line coincides with the loci of the response function extrema, because all response functions can be asymptotically expressed as functions of the diverging correlation length. We find that the method of identifying the Widom line as the loci of heat capacity ...
Financial networks are dynamic and to assess systemic importance and avert losses we needs models... more Financial networks are dynamic and to assess systemic importance and avert losses we needs models which take the time variations of the links and nodes into account. We develop a model that can predict the response of the financial network to a shock and propose a measure for the systemic importance of the banks, which we call BankRank. Using the European Bank Authority 2011 stress test exposure data, we apply our model to the bipartite network of the largest institutional holders of troubled European countries (Greece, Italy, Portugal, Spain, and Ireland). Simulation of the states in our model reveal that it has "calm" state, where shocks do not cause very major losses, and "panicked" states, in which devastating damages occur. Fitting the parameters to Eurocrisis data shows that, before the crisis, the system was mostly in the "calm" regime while during the Eurocrisis it went into the "panicked" regime. The numerical solutions of the our mod...
We study by discrete molecular dynamics simulations the relation between the thermodynamics and t... more We study by discrete molecular dynamics simulations the relation between the thermodynamics and the diffusive behavior in solutions of hard spheres in Jagla particles, close to their liquid-liquid critical point. For comparison, we also show the same properties in the bulk Jagla particles system. The hard spheres and the Jagla model are used as spherically symmetric potentials for small hydrophobic solutes in water. We find that the fragile to strong dynamic transition observed when studying the diffusive behavior is always coupled to the low density to high density liquid transition. Above the liquid-liquid critical pressure the diffusivity crossover happens exactly at the Widom line of the systems, where the thermodynamic response functions show maxima. Below the liquid-liquid critical pressure, the diffusivity crossover corresponds to the crossing of the limit of mechanical stability lines and it shows hysteresis when going from high to low temperatures or vice versa. These findi...
We study a system composed of two interdependent lattice networks A and B, where nodes in network... more We study a system composed of two interdependent lattice networks A and B, where nodes in network A depend on a node within a certain shuffling distance r of its corresponding counterpart in network B and vice versa. We find, using numerical simulation that percolation in the two interdependent lattice networks system shows that for small r the phase transition is second order while for larger r it is a first order.
The Journal of chemical physics, Jan 14, 2015
We discuss the dynamic behavior of two silica models, the BKS model (by van Beest, Kramer, and va... more We discuss the dynamic behavior of two silica models, the BKS model (by van Beest, Kramer, and van Santen) and the WAC model (by Woodcock, Angell, and Cheeseman). Although BKS is considered the more realistic model for liquid silica, the WAC model has the unique property that it is very close to having a liquid-liquid critical point (LLCP), and this makes it particularly useful in studying the dynamics of models that do have a LLCP. We find that the diffusivity is a good indicator of how close a liquid is to criticality-the Si diffusivity shows a jump of 3-4 orders of magnitude when the pressure is reduced, which may be interpreted as an abrupt (though not first-order) transition from a high-density liquid state to a low-density liquid state. We show that this transition is captured by the Adam-Gibbs relation, which also allows us to estimate the configurational entropy of the system.
The Journal of chemical physics, Jan 14, 2014
Previous research has indicated the possible existence of a liquid-liquid critical point (LLCP) i... more Previous research has indicated the possible existence of a liquid-liquid critical point (LLCP) in models of silica at high pressure. To clarify this interesting question we run extended molecular dynamics simulations of two different silica models (WAC and BKS) and perform a detailed analysis of the liquid at temperatures much lower than those previously simulated. We find no LLCP in either model within the accessible temperature range, although it is closely approached in the case of the WAC potential near 4000 K and 5 GPa. Comparing our results with those obtained for other tetrahedral liquids, and relating the average Si-O-Si bond angle and liquid density at the model glass temperature to those of the ice-like β-cristobalite structure, we conclude that the absence of a critical point can be attributed to insufficient "stiffness" in the bond angle. We hypothesize that a modification of the potential to mildly favor larger average bond angles will generate a LLCP in a te...
Physical review letters, Jan 4, 2014
Using linear scaling theory, we study the behavior of response functions extrema in the vicinity ... more Using linear scaling theory, we study the behavior of response functions extrema in the vicinity of the critical point. We investigate how the speed of convergence of the loci of response function extrema to the Widom line depends on the parameters of the linear scaling theory. We find that when the slope of the coexistence line is near zero, the line of specific heat maxima does not follow the Widom line but instead follows the coexistence line. This has relevance for the detection of liquid-liquid critical points, which can exhibit a near-horizontal coexistence line. Our theoretical predictions are confirmed by computer simulations of a family of spherically symmetric potentials.
Physical review. E, Statistical, nonlinear, and soft matter physics, 2011
We study a problem of failure of two interdependent networks in the case of identical degrees of ... more We study a problem of failure of two interdependent networks in the case of identical degrees of mutually dependent nodes. We assume that both networks (A and B) have the same number of nodes N connected by the bidirectional dependency links establishing a one-to-one correspondence between the nodes of the two networks in a such a way that the mutually dependent nodes have the same number of connectivity links; i.e., their degrees coincide. This implies that both networks have the same degree distribution P(k). We call such networks correspondently coupled networks (CCNs). We assume that the nodes in each network are randomly connected. We define the mutually connected clusters and the mutual giant component as in earlier works on randomly coupled interdependent networks and assume that only the nodes that belong to the mutual giant component remain functional. We assume that initially a 1-p fraction of nodes are randomly removed because of an attack or failure and find analytically...
