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.

Neurotoxic effects of thioflavin S-positive amyloid deposits in transgenic mice and Alzheimer's disease

Despite extensive deposition of putatively neurotoxic amyloid-beta (Abeta) protein in the brain, it has not been possible to demonstrate an association of Abeta deposits with neuronal loss in Alzheimer's disease (AD), and neuronal loss is minimal in transgenic mouse models of AD. Using triple immunostaining confocal microscopy and analyzing the images with the cross-correlation density map method from statistical physics, we directly compared Abeta deposition, Abeta morphology, and neuronal architecture. We found dramatic, focal neuronal toxicity associated primarily with thioflavin S-positive fibrillar Abeta deposits in both AD and PSAPP mice. These results, along with computer simulations, suggest that Abeta develops neurotoxic properties in vivo when it adopts a fibrillar beta-pleated sheet conformation.

Traveling length and minimal traveling time for flow through percolation networks with long-range spatial correlations

We study the distributions of traveling length l and minimal traveling time t(min) through two-dimensional percolation porous media characterized by long-range spatial correlations. We model the dynamics of fluid displacement by the convective movement of tracer particles driven by a pressure difference between two fixed sites ("wells") separated by Euclidean distance r. For strongly correlated pore networks at criticality, we find that the probability distribution functions P(l) and P(t(min)) follow the same scaling ansatz originally proposed for the uncorrelated case, but with quite different scaling exponents. We relate these changes in dynamical behavior to the main morphological difference between correlated and uncorrelated clusters, namely, the compactness of their backbones. Our simulations reveal that the dynamical scaling exponents d(l) and d(t) for correlated geometries take values intermediate between the uncorrelated and homogeneous limiting cases, where l(*) approximately r(d(l)) and t(*)(min) approximately r(d(t)), and l(*) and t(*)(min) are the most probable values of l and t(min), respectively.

Dynamics and configurational entropy in the Lewis-Wahnström model for supercooled orthoterphenyl

We study thermodynamic and dynamic properties of a rigid model of the fragile glass-forming liquid orthoterphenyl. This model, introduced by Lewis and Wahnström in 1993, collapses each phenyl ring to a single interaction site; the intermolecular site-site interactions are described by the Lennard-Jones potential whose parameters have been selected to reproduce some bulk properties of the orthoterphenyl molecule. A system of N=343 molecules is considered in a wide range of densities and temperatures, reaching simulation times up to 1 micros. Such long trajectories allow us to equilibrate the system at temperatures below the mode coupling temperature T(c) at which the diffusion constant reaches values of order 10(-10) cm(2)/s and thereby to sample in a significant way the potential energy landscape in the entire temperature range. Working within the inherent structures thermodynamic formalism, we present results for the temperature and density dependence of the number, depth and shape of the basins of the potential energy surface. We evaluate the total entropy of the system by thermodynamic integration from the ideal-noninteracting-gas state and the vibrational entropy approximating the basin free energy with the free energy of 6N-3 harmonic oscillators. We evaluate the configurational part of the entropy as a difference between these two contributions. We study the connection between thermodynamical and dynamical properties of the system. We confirm that the temperature dependence of the configurational entropy and of the diffusion constant, as well as the inverse of the characteristic structural relaxation time, are strongly connected in supercooled states; we demonstrate that this connection is well represented by the Adam-Gibbs relation, stating a linear relation between logD and the quantity 1/TS(c). This relation is found to hold both above and below the critical temperature T(c)-as previously found in the case of silica-supporting the hypothesis that a connection exists between the number of basins and the connectivity properties of the potential energy surface.

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.

When human walking becomes random walking: fractal analysis and modeling of gait rhythm fluctuations

We present a random walk, fractal analysis of the stride-to-stride fluctuations in the human gait rhythm. The gait of healthy young adults is scale-free with long-range correlations extending over hundreds of strides. This fractal scaling changes characteristically with maturation in children and older adults and becomes almost completely uncorrelated with certain neurologic diseases. Stochastic modeling of the gait rhythm dynamics, based on transitions between different "neural centers", reproduces distinctive statistical properties of the gait pattern. By tuning one model parameter, the hopping (transition) range, the model can describe alterations in gait dynamics from childhood to adulthood including a decrease in the correlation and volatility exponents with maturation.

