Biomedical subjects

H Eugene Stanley

Publications and source records attributed to H Eugene Stanley.

At least 19 recordsLinked to original sources

PubMed2004

Common scale-invariant patterns of sleep-wake transitions across mammalian species.

Although mammals of different species have different sleep patterns, brief sleep-wake transitions commonly are observed across species and appear to occur randomly throughout the sleeping period. The dynamical patterns and functions of these brief awakenings from sleep are not well understood, and they often are viewed as disruptions (random or pathologic) of the sleep process. In this article, we hypothesize that brief awakenings from sleep may reflect aspects of the endogenous sleep control mechanism and thus may exhibit certain robust dynamical patterns across species. We analyze sleep recordings from mice, rats, cats, and humans, and we compare the distributions of sleep and wake episode durations. For all four species, we find that durations of brief wake episodes during the sleep period exhibit a scale-free power-law behavior with an exponent alpha that remains the same for all species (alpha approximately equal to 2.2). In contrast, sleep episode durations for all four species follow exponential distributions with characteristic time scales, which change across species in relation to body mass and metabolic rate. Our findings suggest common dynamical features of brief awakenings and sleep durations across species and may provide insights into the dynamics of the neural circuits controlling sleep.

Animals↗

PubMed2004

Effect of disorder strength on optimal paths in complex networks.

We study the transition between the strong and weak disorder regimes in the scaling properties of the average optimal path l(opt) in a disordered Erdos-Rényi (ER) random network and scale-free (SF) network. Each link i is associated with a weight tau(i) identical withexp (a r(i) ) , where r(i) is a random number taken from a uniform distribution between 0 and 1 and the parameter a controls the strength of the disorder. We find that for any finite a , there is a crossover network size N* (a) at which the transition occurs. For N< /=4 , and l(opt) approximately N (lambda-3) (/ (lambda-1) ) for SF networks with 3 >N* (a) the scaling behavior is in the weak disorder regime, with l(opt) approximately ln N for ER networks and SF networks with lambda>3 . In order to study the transition we propose a measure which indicates how close or far the disordered network is from the limit of strong disorder. We propose a scaling ansatz for this measure and demonstrate its validity. We proceed to derive the scaling relation between N* (a) and a . We find that N* (a) approximately a(3) for ER networks and for SF networks with lambda>/=4 , and N* (a) approximately a (lambda-1) (/ (lambda-3) ) for SF networks with 3<lambda<4 .

Journal Article↗

PubMed2004

Universality of the optimal path in the strong disorder limit.

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.

Journal Article↗

PubMed2004

Glass-transition temperature of water: a simulation study.

We report a computer simulation study of the glass transition for water using the extended simple point charge potential. To mimic the difference between standard and hyperquenched glass, we generate glassy configurations with different cooling rates, and we calculate the temperature dependence of the specific heat on heating. The absence of crystallization phenomena allows us, for properly annealed samples, to detect in the specific heat the simultaneous presence of a weak prepeak ("shadow transition") and an intense glass transition peak at higher temperature. Our results support the view-point that the glass transition temperature is higher than the conventionally accepted value 136 K. We also compare our simulation results with the Tool-Narayanaswamy-Moynihan phenomenological model.

Journal Article↗

PubMed2004

Cooling rate, heating rate, and aging effects in glassy water.

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.

Journal Article↗

PubMed2004

Heuristic segmentation of a nonstationary time series.

Many phenomena, both natural and human influenced, give rise to signals whose statistical properties change under time translation, i.e., are nonstationary. For some practical purposes, a nonstationary time series can be seen as a concatenation of stationary segments. However, the exact segmentation of a nonstationary time series is a hard computational problem which cannot be solved exactly by existing methods. For this reason, heuristic methods have been proposed. Using one such method, it has been reported that for several cases of interest-e.g., heart beat data and Internet traffic fluctuations-the distribution of durations of these stationary segments decays with a power-law tail. A potential technical difficulty that has not been thoroughly investigated is that a nonstationary time series with a (scalefree) power-law distribution of stationary segments is harder to segment than other nonstationary time series because of the wider range of possible segment lengths. Here, we investigate the validity of a heuristic segmentation algorithm recently proposed by Bernaola-Galván et al. [Phys. Rev. Lett. 87, 168105 (2001)] by systematically analyzing surrogate time series with different statistical properties. We find that if a given nonstationary time series has stationary periods whose length is distributed as a power law, the algorithm can split the time series into a set of stationary segments with the correct statistical properties. We also find that the estimated power-law exponent of the distribution of stationary-segment lengths is affected by (i) the minimum segment length and (ii) the ratio R identical with sigma(epsilon)/sigma(x), where sigma(x) is the standard deviation of the mean values of the segments and sigma(epsilon) is the standard deviation of the fluctuations within a segment. Furthermore, we determine that the performance of the algorithm is generally not affected by uncorrelated noise spikes or by weak long-range temporal correlations of the fluctuations within segments.