Physical review. E, Statistical, nonlinear, and soft matter physics, 2006
We present a unified scaling theory for the optimal path connecting opposite edges of a disordere... more We present a unified scaling theory for the optimal path connecting opposite edges of a disordered lattice of size L. Each bond of the lattice is assigned a cost exp(ar), where r is a uniformly distributed random variable and a is disorder strength. The optimal path minimizes the sum of the costs of the bonds along the path. We argue that for L>a(nu) , where nu is the correlation exponent of percolation, the path becomes equivalent to a directed polymer on an effective lattice consisting of blobs of size xi=a(nu). It is self-affined and characterized by the roughness exponent of directed polymers chi. For L<a(nu), or on the length scales below the blob size xi, the path behaves as an optimal path in the strong disorder limit. It has a self-similar fractal shape with fractal dimension d(opt). We derived the scaling relations for the length of the path, its transversal displacement, the average cost and its fluctuation. We test our scaling theoretical predictions by numerical si...
Physical Review Letters, 2003
We study the optimal distance in networks, lopt, defined as the length of the path minimizing the... more We study the optimal distance in networks, lopt, defined as the length of the path minimizing the total weight, in the presence of disorder. Disorder is introduced by assigning random weights to the links or nodes. For strong disorder, where the maximal weight along the path dominates the sum, we find that lopt˜N1/3 in both Erdos-Rényi (ER) and Watts-Strogatz (WS)
Physical Review E, 2000
We explore if there exist universal statistical patterns that are different in coding and noncodi... more We explore if there exist universal statistical patterns that are different in coding and noncoding DNA and can be found in all living organisms, regardless of their phylogenetic origin. We find that (i) the mutual information function I has a significantly different functional form in coding and noncoding DNA. We further find that (ii) the probability distributions of the average
Physical Review E, 2014
We study the mutual percolation of a system composed of two interdependent random regular network... more We study the mutual percolation of a system composed of two interdependent random regular networks. We introduce a notion of distance to explore the effects of the proximity of interdependent nodes on the cascade of failures after an initial attack. We find a non-trivial relation between the nature of the transition through which the networks disintegrate and the parameters of the system, which are the degree of the nodes and the maximum distance between interdependent nodes. We explain this relation by solving the problem analytically for the relevant set of cases.
Physical Review E, 1999
During slow inflation of lung lobes, we measure a sequence of short explosive transient sound wav... more During slow inflation of lung lobes, we measure a sequence of short explosive transient sound waves called ``crackles,'' each consisting of an initial spike followed by ringing. The crackle time series is irregular and intermittent, with the number of spikes of size s following a power law, n(s)~s-alpha, with alpha=2.77+/-0.05. We develop a model of crackle wave generation and propagation
Physical review. E, Statistical, nonlinear, and soft matter physics, 2004
We study numerically the optimal paths in two and three dimensions on various disordered lattices... more We study numerically the optimal paths in two and three dimensions on various disordered lattices in the limit of strong disorder. We find that the length l of the optimal path scales with geometric distance r , as l approximately r (d(opt) ) with d(opt) =1.22+/-0.01 for d=2 and 1.44+/-0.02 for d=3 , independent of whether the optimization is on a path of weighted bonds or sites, and independent of the lattice or its coordination number. Our finding suggests that the exponent d(opt) is universal, depending only on the dimension of the system.
Physical Review E, 2000
On two-dimensional percolation clusters at the percolation threshold, we study σ(MB, r) , the ave... more On two-dimensional percolation clusters at the percolation threshold, we study σ(MB, r) , the average conductance of the backbone, defined by two points separated by Euclidean distance r, of mass MB. We find that with increasing MB and for fixed r, σ(MB, r) asymptotically decreases to a constant, in contrast with the behavior of homogeneous sytems and non-random fractals (such as the Sierpinski gasket) in which conductance increases with increasing MB. We explain this behavior by studying the distribution of shortest paths between the two points on clusters with a given MB. We also study the dependence of conductance on MB slightly above the percolation threshold.
Physical Review E, 2006
Using collision driven discrete molecular dynamics (DMD), we investigate the thermodynamics and d... more Using collision driven discrete molecular dynamics (DMD), we investigate the thermodynamics and dynamics of systems of 500 dumbbell molecules interacting by a purely repulsive ramp-like discretized potential, consisting of $n$ steps of equal size. We compare the behavior of the two systems, with $n = 18$ and $n = 144$ steps. Each system exhibits both thermodynamic and dynamic anomalies, a
Biophysical Journal, 2002
The concept of the protein transition state ensemble (TSE), a collection of the conformations tha... more The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50% probability to convert rapidly to the folded state and 50% chance to rapidly unfold, constitutes the basis of the modern interpretation of protein engineering experiments. It has been conjectured that conformations constituting the TSE in many proteins are the expanded and distorted forms
Folding and Design, 1998
Background: Many attempts have been made to resolve in time the folding of model proteins in comp... more Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are computationally heavy (traditional MD). Results: We use a recently-proposed approach of Zhou and Karplus to study the
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Papers by Sergey Buldyrev