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At least 667 records · Page 37Linked to original sources

arXiv2003

Thermodynamic and Kinetic Analysis of Sensitivity Amplification in Biological Signal Transduction

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, $ΔG$ (phosphorylation potential), controls the amplification and sensitivity of the switch-like cellular module; the response coefficient of the sensitivity amplification approaches the optimal 1 and the Hill coefficient increases with increasing $ΔG$. We discover that zero-order ultrasensitivity is mathematically equivalent to allosteric cooperativity. Furthermore, we show that the high amplification in ultrasensitivity is mechanistically related to the proofreading kinetics for protein biosynthesis. Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein.

physics.bio-ph↗

arXiv2000

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↗

arXiv2000

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↗

arXiv2001

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↗

arXiv2001

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↗

arXiv2003

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↗

arXiv1998

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↗

arXiv1999

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↗

arXiv1999

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↗

arXiv1999

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↗

arXiv2000

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↗

arXiv2000

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↗

arXiv2000

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↗

arXiv2001

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↗

arXiv2001

Justification of Sexual Reproduction by Modified Penna Model of Ageing

We generalize the standard Penna bit-string model of biological ageing by assuming that each deleterious mutation diminishes the survival probability in every time interval by a small percentage. This effect is added to the usual lethal but age-dependent effect of the same mutation. We then find strong advantages or disadvantages of sexual reproduction (with males and females) compared to asexual cloning, depending on parameters.

cond-mat.stat-mech↗

arXiv2001

Phenomenological Theory of Survival

Theoretical analysis proves that human survivability is dominated by an unusual physical, rather than biological, mechanism, which yields an exact law. The law agrees with all experimental data, but, contrary to existing theories, it is the same for an entire species, i.e., it is independent of the population, its phenotypes, environment and history. The law implies that the survivability changes with environment via phase transitions, which are simultaneous for all generations. They allow for a rapid (within few percent of the life span) and significant increase in the life expectancy even above its value at a much earlier age.

physics.bio-ph↗

arXiv2001

Simulated emergence of cyclic sexual-asexual reproduction

Motivated by the cyclic pattern of reproductive regimes observed in some species of green flies (``{\it aphids}''), we simulate the evolution of a population enduring harsh seasonal conditions for survival. The reproductive regime of each female is also seasonal in principle and genetically acquired, and can mutate for each newborn with some small probability. The results show a sharp transition at a critical value of the survival probability in the winter, between a reproductive regime in the fall that is predominantly sexual, for low values of this probability, or asexual, for high values.

cond-mat.stat-mech↗

arXiv2001

Multifractal characterisation of length sequences of coding and noncoding segments in a complete genome

The coding and noncoding length sequences constructed from a complete genome are characterised by multifractal analysis. The dimension spectrum $D_{q}$ and its derivative, the 'analogous' specific heat $C_{q}$, are calculated for the coding and noncoding length sequences of bacteria, where $q$ is the moment order of the partition sum of the sequences. From the shape of the $% D_{q}$ and $C_{q}$ curves, it is seen that there exists a clear difference between the coding/noncoding length sequences of all organisms considered and a completely random sequence. The complexity of noncoding length sequences is higher than that of coding length sequences for bacteria. Almost all $D_{q}$ curves for coding length sequences are flat, so their multifractality is small whereas almost all $D_{q}$ curves for noncoding length sequences are multifractal-like. We propose to characterise the bacteria according to the types of the $C_{q}$ curves of their noncoding length sequences.

physics.bio-ph↗