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S V Buldyrev

Publications and source records attributed to S V Buldyrev.

At least 19 recordsLinked to original sources
PubMed2002

Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly.

We investigate the phase behavior of a single-component system in three dimensions with spherically-symmetric, pairwise-additive, soft-core interactions with an attractive well at a long distance, a repulsive soft-core shoulder at an intermediate distance, and a hard-core repulsion at a short distance, similar to potentials used to describe liquid systems such as colloids, protein solutions, or liquid metals. We showed [Nature (London) 409, 692 (2001)] that, even with no evidence of the density anomaly, the phase diagram has two first-order fluid-fluid phase transitions, one ending in a gas-low-density-liquid (LDL) critical point, and the other in a gas-high-density-liquid (HDL) critical point, with a LDL-HDL phase transition at low temperatures. Here we use integral equation calculations to explore the three-parameter space of the soft-core potential and perform molecular dynamics simulations in the interesting region of parameters. For the equilibrium phase diagram, we analyze the structure of the crystal phase and find that, within the considered range of densities, the structure is independent of the density. Then, we analyze in detail the fluid metastable phases and, by explicit thermodynamic calculation in the supercooled phase, we show the absence of the density anomaly. We suggest that this absence is related to the presence of only one stable crystal structure.

Journal Article↗
PubMed2002

Confirmation of anomalous dynamical arrest in attractive colloids: a molecular dynamics study.

Previous theoretical simulation and experimental studies have indicated that particles with a short-ranged attraction exhibit a range of dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singularity in the density correlation functions, and the existence of "attractive" and "repulsive" glasses. Here we carry out extensive molecular dynamics calculations on dense systems interacting via a square-well potential. This is one of the simplest systems with the required properties, and may be regarded as canonical for interpreting the phase diagram, and now also the dynamical arrest. We confirm the theoretical predictions for reentrance, logarithmic singularity, and give a direct evidence of the existence, independent of theory, of two distinct glasses. We now regard the previous predictions of these phenomena as having been established.

Journal Article↗
PubMed2002

Evidence for an unusual dynamical-arrest scenario in short-ranged colloidal systems.

Extensive molecular dynamics simulation studies of particles interacting via a short-ranged attractive square-well potential are reported. The calculated loci of constant diffusion coefficient D in the temperature-packing fraction plane show a reentrant behavior, i.e., an increase of diffusivity on cooling, confirming an important part of the high volume-fraction dynamical-arrest scenario earlier predicted by theory for particles with short-ranged potentials. The more efficient localization mechanism induced by the short-range bonding provides, on average, additional free volume as compared to the hard-sphere case and results in faster dynamics.

Journal Article↗
PubMed2002

Self-organized complexity in economics and finance.

This article discusses some of the similarities between work being done by economists and by physicists seeking to contribute to economics. We also mention some of the differences in the approaches taken and seek to justify these different approaches by developing the argument that by approaching the same problem from different points of view, new results might emerge. In particular, we review two newly discovered scaling results that appear to be universal, in the sense that they hold for widely different economies as well as for different time periods: (i) the fluctuation of price changes of any stock market is characterized by a probability density function, which is a simple power law with exponent -4 extending over 10(2) SDs (a factor of 10(8) on the y axis); this result is analogous to the Gutenberg--Richter power law describing the histogram of earthquakes of a given strength; and (ii) for a wide range of economic organizations, the histogram shows how size of organization is inversely correlated to fluctuations in size with an exponent approximately 0.2. Neither of these two new empirical laws has a firm theoretical foundation. We also discuss results that are reminiscent of phase transitions in spin systems, where the divergent behavior of the response function at the critical point (zero magnetic field) leads to large fluctuations.

Journal Article↗
PubMed2001

Average time spent by Lévy flights and walks on an interval with absorbing boundaries.

We consider a Lévy flyer of order alpha that starts from a point x(0) on an interval [O,L] with absorbing boundaries. We find a closed-form expression for the average number of flights the flyer takes and the total length of the flights it travels before it is absorbed. These two quantities are equivalent to the mean first passage times for Lévy flights and Lévy walks, respectively. Using fractional differential equations with a Riesz kernel, we find exact analytical expressions for both quantities in the continuous limit. We show that numerical solutions for the discrete Lévy processes converge to the continuous approximations in all cases except the case of alpha-->2, and the cases of x(0)-->0 and x(0)-->L. For alpha>2, when the second moment of the flight length distribution exists, our result is replaced by known results of classical diffusion. We show that if x(0) is placed in the vicinity of absorbing boundaries, the average total length has a minimum at alpha=1, corresponding to the Cauchy distribution. We discuss the relevance of this result to the problem of foraging, which has received recent attention in the statistical physics literature.