Scale invariance in the nonstationarity of human heart rate

We introduce a segmentation algorithm to probe the temporal organization of heterogeneities in human heartbeat interval time series. We find that the lengths of segments with different local mean heart rates follow a power-law distribution and show that this scale-invariant structure is not a simple consequence of the long-range correlations present in the data. The differences in mean heart rates between consecutive segments display a common functional form, but with different parameters for healthy individuals and for heart-failure patients. These findings suggest that there is relevant physiological information hidden in the heterogeneities of the heartbeat time series.

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.

Dynamics of supercooled water in configuration space

We study the potential energy surface (PES) sampled by a liquid modeled via the widely studied extended simple point charge (SPC/E) model for water. We characterize the curvature of the PES by calculating the instantaneous normal mode (INM) spectrum for a wide range of densities and temperatures. We discuss the information contained in the INM density of states, which requires additional processing to be unambiguously associated with the long-time dynamics. For the SPC/E model, we find that the slowing down of the dynamics in the supercooled region-where the ideal mode coupling theory has been used to describe the dynamics-is controlled by the reduction in the number of directions in configuration space that allow a structural change. We find that the fraction f(dw) of the double-well directions in configuration space determines the value of the diffusion constant D, thereby relating a property of the PES to a macroscopic dynamic quantity; specifically, it appears that square root D is approximately linear in f(dw). Our findings are consistent with the hypothesis that, at the mode coupling crossover temperature, dynamical processes based on the free exploration of configuration space vanish, and processes requiring activation dominate. Hence, the reduction of the number of directions allowing free exploration of configuration space is the mechanism of diffusion implicitly implemented in the ideal mode coupling theory. Additionally, we find a direct relationship between the number of basins sampled by the system and the number of free directions. In this picture, diffusion appears to be related to geometrical properties of the PES, and to be entropic in origin.

Quantifying and interpreting collective behavior in financial markets

Firms having similar business activities are correlated. We analyze two different cross-correlation matrices C constructed from (i) 30-min price fluctuations of 1000 US stocks for the two-year period 1994-95 and (ii) one-day price fluctuations of 422 US stocks for the 35-year period 1962-96. We find that the eigenvectors of C corresponding to the largest eigenvalues allow us to partition the set of all stocks into distinct subsets. These subsets are similar to business sectors, and are stable for extended periods of time. We find that price fluctuations of these subsets are characterized by power-law decaying time correlations, reminiscent of strongly interacting systems.

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.

Noise effects on the complex patterns of abnormal heartbeats

Patients at high risk for sudden death often exhibit complex heart rhythms in which abnormal heartbeats are interspersed with normal heartbeats. We analyze such a complex rhythm in a single patient over a 12-h period and show that the rhythm can be described by a theoretical model consisting of two interacting oscillators with stochastic elements. By varying the magnitude of the noise, we show that for an intermediate level of noise, the model gives best agreement with key statistical features of the dynamics.

Percolation threshold, Fisher exponent, and shortest path exponent for four and five dimensions

We develop a method of constructing percolation clusters that allows us to build very large clusters using very little computer memory by limiting the maximum number of sites for which we maintain state information to a number of the order of the number of sites in the largest chemical shell of the cluster being created. The memory required to grow a cluster of mass s is of the order of s(straight theta) bytes where straight theta ranges from 0.4 for two-dimensional (2D) lattices to 0.5 for six (or higher)-dimensional lattices. We use this method to estimate d(min), the exponent relating the minimum path l to the Euclidean distance r, for 4D and 5D hypercubic lattices. Analyzing both site and bond percolation, we find d(min)=1.607+/-0.005 (4D) and d(min)=1.812+/-0.006 (5D). In order to determine d(min) to high precision, and without bias, it was necessary to first find precise values for the percolation threshold, p(c): p(c)=0.196889+/-0.000003 (4D) and p(c)=0.14081+/-0.00001 (5D) for site and p(c)=0.160130+/-0.000003 (4D) and p(c)=0.118174+/-0.000004 (5D) for bond percolation. We also calculate the Fisher exponent tau determined in the course of calculating the values of p(c): tau=2.313+/-0.003 (4D) and tau=2.412+/-0.004 (5D).

