Landscape Paradigms in Physics and Biology: Introduction and Overview
A brief introductory overview in general terms is given of concepts, issues and applications of the paradigm of rugged landscapes in the contexts of physics and biology.
cond-mat↗
SEARCH · Searcharxiv
Results for “q-bio”
Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
The Modular Structure of Kauffman Networks
This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced and studied in our first paper, are subdivided. We show that the phase transition in Random Boolean Networks can also be described as a percolation transition. The statistical properties of the clusters of relevant elements (that we call modules) give an insight on the scaling behavior of the attractors of the critical networks that, according to Kauffman, have a biological analogy as a model of genetic regulatory systems.
cond-mat.dis-nn↗
A Robust Method for Detecting Interdependences: Application to Intracranially Recorded EEG
We present a measure for characterizing statistical relationships between two time sequences. In contrast to commonly used measures like cross-correlations, coherence and mutual information, the proposed measure is non-symmetric and provides information about the direction of interdependence. It is closely related to recent attempts to detect generalized synchronization. However, we do not assume a strict functional relationship between the two time sequences and try to define the measure so as to be robust against noise, and to detect also weak interdependences. We apply our measure to intracranially recorded electroencephalograms of patients suffering from severe epilepsies.
chao-dyn↗
A Sucrose Solution Application to the Study of Model Biological Membranes
The small-angle X-ray and neutron scattering, time resolved X-ray small-angle and wide-angle diffraction coupled with differential scanning calorimetry have been applied to the investigation of unilamellar and multilamellar dimyristoylphosphatidylcholine (DMPC) vesicles in sucrose buffers with sucrose concentrations from 0 to 60%. Sucrose buffer decreased vesicle size and polydispersity and increased an X-ray contrast between phospholipid membrane and bulk solvent sufficiently. No influence of sucrose on the membrane thickness or mutual packing of hydrocarbon chains has been detected. The region of sucrose concentrations 30%-40% created the best experimental conditions for X-ray small-angle experiments with phospholipid vesicles.
physics.bio-ph↗
A Diffusion-Based Approach to Geminate Recombination of Heme Proteins with Small Ligands
A model of postphotodissociative monomolecular (geminate) recombination of heme proteins with small ligands (NO, O2 or CO) is represented. The non-exponential decay with time for the probability to find a heme in unbound state is interpreted in terms of diffusion-like migration of ligabs physics/0212040 and between protein cavities. The temporal behavior for the probability is obtained from numerical simulation and specified by two parameters: the time τ_{reb} of heme-ligand rebinding for the ligand localized inside the heme pocket and the time τ_{esc} of ligand escape from the pocket. The model is applied in the analysis of available experimental data for geminate reoxygenation of human hemoglobin HbA. Our simulation is in good agreement with the measurements. The analysis shows that the variation in pH of the solution (6.0<pH<9.4) results in considerable changes for τ_{reb} from 0.36 ns (at pH=8.5) up to 0.5 ns (pH=6.0) but effects slightly on the time τ_{esc} (τ_{esc} ~ 0.88 ns).
physics.bio-ph↗
The Genetic Code as a Periodic Table: Algebraic Aspects
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of amino acid conformational parameters. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.
physics.bio-ph↗
Entropy concepts and DNA investigations
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a maximum of heterogeneity. It falls in the block length interval [5,7]. Maximum distinction between natural and artificial sequences is shifted on 1-3 position from the maximum of heterogeneity to the right as for metric as for topological entropy. This point on the specificity of real DNA sequences in the interval.
cond-mat.stat-mech↗
Analysis of DNA chains by means of factorial moments
By means of the concept of Factorial Moments we examine DNA sequences from Yeast to distinguish coding and non-coding regions. It is found that the FM may be a powerful tool for analysis of DNA sequences. PACS numbers: 87.15.Cc,87.10.+e,87.14.Gg
cond-mat.soft↗
An optimal Q-state neural network using mutual information
Starting from the mutual information we present a method in order to find a hamiltonian for a fully connected neural network model with an arbitrary, finite number of neuron states, Q. For small initial correlations between the neurons and the patterns it leads to optimal retrieval performance. For binary neurons, Q=2, and biased patterns we recover the Hopfield model. For three-state neurons, Q=3, we find back the recently introduced Blume-Emery-Griffiths network hamiltonian. We derive its phase diagram and compare it with those of related three-state models. We find that the retrieval region is the largest.