Journal Article↗
PubMed2001

Avalanche dynamics of crackle sound in the lung.

We analyze a sequence of short transient sound waves, called "crackles," which are associated with explosive openings of airways during lung inflation. The distribution of time intervals between consecutive crackles Delta(t) shows two regimes of power law behavior. We develop an avalanche model which fits the data over five decades of Delta(t). We find that the regime for large Delta(t) is related to the dynamics of distinct avalanches in a Cayley tree, and the regime for small Delta(t) is determined by the dynamics of crackle propagation within a single avalanche. We also obtain a mean-field solution of the model which provides information about lung inflation.

Acoustics↗
PubMed2001

Characterization of the branching structure of the lung from "macroscopic" pressure-volume measurements.

We analyze the problem of fluid flow in a bifurcating structure containing random blockages that can be removed by fluid pressure. We introduce an asymmetric tree model and find that the predicted pressure-volume relation is connected to the distribution Pi(n) of the generation number n of the tree's terminal segments. We use this relation to explore the branching structure of the lung by analyzing experimental pressure-volume data from dog lungs. The Pi(n) extracted from the data using the model agrees well with experimental data on the branching structure. We can thus obtain information about the asymmetric structure of the lung from macroscopic, noninvasive pressure-volume measurements.

Animals↗
PubMed2001

Dynamics of viscous penetration in percolation porous media.

We investigate the dynamics of viscous penetration in two-dimensional percolation networks at criticality for the case in which the ratio between the viscosities of displaced and injected fluids is very large. We report extensive numerical simulations that indicate that the scaling exponents for the breakthrough time distribution are the same as the previously reported values computed for the case of unit viscosity ratio. Our results are consistent with the possibility that viscous displacement through critical percolation networks constitutes a single universality class, independent of the viscosity ratio. We also find that the distributions of mass and breakthrough time of the invaded clusters have the same scaling form, but with different critical exponents.

Journal Article↗
PubMed2001

Waterlike anomalies for core-softened models of fluids: two-dimensional systems.

We use molecular-dynamics simulations in two dimensions to investigate the possibility that a core-softened potential can reproduce static and dynamic anomalies found experimentally in liquid water: (i) the increase in specific volume upon cooling, (ii) the increase in isothermal compressibility upon cooling, and (iii) the increase in the diffusion coefficient with pressure. We relate these anomalies to the shape of the potential. We obtain the phase diagram of the system and identify two solid phases: a square crystal (high-density phase) and a triangular crystal (low-density phase). We also discuss the relation between the anomalies observed and the polymorphism of the solid. Finally, we compare the phase diagram of our model system with experimental data, noting especially the line of temperatures of maximum density, the line of pressures of maximum diffusion constant, and the line of temperatures of minimum isothermal compressibility.

Journal Article↗
PubMed2001

Thermodynamically important contacts in folding of model proteins.

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.

Amino Acids↗
PubMed2001

Generic mechanism for generating a liquid-liquid phase transition.

Recent experimental results indicate that phosphorus--a single-component system--can have a high-density liquid (HDL) and a low-density liquid (LDL) phase. A first-order transition between two liquids of different densities is consistent with experimental data for a variety of materials, including single-component systems such as water, silica and carbon. Molecular dynamics simulations of very specific models for supercooled water, liquid carbon and supercooled silica predict a LDL-HDL critical point, but a coherent and general interpretation of the LDL-HDL transition is lacking. Here we show that the presence of a LDL and a HDL can be directly related to an interaction potential with an attractive part and two characteristic short-range repulsive distances. This kind of interaction is common to other single-component materials in the liquid state (in particular, liquid metals), and such potentials are often used to describe systems that exhibit a density anomaly. However, our results show that the LDL and HDL phases can occur in systems with no density anomaly. Our results therefore present an experimental challenge to uncover a liquid-liquid transition in systems like liquid metals, regardless of the presence of a density anomaly.

Journal Article↗
PubMed2000

Optimization of coding potentials using positional dependence of nucleotide frequencies.