Plaque-induced abnormalities in neurite geometry in transgenic models of Alzheimer disease: implications for neural system disruption

Neurites that pass through amyloid-beta deposits in Alzheimer disease (AD) undergo 3 changes: they develop phosphorylated tau immunoreactivity; the density of SMI-32-positive dendrites diminishes; and they also develop a marked alteration in their geometric features, changing from being nearly straight to being quite curvy. The extent to which the latter 2 phenomena are related to phosphorylated tau is unknown. We have now examined whether amyloid-beta deposits in APP695Sw transgenic mice, which have only rare phosphorylated tau containing neurites. develop these changes. We found that dendritic density is diminished within the boundaries of amyloid-beta plaques, with the greatest loss (about 80%, p < 0.001) within the boundaries of thioflavine S cores. Remaining dendrites within plaques develop substantial morphological alterations quantitatively similar to those seen in AD. A statistically significant but smaller degree of change in geometry was seen in the immediate vicinity around plaques, suggesting a propagation of cytoskeletal disruption from the center of the plaque outward. We examined the possible physiological consequences of this change in dendritic geometry using a standard cable-theory model. We found a predicted delay of several milliseconds in about one quarter of the dendrites passing through a thioflavine S plaque. These results are consistent with previous observations in AD, and suggest that thioflavine S-positive amyloid-beta deposits have a marked effect on dendritic microarchitecture in the cortex, even in the relative absence of phosphorylated tau alterations.

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.

Effect of trends on detrended fluctuation analysis

Detrended fluctuation analysis (DFA) is a scaling analysis method used to estimate long-range power-law correlation exponents in noisy signals. Many noisy signals in real systems display trends, so that the scaling results obtained from the DFA method become difficult to analyze. We systematically study the effects of three types of trends--linear, periodic, and power-law trends, and offer examples where these trends are likely to occur in real data. We compare the difference between the scaling results for artificially generated correlated noise and correlated noise with a trend, and study how trends lead to the appearance of crossovers in the scaling behavior. We find that crossovers result from the competition between the scaling of the noise and the "apparent" scaling of the trend. We study how the characteristics of these crossovers depend on (i) the slope of the linear trend; (ii) the amplitude and period of the periodic trend; (iii) the amplitude and power of the power-law trend, and (iv) the length as well as the correlation properties of the noise. Surprisingly, we find that the crossovers in the scaling of noisy signals with trends also follow scaling laws--i.e., long-range power-law dependence of the position of the crossover on the parameters of the trends. We show that the DFA result of noise with a trend can be exactly determined by the superposition of the separate results of the DFA on the noise and on the trend, assuming that the noise and the trend are not correlated. If this superposition rule is not followed, this is an indication that the noise and the superposed trend are not independent, so that removing the trend could lead to changes in the correlation properties of the noise. In addition, we show how to use DFA appropriately to minimize the effects of trends, how to recognize if a crossover indicates indeed a transition from one type to a different type of underlying correlation, or if the crossover is due to a trend without any transition in the dynamical properties of the noise.

Behavioral-independent features of complex heartbeat dynamics

We test whether the complexity of the cardiac interbeat interval time series is simply a consequence of the wide range of scales characterizing human behavior, especially physical activity, by analyzing data taken from healthy adult subjects under three conditions with controls: (i) a "constant routine" protocol where physical activity and postural changes are kept to a minimum, (ii) sympathetic blockade, and (iii) parasympathetic blockade. We find that when fluctuations in physical activity and other behavioral modifiers are minimized, a remarkable level of complexity of heartbeat dynamics remains, while for neuroautonomic blockade the multifractal complexity decreases.