cond-mat.dis-nn↗
Information decomposition of symbolic sequences
We developed a non-parametric method of Information Decomposition (ID) of a content of any symbolical sequence. The method is based on the calculation of Shannon mutual information between analyzed and artificial symbolical sequences, and allows the revealing of latent periodicity in any symbolical sequence. We show the stability of the ID method in the case of a large number of random letter changes in an analyzed symbolic sequence. We demonstrate the possibilities of the method, analyzing both poems, and DNA and protein sequences. In DNA and protein sequences we show the existence of many DNA and amino acid sequences with different types and lengths of latent periodicity. The possible origin of latent periodicity for different symbolical sequences is discussed.
math.SP↗
A crystal base for the genetic code
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases, tensor product of U_{q \to 0}(sl(2) \oplus sl(2)) representations. Such a construction might be compared to the baryon classification from quark building blocks in elementary particles physics, one of the main differences standing in the property of a crystal base to provide a natural order in the state constituents, this order being crucial in the codon. Then an operator ensuring the correspondence codon/amino-acid can be constructed out of the above algebra. It will be called the reading operator, and be such that two codons relative to the same (resp. different) amino-acid(s) acquire the same (resp. different) eigenvalue(s).
physics.bio-ph↗
Helicoidal model for DNA opening
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the helicoidal structure of the molecule. The small amplitude dynamics of the model is studied analytically : we derive small amplitude envelope solutions made of a breather in the radial variables combined with a kink in the angular variables, showing the role of the topological constraints associated to the helicoidal geometry. We check the stability of the solutions by numerical integration of the motion equations.
chao-dyn↗
Fractals from genomes: exact solutions of a biology-inspired problem
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be described. This scheme leads to a class of self-similar and self-overlapping fractals in the limit of infinitely long constotuent strings. The calculation of their exact dimensions and the counting of true and redundant avoided strings at different string lengths turn out to be one and the same problem. We give exact solution of the problem using two independent methods: the Goulden-Jackson cluster method in combinatorics and the method of formal language theory.
cond-mat.soft↗
On the structure pf genealogical trees in the presence of selection
We investigate through numerical simulations the effect of selection on two summary statistics for nucleotide variation in a sample of two genes from a population of N asexually reproducing haploid individuals. One is the mean time since two individuals had their most recent common ancestor ($\bar{T_s}$), and the other is the mean number of nucleotide differences between two genes in the sample ($\bar{d_s}$). In the case of diminishing epistasis, in which the deleterious effect of a new mutation is attenuated, we find that the scale of $\bar{d_s}$ with the population size depends on the mutation rate, leading then to the onset of a sharp threshold phenomenon as N becomes large.
cond-mat.stat-mech↗
Comparative statistical analysis of bacteria genomes in "word" context
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results obtained in the absent words investigation show the considerably nonrandom character of DNA texts. In character of autocorrelation function behavior in several genomes period 3 oscillations were found. Short range autocorrelations are present in short ($n=3$) words and practically absent in longer words.
cond-mat↗
Yang-Lee zeros and the helix-coil transition in a continuum model of polyalanine
We calculate the Yang-Lee zeros for characteristic temperatures of the helix-coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm-Bragg theory and supports recent claims that polyalanine exhibits a true phase transition. New estimates for critical exponents are presented and the relation of our results to the Lee-Yang theorem is discussed.
cond-mat.stat-mech↗
A protein model exhibiting three folding transitions
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of this mechanism (somewhat speculative), the model exhibits fundamental aspects of protein thermodynamics, as cold, and warm unfolding of the polypeptide chain, and hence decreasing the temperature below the cold unfolding the protein folds again, accordingly the heat capacity has three characteristic peaks. The cold and warm unfolding has a sharpness close to a two-state system, while the cold folding is a transition where the intermediate states in the folding is energetical close to the folded/unfolded states, yielding a less sharp transition. The entropy of the protein chain causes both the cold folding and the warm unfolding.
cond-mat↗
An Unusual Antagonistic Pleiotropy in the Penna Model for Biological Ageing
We combine the Penna Model for biological aging, which is based on the mutation-accumulation theory, with a sort of antagonistic pleiotropy. We show that depending on how the pleiotropy is introduced, it is possible to reproduce both the humans mortality, which increases exponentially with age, and fruitfly mortality, which decelerates at old ages, allowing the appearance of arbitrarily old Methuselah's.
cond-mat.stat-mech↗