Algorithms↗

PubMed2004

Multiple folding pathways of the SH3 domain.

Experimental observations suggest that proteins follow different folding pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the c-Crk SH3 domain over a broad range of temperatures, and identify distinct pathways in the folding transition. We determine the kinetic partition temperature-the temperature for which the c-Crk SH3 domain undergoes a rapid folding transition with minimal kinetic barriers-and observe that below this temperature the model protein may undergo a folding transition by multiple folding pathways via only one or two intermediates. Our findings suggest the hypothesis that the SH3 domain, a protein fold for which only two-state folding kinetics was observed in previous experiments, may exhibit intermediate states under conditions that strongly stabilize the native state.

Animals↗

PubMed2003

Dynamical robustness of Lévy search strategies.

We study the role of dynamical constraints in the general problem of finding the best statistical strategy for random searching when the targets can be detected only in the limited vicinity of the searcher. We find that the optimal search strategy depends strongly on the delay time tau during which a previously visited site becomes unavailable. We also find that the optimal search strategy is always described for large step lengths l by a power-law distribution P(l) approximately l(-mu), with 1<mu(tau)</=2. Our findings appear to remain valid even if arbitrary energy costs of locomotion are considered.

Feeding Behavior↗

PubMed2003

Minimal Brownian ratchet: an exactly solvable model.

We develop an analytically solvable three-state discrete-time minimal Brownian ratchet (MBR), where the transition probabilities between states are asymmetric. By solving the master equations, we obtain the steady-state probabilities. Generally, the steady-state solution does not display detailed balance, giving rise to an induced directional motion in the MBR. For a reduced two-dimensional parameter space, we find the null curve on which the net current vanishes and detailed balance holds. A system on this curve is said to be balanced. On the null curve, an additional source of external random noise is introduced to show that a directional motion can be induced under the zero overall driving force.

Journal Article↗

PubMed2003

Mechanism for the alpha-helix to beta-hairpin transition.

The aggregation of alpha-helix-rich proteins into beta-sheet-rich amyloid fibrils is associated with fatal diseases, such as Alzheimer's disease and prion disease. During an aggregation process, protein secondary structure elements-alpha-helices-undergo conformational changes to beta-sheets. The fact that proteins with different sequences and structures undergo a similar transition on aggregation suggests that the sequence nonspecific hydrogen bond interaction among protein backbones is an important factor. We perform molecular dynamics simulations of a polyalanine model, which is an alpha-helix in its native state and observe a metastable beta-hairpin intermediate. Although a beta-hairpin has larger potential energy than an alpha-helix, the entropy of a beta-hairpin is larger because of fewer constraints imposed by the hydrogen bonds. In the vicinity of the transition temperature, we observe the interconversion of the alpha-helix and beta-sheet states via a random coil state. We also study the effect of the environment by varying the relative strength of side-chain interactions for a designed peptide-an alpha-helix in its native state. For a certain range of side-chain interaction strengths, we find that the intermediate beta-hairpin state is destabilized and even disappears, suggesting an important role of the environment in the aggregation propensity of a peptide.

Amino Acid Sequence↗

PubMed2003

Optimal paths in disordered complex networks.

We study the optimal distance in networks, l(opt), 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 l(opt) approximately N(1/3) in both Erdos-Rényi (ER) and Watts-Strogatz (WS) networks. For scale-free (SF) networks, with degree distribution P(k) approximately k(-lambda), we find that l(opt) scales as N((lambda-3)/(lambda-1)) for 3 or =4. Thus, for these networks, the small-world nature is destroyed. For 2<lambda<3, our numerical results suggest that l(opt) scales as ln(lambda-1N. We also find numerically that for weak disorder l(opt) approximately ln(N for both the ER and WS models as well as for SF networks.

Communication↗

PubMed2003

Possible mechanism for cold denaturation of proteins at high pressure.

We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the pressure where water freezes to the dense ice phase (approximately 2 kbars) the mechanism for cold denaturation with decreasing temperature is the loss of local low-density water structure. We find our results in agreement with data of bovine pancreatic ribonuclease A.

Animals↗

PubMed2003

Potential-energy landscape study of the amorphous-amorphous transformation in H(2)O.

We study the potential energy landscape explored during a compression-decompression cycle for the simple point charge extended model of water. During the cycle, the system changes from low density amorphous (LDA) ice to high density amorphous ice. After the cycle, the system does not return to the same region of the landscape, supporting the interesting possibility that more than one significantly different configuration corresponds to LDA. We find that the regions of the landscape explored during this transition have properties remarkably different from those explored in thermal equilibrium in the liquid phase.