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.

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.

Thermodynamic and structural aspects of the potential energy surface of simulated water

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition is a topic of considerable interest. The potential energy surface of model liquids has been increasingly studied, since it provides a connection between the configurational component of the partition function on the one hand, and the system dynamics on the other. This connection is most obvious at low temperatures, where the motion of the system can be partitioned into vibrations within a basin of attraction and infrequent interbasin transitions. In this work, we present a description of the potential energy surface properties of supercooled liquid water. The dynamics of this model have been studied in great detail in recent years. We locate the minima sampled by the liquid by "quenches" from equilibrium configurations generated via molecular dynamics simulations, and then calculate the temperature and density dependence of the basin energy, degeneracy, and shape. The temperature dependence of the energy of the minima is qualitatively similar to simple liquids, but has anomalous density dependence. The unusual density dependence is also reflected in the configurational entropy, the thermodynamic measure of degeneracy. Finally, we study the structure of simulated water at the minima, which provides insight on the progressive tetrahedral ordering of the liquid on cooling.

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.

Magnitude and sign correlations in heartbeat fluctuations

We propose an approach for analyzing signals with long-range correlations by decomposing the signal increment series into magnitude and sign series and analyzing their scaling properties. We show that signals with identical long-range correlations can exhibit different time organization for the magnitude and sign. We find that the magnitude series relates to the nonlinear properties of the original time series, while the sign series relates to the linear properties. We apply our approach to the heartbeat interval series and find that the magnitude series is long-range correlated, while the sign series is anticorrelated and that both magnitude and sign series may have clinical applications.

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.

Free energy surface of supercooled water

We present a detailed analysis of the free energy surface of a well characterized rigid model for water in supercooled states. We propose a functional form for the liquid free energy, supported by recent theoretical predictions [Y. Rosenfeld and P. Tarazona, Mol. Phys. 95, 141 (1998)], and use it to locate the position of a liquid-liquid critical point at T(C')=130+/-5 K, P(C')=290+/-30 MPa, and rho(C')=1.10+/-0.03 g/cm(3). The observation of the critical point strengthens the possibility that the extended simple point charge model of water may undergo a liquid-liquid phase transition. Finally, we discuss the possibility that the approach to the liquid-liquid critical point could be pre-empted by the glass transition.

Size distribution of recruited alveolar volumes in airway reopening

In 11 isolated dog lung lobes, we studied the size distribution of recruited alveolar volumes that become available for gas exchange during inflation from the collapsed state. Three catheters were wedged into 2-mm-diameter airways at total lung capacity. Small-amplitude pseudorandom pressure oscillations between 1 and 47 Hz were led into the catheters, and the input impedances of the regions subtended by the catheters were continuously recorded using a wave tube technique during inflation from -5 cm H(2)O transpulmonary pressure to total lung capacity. The impedance data were fit with a model to obtain regional tissue elastance (Eti) as a function of inflation. First, Eti was high and decreased in discrete jumps as more groups of alveoli were recruited. By assuming that the number of opened alveoli is inversely proportional to Eti, we calculated from the jumps in Eti the distribution of the discrete increments in the number of opened alveoli. This distribution was in good agreement with model simulations in which airways open in cascade or avalanches. Implications for mechanical ventilation may be found in these results.

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.

Classes of small-world networks

We study the statistical properties of a variety of diverse real-world networks. We present evidence of the occurrence of three classes of small-world networks: (a) scale-free networks, characterized by a vertex connectivity distribution that decays as a power law; (b) broad-scale networks, characterized by a connectivity distribution that has a power law regime followed by a sharp cutoff; and (c) single-scale networks, characterized by a connectivity distribution with a fast decaying tail. Moreover, we note for the classes of broad-scale and single-scale networks that there are constraints limiting the addition of new links. Our results suggest that the nature of such constraints may be the controlling factor for the emergence of different classes of networks.

