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At least 811 records · Page 45Linked to original sources

arXiv1998

Error threshold in finite populations

A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage disequilibrium at the population level is neglected. In particular, for the single-sharp-peak replication landscape we investigate the dependence of the error threshold on the population size and find that the replication accuracy at threshold increases linearly with the reciprocal of the population size for sufficiently large populations. Furthermore, in the deterministic limit our formulation yields the exact steady-state of the quasispecies model, indicating then the population composition is a random combination of the molecules.

cond-mat.stat-mech↗

arXiv1998

Mapping of mutation-sensitive sites in protein-like chains

In this work we have studied, with the help of a simple on-lattice model, the distribution pattern of sites sensitive to point mutations ('hot' sites) in protein-like chains. It has been found that this pattern depends on the regularity of the matrix that rules the interaction between different kinds of residues. If the interaction matrix is dominated by the hydrophobic effect (Miyazawa Jernigan like matrix), this distribution is very simple - all the 'hot' sites can be found at the positions with maximum number of closest nearest neighbors (bulk). If random or nonlinear corrections are added to such an interaction matrix the distribution pattern changes. The rising of collective effects allows the 'hot' sites to be found in places with smaller number of nearest neighbors (surface) while the general trend of the 'hot' sites to fall into a bulk part of a conformation still holds.

cond-mat.stat-mech↗

arXiv1998

Bending and Twisting Elasticity: a Revised Marko-Siggia Model on DNA Chirality

A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27, 981 (1994)] is proposed, which includes the WLC bending energy and a new chiral twisting energy term. It is predicted that the mean helical repeat length (HRL) for short DNA rings increases with the decreasing of chain length; while for very long chains, their mean HRL is the same, independent of both the chain length and whether the ends are closed, it is longer than the value for rectilinear DNAs. Our results are in good agreement with experiments.

cond-mat.soft↗

arXiv1998

Quantitative analysis by renormalized entropy of invasive electroencephalograph recordings in focal epilepsy

Invasive electroencephalograph (EEG) recordings of ten patients suffering from focal epilepsy were analyzed using the method of renormalized entropy. Introduced as a complexity measure for the different regimes of a dynamical system, the feature was tested here for its spatio-temporal behavior in epileptic seizures. In all patients a decrease of renormalized entropy within the ictal phase of seizure was found. Furthermore, the strength of this decrease is monotonically related to the distance of the recording location to the focus. The results suggest that the method of renormalized entropy is a useful procedure for clinical applications like seizure detection and localization of epileptic foci.

physics.med-ph↗

arXiv1998

Nonstationary Stochastic Resonance in a Single Neuron-Like System

Stochastic resonance holds much promise for the detection of weak signals in the presence of relatively loud noise. Following the discovery of nondynamical and of aperiodic stochastic resonance, it was recently shown that the phenomenon can manifest itself even in the presence of nonstationary signals. This was found in a composite system of differentiated trigger mechanisms mounted in parallel, which suggests that it could be realized in some elementary neural networks or nonlinear electronic circuits. Here, we find that even an individual trigger system may be able to detect weak nonstationary signals using stochastic resonance. The very simple modification to the trigger mechanism that makes this possible is reminiscent of some aspects of actual neuron physics. Stochastic resonance may thus become relevant to more types of biological or electronic systems injected with an ever broader class of realistic signals.

cond-mat↗

arXiv1998

Cooperative dynamics in auditory brain response

Simultaneous estimates of the activity in the left and right auditory cortex of five normal human subjects were extracted from Multichannel Magnetoencephalography recordings. Left, right and binaural stimulation were used, in separate runs, for each subject. The resulting time-series of left and right auditory cortex activity were analysed using the concept of mutual information. The analysis constitutes an objective method to address the nature of inter-hemispheric correlations in response to auditory stimulations. The results provide a clear evidence for the occurrence of such correlations mediated by a direct information transport, with clear laterality effects: as a rule, the contralateral hemisphere leads by 10-20ms, as can be seen in the average signal. The strength of the inter-hemispheric coupling, which cannot be extracted from the average data, is found to be highly variable from subject to subject, but remarkably stable for each subject.

physics.bio-ph↗

arXiv1998

Fractal Analysis of Protein Potential Energy Landscapes

The fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the exponent γ, is almost independent of temperature and increases with time, more slowly the larger the protein. Perhaps the most striking observation of this study is the apparent universality of the fractal dimension, which depends only weakly on the type of molecular system. We explain this behavior by assuming that fractality is caused by a self-generated dynamical noise, a consequence of intermode coupling due to anharmonicity. Global topological features of the potential energy landscape are found to have little effect on the observed fractal behavior.

