PubMed Health⌕ Search

Biomedical subjects

P Grassberger

Publications and source records attributed to P Grassberger.

13 recordsLinked to original sources
PubMed2001

Coarsening in the presence of kinetic disorders: analogy to granular compaction.

We study the zero temperature dynamics in an Ising chain in the presence of a dynamically induced field that favors locally the " -" phase compared to the " +" phase. At late times, while the " +" domains coarsen as t(1/2), the " -" domains coarsen as t(1/2)log(t). Hence, at late times, the magnetization decays slowly as m(t) = -1+const/log(t). We establish this behavior both analytically within an independent interval approximation and numerically. Our model can be viewed as a simple model for granular compaction, where the system decays into a fully compact state (with all spins " -") in a slow logarithmic manner as seen in recent experiments on granular systems.

Journal Article↗
PubMed2001

Exactness of the annealed and the replica symmetric approximations for random heteropolymers.

We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest-neighbor pairs. For each pair, the interaction energy is an independent Gaussian variable with mean value B and variance Delta(2). For this model the annealed approximation is expected to become exact for low disorder, at sufficiently high dimension and in the thermodynamic limit. We show that corrections to the annealed approximation in the three-dimensional high-temperature phase are small, but do not vanish in the thermodynamic limit, and are in good agreement with our replica symmetric calculations. Such corrections derive from the fact that the overlap between two typical chains is nonzero. We explain why previous authors had come to the opposite conclusion, and discuss consequences for the thermodynamics of the model. Numerical results were obtained by simulating chains of length N<or=1400 by means of the recent PERM algorithm, in the coil and molten globular phases, well above the freezing temperature.

Algorithms↗
PubMed2000

Learning driver-response relationships from synchronization patterns.

We test recent claims that causal (driver-response) relationships can be deduced from interdependencies between simultaneously measured time series. We apply two recently proposed interdependence measures that should give results similar to cross predictabilities used by previous authors. The systems that we study are asymmetrically coupled simple models (Lorenz, Roessler, and Hénon models), the couplings being such that they lead to generalized synchronization. If the data were perfect (noise-free, infinitely long), we should be able to detect, at least in some cases, which of the coupled systems is the driver and which the response. This might no longer be true if the time series has finite length. Instead, estimated interdependencies depend strongly on which of the systems has a higher effective dimension at the typical neighborhood sizes used to estimate them, and causal relationships are more difficult to detect. We also show that slightly different variants of the interdependence measure can have quite different sensitivities.

Electroencephalography↗
PubMed2000

Scaling of waves in the bak-tang-wiesenfeld sandpile model

We study probability distributions of waves of topplings in the Bak-Tang-Wiesenfeld model on hypercubic lattices for dimensions D>/=2. Waves represent relaxation processes which do not contain multiple toppling events. We investigate bulk and boundary waves by means of their correspondence to spanning trees, and by extensive numerical simulations. While the scaling behavior of avalanches is complex and usually not governed by simple scaling laws, we show that the probability distributions for waves display clear power-law asymptotic behavior in perfect agreement with the analytical predictions. Critical exponents are obtained for the distributions of radius, area, and duration of bulk and boundary waves. Relations between them and fractal dimensions of waves are derived. We confirm that the upper critical dimension D(u) of the model is 4, and calculate logarithmic corrections to the scaling behavior of waves in D=4. In addition, we present analytical estimates for bulk avalanches in dimensions D>/=4 and simulation data for avalanches in D</=3. For D=2 they seem not easy to interpret.

Journal Article↗
PubMed2000

Simple model for the DNA denaturation transition.

We study pairs of interacting self-avoiding walks ¿omega(1), omega(2)¿ on the 3d simple cubic lattice. They have a common origin omega(1)(0)=omega 20, and are allowed to overlap only at the same monomer position along the chain: omega(1)(i) not equal omega(2)(j) for i not equal j, while omega(1)(i)=omega(2)(i) is allowed. The latter overlaps are indeed favored by an energetic gain epsilon. This is inspired by a model introduced long ago by Poland and Sheraga [J. Chem. Phys. 45, 1464 (1966)] for the denaturation transition in DNA where, however, self avoidance was not fully taken into account. For both models, there exists a temperature T(m) above which the entropic advantage to open up overcomes the energy gained by forming tightly bound two-stranded structures. Numerical simulations of our model indicate that the transition is of first order (the energy density is discontinuous), but the analog of the surface tension vanishes and the scaling laws near the transition point are exactly those of a second-order transition with crossover exponent straight phi=1. Numerical and exact analytic results show that the transition is second order in modified models where the self-avoidance is partially or completely neglected.

Computer Simulation↗
PubMed2000

Kulback-Leibler and renormalized entropies: applications to electroencephalograms of epilepsy patients.

Recently, "renormalized entropy" was proposed as a novel measure of relative entropy [P. Saparin et al., Chaos, Solitons and Fractals 4, 1907 (1994)] and applied to several physiological time sequences, including electroencephalograms (EEGs) of patients with epilepsy. We show here that this measure is just a modified Kullback-Leibler (KL) relative entropy, and it gives similar numerical results to the standard KL entropy. The latter better distinguishes frequency contents of, e.g., seizure and background EEGs than renormalized entropy. We thus propose that renormalized entropy might not be as useful as claimed by its proponents. In passing, we also make some critical remarks about the implementation of these methods.

Biophysical Phenomena↗
PubMed1998

Testing a new Monte Carlo algorithm for protein folding.

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (PERM) (Grassberger, Phys. Rev. E 56:3682, 1997) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare it to published Monte Carlo studies of the properties of particular sequences. In all cases our method is faster than the previous ones, and in several cases we find new minimal energy states. In addition to producing more reliable candidates for ground states, our method gives detailed information about the thermal spectrum and thus allows one to analyze thermodynamic aspects of the folding behavior of arbitrary sequences.

Algorithms↗