Statistical properties of share volume traded in financial markets

We quantitatively investigate the ideas behind the often-expressed adage "it takes volume to move stock prices," and study the statistical properties of the number of shares traded Q(Deltat) for a given stock in a fixed time interval Deltat. We analyze transaction data for the largest 1000 stocks for the two-year period 1994-95, using a database that records every transaction for all securities in three major US stock markets. We find that the distribution P(Q(Deltat)) displays a power-law decay, and that the time correlations in Q(Deltat) display long-range persistence. Further, we investigate the relation between Q(Deltat) and the number of transactions N(Deltat) in a time interval Deltat, and find that the long-range correlations in Q(Deltat) are largely due to those of N(Deltat). Our results are consistent with the interpretation that the large equal-time correlation previously found between Q(Deltat) and the absolute value of price change |G(Deltat)| (related to volatility) are largely due to N(Deltat).

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.

Quantifying nonstationary radioactivity concentration fluctuations near chernobyl: A complete statistical description

We analyze nonstationary 137Cs atmospheric activity concentration fluctuations measured near Chernobyl after the 1986 disaster and find three new results: (i) the histogram of fluctuations is well described by a log-normal distribution; (ii) there is a pronounced spectral component with period T=1yr, and (iii) the fluctuations are long-range correlated. These findings allow us to quantify two fundamental statistical properties of the data: the probability distribution and the correlation properties of the time series. We interpret our findings as evidence that the atmospheric radionuclide resuspension processes are tightly coupled to the surrounding ecosystems and to large time scale weather patterns.

Finding borders between coding and noncoding DNA regions by an entropic segmentation method

We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses only the general statistical properties of coding DNA. We find that this method is highly accurate in finding borders between coding and noncoding regions and requires no "prior training" on known data sets. Our results appear to be more accurate than those obtained with moving windows in the discrimination of coding from noncoding DNA.

Hydrogen-bond dynamics for the extended simple point-charge model of water

We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We analyze the dynamics using energetic and geometric definitions of a hydrogen bond, and employ two analysis methods: (i) a history-dependent correlation function, related to the distribution of bond lifetimes, and (ii) a history-independent correlation function. For method (i) we find an approximately Arrhenius temperature dependence of the bond lifetime, and find that the distribution of bond lifetimes is extremely sensitive to the choice of bond definition. For method (ii) we find-independent of bond definition-that the dynamics are consistent with the predictions of the mode-coupling theory, suggesting that the slow dynamics of hydrogen bonds can be explained in the same framework as standard transport quantities. Our results allow us to clarify the significance of the choice of both bond definition and analysis technique.

PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals

The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the National Institutes of Health, is intended to stimulate current research and new investigations in the study of cardiovascular and other complex biomedical signals. The resource has 3 interdependent components. PhysioBank is a large and growing archive of well-characterized digital recordings of physiological signals and related data for use by the biomedical research community. It currently includes databases of multiparameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and from patients with a variety of conditions with major public health implications, including life-threatening arrhythmias, congestive heart failure, sleep apnea, neurological disorders, and aging. PhysioToolkit is a library of open-source software for physiological signal processing and analysis, the detection of physiologically significant events using both classic techniques and novel methods based on statistical physics and nonlinear dynamics, the interactive display and characterization of signals, the creation of new databases, the simulation of physiological and other signals, the quantitative evaluation and comparison of analysis methods, and the analysis of nonstationary processes. PhysioNet is an on-line forum for the dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. It provides facilities for the cooperative analysis of data and the evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software via the World Wide Web (http://www.physionet. org), PhysioNet offers services and training via on-line tutorials to assist users with varying levels of expertise.

Instantaneous normal mode analysis of supercooled water

We use the instantaneous normal mode approach to provide a description of the local curvature of the potential energy surface of a model for water. We focus on the region of the phase diagram in which the dynamics may be described by mode-coupling theory. We find that the diffusion constant depends on the fraction of directions in configuration space connecting different local minima, supporting the hypothesis that the dynamics are controlled by the geometric properties of configuration space. Furthermore, we find a relation between the number of basins accessed in equilibrium and the connectivity between them.