cond-mat.soft↗

arXiv1998

Noise and Periodic Modulations in Neural Excitable Media

We have analyzed the interplay between noise and periodic modulations in a mean field model of a neural excitable medium. To this purpose, we have considered two types of modulations; namely, variations of the resistance and oscillations of the threshold. In both cases, stochastic resonance is present, irrespective of if the system is monostable or bistable.

cond-mat.stat-mech↗

arXiv1998

Markov analysis of stochastic resonance in a periodically driven integrate-fire neuron

We model the dynamics of the leaky integrate-fire neuron under periodic stimulation as a Markov process with respect to the stimulus phase. This avoids the unrealistic assumption of a stimulus reset after each spike made in earlier work and thus solves the long-standing reset problem. The neuron exhibits stochastic resonance, both with respect to input noise intensity and stimulus frequency. The latter resonance arises by matching the stimulus frequency to the refractory time of the neuron. The Markov approach can be generalized to other periodically driven stochastic processes containing a reset mechanism.

physics.bio-ph↗

arXiv1999

Modelling of spatio-temporal patterns in bacterial colonies

A diffusion-reaction model for the growth of bacterial colonies is presented. The often observed cooperative behavior developed by bacteria which increases their motility in adverse growth conditions is here introduced as a nonlinear diffusion term. The presence of this mechanism depends on a response which can present hysteresis. By changing only the concentrations of agar and initial nutrient, numerical integration of the proposed model reproduces the different patterns shown by {\it Bacillus subtilis} OG-01.

cond-mat↗

arXiv1999

Folding in two-dimenensional off-lattice models of proteins

Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties.

cond-mat.soft↗

arXiv1998

Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations

A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification, which is noteworthy for its independence from stationarity constraints, as well as its ability to detect transients, and both linear and nonlinear state changes. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence measures is also discussed.

physics.bio-ph↗

arXiv1999

Multiscale analysis of blood pressure signals

We describe the multiresolution wavelet analysis of blood pressure waves in vasovagal syncope-affected patients compared with those in healthy people, using Haar and Gaussian bases. A comparison between scale-dependent and scale-independent measures discriminating the two classes of subjects is made. What emerges is a sort of equivalence between these two methodological approaches, that is, both methods reach the same statistical significance of separation between the two classes.

cond-mat.dis-nn↗

arXiv1999

Protein Ground State Candidates in a Simple Model: An Exact Enumeration

The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the native states of all proteins for a wide range of energy parameters. In this way, we show that there are some sequences, which have an absolute native state. Moreover, we study the scale-dependence of the number of the members of the reduced set, the number of ground state candidates, and the number of perfectly stable sequences by comparing the results for sequences with lengths of 6 up to 20.

cond-mat.soft↗

arXiv1999

Thermal Noise Can Facilitate Energy Conversion by Ratchet System?

Molecular motors in biological systems are expected to use ambient fluctuation. In a recent Letter [Phys. Rev. Lett. {\bf 80}, 5251 (1998)], it was showed that the following question was unsolved, ``Can thermal noise facilitate energy conversion by ratchet system?'' We consider it using stochastic energetics, and show that there exist systems where thermal noise helps the energy conversion.

cond-mat.stat-mech↗

arXiv1999

Oscillatory behaviour in a lattice prey-predator system

Using Monte Carlo simulations we study a lattice model of a prey-predator system. We show that in the three-dimensional model populations of preys and predators exhibit coherent periodic oscillations but such a behaviour is absent in lower-dimensional models. Finite-size analysis indicate that amplitude of these oscillations is finite even in the thermodynamic limit. In our opinion, this is the first example of a microscopic model with stochastic dynamics which exhibits oscillatory behaviour without any external driving force. We suggest that oscillations in our model are induced by some kind of stochastic resonance.

cond-mat.stat-mech↗

arXiv1999

Statistics of DNA sequences: a low frequency analysis

We study statistical properties of DNA chains of thirteen microbial complete genomes. We find that the power spectrum of several of the sequences studied flattens off in the low frequency limit. This implies that the correlation length in those sequences is much smaller than the entire DNA chain. Consequently, in contradiction with previous studies, we show that the fractal behavior of DNA chains not always prevail through the entire DNA molecule.

cond-mat.stat-mech↗

arXiv1999

Characterization and control of small-world networks

Recently Watts and Strogatz have given an interesting model of small-world networks. Here we concretise the concept of a ``far away'' connection in a network by defining a {\it far edge}. Our definition is algorithmic and independent of underlying topology of the network. We show that it is possible to control spread of an epidemic by using the knowledge of far edges. We also suggest a model for better advertisement using the far edges. Our findings indicate that the number of far edges can be a good intrinsic parameter to characterize small-world phenomena.

chao-dyn↗