Journal Article↗

PubMed2003

Perimeter growth of a branched structure: application to crackle sounds in the lung.

We study an invasion percolation process on Cayley trees and find that the dynamics of perimeter growth is strongly dependent on the nature of the invasion process, as well as on the underlying tree structure. We apply this process to model the inflation of the lung in the airway tree, where crackling sounds are generated when airways open. We define the perimeter as the interface between the closed and opened regions of the lung. In this context we find that the distribution of time intervals between consecutive openings is a power law with an exponent beta approximately 2. We generalize the binary structure of the lung to a Cayley tree with a coordination number Z between 2 and 4. For Z=4, beta remains close to 2, while for a chain, Z=2 and beta=1, exactly. We also find a mean field solution of the model.

Airway Resistance↗

PubMed2003

Postbreakthrough behavior in flow through porous media.

We numerically simulate the traveling time of a tracer in convective flow between two points (injection and extraction) separated by a distance r in a model of porous media, d=2 percolation. We calculate and analyze the traveling time probability density function for two values of the fraction of connecting bonds p: the homogeneous case p=1 and the inhomogeneous critical threshold case p=p(c). We analyze both constant current and constant pressure conditions at p=p(c). The homogeneous p=1 case serves as a comparison base for the more complicated p=p(c) situation. We find several regions in the probability density of the traveling times for the homogeneous case (p=1) and also for the critical case (p=p(c)) for both constant pressure and constant current conditions. For constant pressure, the first region I(P) corresponds to the short times before the flow breakthrough occurs, when the probability distribution is strictly zero. The second region II(P) corresponds to numerous fast flow lines reaching the extraction point, with the probability distribution reaching its maximum. The third region III(P) corresponds to intermediate times and is characterized by a power-law decay. The fourth region IV(P) corresponds to very long traveling times, and is characterized by a different power-law decaying tail. The power-law characterizing region IV(P) is related to the multifractal properties of flow in percolation, and an expression for its dependence on the system size L is presented. The constant current behavior is different from the constant pressure behavior, and can be related analytically to the constant pressure case. We present theoretical arguments for the values of the exponents characterizing each region and crossover times. Our results are summarized in two scaling assumptions for the traveling time probability density; one for constant pressure and one for constant current. We also present the production curve associated with the probability of traveling times, which is of interest to oil recovery.

Journal Article↗

PubMed2003

A theory of power-law distributions in financial market fluctuations.

Insights into the dynamics of a complex system are often gained by focusing on large fluctuations. For the financial system, huge databases now exist that facilitate the analysis of large fluctuations and the characterization of their statistical behaviour. Power laws appear to describe histograms of relevant financial fluctuations, such as fluctuations in stock price, trading volume and the number of trades. Surprisingly, the exponents that characterize these power laws are similar for different types and sizes of markets, for different market trends and even for different countries--suggesting that a generic theoretical basis may underlie these phenomena. Here we propose a model, based on a plausible set of assumptions, which provides an explanation for these empirical power laws. Our model is based on the hypothesis that large movements in stock market activity arise from the trades of large participants. Starting from an empirical characterization of the size distribution of those large market participants (mutual funds), we show that the power laws observed in financial data arise when the trading behaviour is performed in an optimal way. Our model additionally explains certain striking empirical regularities that describe the relationship between large fluctuations in prices, trading volume and the number of trades.

Journal Article↗

PubMed2003

Fluid transport in branched structures with temporary closures: a model for quasistatic lung inflation.

We analyze the problem of fluid transport through a model system relevant to the inflation of a mammalian lung, an asymmetric bifurcating structure containing random blockages that can be removed by the pressure of the fluid itself. We obtain a comprehensive description of the fluid flow in terms of the topology of the structure and the mechanisms which open the blockages. We show that when calculating averaged flow properties of the fluid, the tree structure can be partitioned into a linear superposition of one-dimensional chains. In particular, we relate the pressure-volume P-V relationship of the fluid to the distribution Pi(n) of the generation number n of the tree's terminal branches, a structural property. We invert this relation to obtain a statistical description of the underlying branching structure of the lung, by analyzing experimental pressure-volume data from dog lungs. The Pi(n) extracted from the experimental P-V data agrees well with available data on lung branching structure. Our general results are applicable to any physical system involving transport in bifurcating structures with removable closures.

Animals↗

PubMed2003

Connection between Adam-Gibbs theory and spatially heterogeneous dynamics.

We investigate the spatially heterogeneous dynamics in the extended simple point charge model of water using molecular dynamics simulations. We relate the average mass n* of mobile particle clusters to the diffusion constant and the configurational entropy. Hence, n* can be interpreted as the mass of the "cooperatively rearranging regions" that form the basis of the Adam-Gibbs theory of the dynamics of supercooled liquids. We also examine the time and temperature dependence of these transient clusters.

Journal Article↗