We study the coding potential of human DNA sequences, using the positional asymmetry function (D(p)) and the positional information function (I(q)). Both D(p)and I(q)are based on the positional dependence of single nucleotide frequencies. We investigate the accuracy of D(p)and I(q)in distinguishing coding and non-coding DNA as a function of the parameters p and q, respectively, and explore at which parameters p(opt)and q(opt)both D(p)and I(q)distinguish coding and non-coding DNA most accurately. We compare our findings with classically used parameter values and find that optimized coding potentials yield comparable accuracies as classical frame-independent coding potentials trained on prior data. We find that p(opt)and q(opt)vary only slightly with the sequence length.

Codon↗
PubMed2000

Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias.

The cortex of the brain is organized into clear horizontal layers, laminae, which subserve much of the connectional anatomy of the brain. We hypothesize that there is also a vertical anatomical organization that might subserve local interactions of neuronal functional units, in accord with longstanding electrophysiological observations. We develop and apply a general quantitative method, inspired by analogous methods in condensed matter physics, to examine the anatomical organization of the cortex in human brain. We find, in addition to obvious laminae, anatomical evidence for tightly packed microcolumnar ensembles containing approximately 11 neurons, with a periodicity of about 80 microm. We examine the structural integrity of this new architectural feature in two common dementing illnesses, Alzheimer disease and dementia with Lewy bodies. In Alzheimer disease, there is a dramatic, nearly complete loss of microcolumnar ensemble organization. The relative degree of loss of microcolumnar ensembles is directly proportional to the number of neurofibrillary tangles, but not related to the amount of amyloid-beta deposition. In dementia with Lewy bodies, a similar disruption of microcolumnar ensemble architecture occurs despite minimal neuronal loss. These observations show that quantitative analysis of complex cortical architecture can be applied to analyze the anatomical basis of brain disorders.

Alzheimer Disease↗
PubMed2000

Identifying the protein folding nucleus using molecular dynamics.

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as "accelerator pedals" used by molecular evolution to control protein folding rate.

Binding Sites↗
PubMed2000

Distributions of dimeric tandem repeats in non-coding and coding DNA sequences.

We study the length distribution functions for the 16 possible distinct dimeric tandem repeats in DNA sequences of diverse taxonomic partitions of GenBank (known human and mouse genomes, and complete genomes of Caenorhabditis elegans and yeast). For coding DNA, we find that all 16 distribution functions are exponential. For non-coding DNA, the distribution functions for most of the dimeric repeats have surprisingly long tails, that fit a power-law function. We hypothesize that: (i) the exponential distributions of dimeric repeats in protein coding sequences indicate strong evolutionary pressure against tandem repeat expansion in coding DNA sequences; and (ii) long tails in the distributions of dimers in non-coding DNA may be a result of various mutational mechanisms. These long, non-exponential tails in the distribution of dimeric repeats in non-coding DNA are hypothesized to be due to the higher tolerance of non-coding DNA to mutations. By comparing genomes of various phylogenetic types of organisms, we find that the shapes of the distributions are not universal, but rather depend on the specific class of species and the type of a dimer.

Animals↗
PubMed2000

Species independence of mutual information in coding and noncoding DNA.

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 [symbol: see text] has a significantly different functional form in coding and noncoding DNA. We further find that (ii) the probability distributions of the average mutual information [symbol: see text] are significantly different in coding and noncoding DNA, while (iii) they are almost the same for organisms of all taxonomic classes. Surprisingly, we find that [symbol: see text] is capable of predicting coding regions as accurately as organism-specific coding measures.

DNA↗
PubMed2000

Average mutual information of coding and noncoding DNA.

One basic problem in the analysis of DNA sequences is the recognition of protein-coding genes. Computer algorithms to facilitate gene identification have become important as genome sequencing projects have turned from mapping to large-scale sequencing, resulting in an exponentially growing number of sequenced nucleotides that await their annotation. Many statistical patterns have been discovered that are different in coding and noncoding DNA, but most of them vary from species to species, and hence require prior training on organism-specific data sets. Here, we investigate if there exist species-independent statistical patterns that are different in coding and noncoding DNA. We introduce an information-theoretic quantity, the average mutual information (AMI), and we find that the probability distribution functions of the AMI are significantly different in coding and noncoding DNA, while they are almost identical for different species. This finding suggests that the AMI might be useful for the recognition of protein-coding regions in genomes for which training sets do not exist.

Algorithms↗