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At least 451 records · Page 25Linked to original sources
arXiv2000

Crystalizing the genetic code

New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An operator which gives the correspondence between the amino-acids and the codons is now obtained for any known genetic code. The free energy released by base pairing of dinucleotides as well as the relative hydrophilicity and hydrophobicity of the dinucleosides are also computed. For the vertebrate series, a universal behaviour in the ratios of codon usage frequencies is put in evidence and is shown to fit nicely in our model. Then a first attempt to represent the mutations relative to the deletion of a pyrimidine by action of a suitable crystal spinor operator is proposed. Finally recent theoretical descriptions are reviewed and compared with our model.

physics.bio-ph↗
arXiv2000

Mechanism of Discordant Alternans in Spatially Homogeneous Tissue

Discordant alternans,the phenomenon of 2 separate cardiac tissue locations exhibiting action potential duration (APD) alternans of opposite phase, appears to be a potential mechanism for electrocardiographic T wave alternans, but its initiation mechanism is unknown. We studied behavior of one- and two- dimensional cardiac tissue spatially homogenous in all respects, including APD restitution and conduction velocity restitution, using the Beeler Reuter ion channel model. We found that discordant alternans was initiated when spatial gradients of APD arose dynamically, such as from fixed rate pacing of a cable end (sinus node scenario), or from fixed rate pacing at one site preceded by a single excitation wavefront from another site (ectopic focus scenario). In the sinus node scenario, conduction velocity restitution was necessary to initiate discordant alternans. Alternating regimes of concordant and discordant alternans arose along the length of the cable, with regimes delimited by nodes of fixed APD. The number of observable nodes depended upon pacing rate and tissue length. Differences in beat to beat conduction velocity values at steady state were small. In the ectopic focus scenario, variable conduction velocity was not required for induction of discrodant alternans. In both scenarios, stability of node position was dependent upon electrotonic coupling. Other mathematical models produced qualitatively similar results. We conclude that spatial inhomogeneities of electrical restitution are not requiredd to produce discordant alternans; rather, discordant alternans can arise dynamicaly from interaction of APD and conduction veolocity resstitution with single site pacing, or from APD restitution alone in two site pacing.

physics.bio-ph↗
arXiv2000

Signal Selection Based on Stochastic Resonance

Noise aids the encoding of continuous signals into pulse sequences by way of stochastic resonance and endows the encoding device with a preferred frequency. We study encoding by a threshold device based on the Ornstein-Uhlenbeck process, equivalent to the leaky integrate-and-fire neuron model. Preferred frequency, optimum noise intensity, and optimum signal-to-noise ratio are shown to be linearly related to the AC amplitude of the input signal. The DC component of the input tunes the device either into transmission (preferred frequency nearly independent of signal amplitude) or selection mode (frequency rising with amplitude). We argue that this behavior may facilitate selective signal processing in neurons.

physics.bio-ph↗
arXiv2000

Quasispecies evolution on a fitness landscape with a fluctuating peak

A quasispecies evolving on a fitness landscape with a single peak of fluctuating height is studied. In the approximation that back mutations can be ignored, the rate equations can be solved analytically. It is shown that the error threshold on this class of dynamic landscapes is defined by the time average of the selection pressure. In the case of a periodically fluctuating fitness peak we also study the phase-shift and response amplitude of the previously documented low-pass filter effect. The special case of a small harmonic fluctuation is treated analytically.

physics.bio-ph↗
arXiv2000

Optimal Mutation Rates in Dynamic Environments

In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal mutation rate is derived. Surprisingly it turns out that the optimal mutation rate per genome is approximately independent of genome length, something that also has been observed in nature. Simulations confirm the theoretical predictions. We also suggest an explanation for the difference in mutation frequency between RNA and DNA based organisms.

physics.bio-ph↗
arXiv2000

Contraction of a Bundle of Actin Filaments: 50 years after Szent-Gyorgyi

Biological systems are among the most challenging subjects for theoretical physicists, as well as experimentalists or simulationists. Physical principles should have been both constraints and guide-lines for the evolution of living systems over billions of years. One generally aims at clarifying what physical principles, possibly new ones, are behind the phenomena of biological interest and at understanding how they work within the entire biological world. In the present talk we describe an example of such an effort. Since the discovery of `superprecipitation' by Szent-Gyorgyi's group in 1940's, it has been a long puzzle how an assemblage of actin filaments with random orientation can contract in the presence of the two-headed myosin molecules undergoing actin-activated ATP-hydrolysis reaction. It is widely accepted that during the contraction the two-headed myosin mediates the relative sliding of two actin filaments whose polarity directions are not parallel but rather anti-parallel. But this fact solely does not account for the shortening. We propose a dynamical model which, upon numerical simulation, exhibits the shortening of an bundle of the actin filaments which are initially dirstributed randomly both in space along a line and in polarity direction. In the course of shortening several clusters of actins appears along the bundle. The model also shows the sorting of the actin filaments according to their polarity in the late stage. These findings are in accordance with the recent experiment by Takiguchi.

physics.bio-ph↗
arXiv2000

Optimal Mutation Rates on Static Fitness Landscpes

We study the evolution of mutation rates for an asexual population living on a static fitness landscape, consisting of multiple peaks forming an evolutionary staircase. The optimal mutation rate is found by maximizing the diffusion towards higher fitness. Surprisingly the optimal genomic copying fidelity is given by Q = e^(-1/ln(n)) (where n is the genome length), independent of all other parameters in the model. Simulations confirm this theoretical result. We also discuss the relation between the optimal mutation rate on static and dynamic fitness landscapes.

physics.bio-ph↗
arXiv2000

Large Scale-Invariant Fluctuations in Normal Blood Cell Counts: A sign of criticality?

All types of blood cells are formed by differentiation from a small self-maintaining population of pluri-potential stem cells in the bone marrow. Despite abundant information on the molecular aspects of division, differentiation, commitment and maturation of these cells, comparatively little is known about the dynamics of the system as a whole, and how it works to maintain this complex ``ecology'' in the observed normal ranges throughout life. Here we report unexpected large, scale-free, fluctuations detected from the first long-term analysis of the day-to-day variability of a healthy animal's blood cell counts measured over one thousand days. This scale-invariance cannot be accounted for by current theoretical models, and resembles some of the scenarios described for self-organized criticality.

physics.bio-ph↗
arXiv2000

Coherence in a simple network: Implication for brain function

In a many body system, constituents interact with each other, forming a recursive pattern of interaction and giving rise to many interesting phenomena. Based upon concepts of the modern many body theory, a model for a generic many body system is developed. A novel approach is proposed to investigate the general features in such a system. An interesting phase transition in the system is found. Possible link to brain dynamics is discussed. It is shown how some of the basic brain processes, such as learning and memory, find therein a natural explanation.

physics.bio-ph↗
arXiv2000

Damage of cellular material under simultaneous application of pressure and pulsed electric field

Influence of pulsed electric field (PEF) simultaneous to pressure treatment on moisture expression from fine-cut cellular raw material has been investigated. Dependencies of specific conductivity $σ$, liquid yield $Y$, instantaneous flow rate $v$ and qualitative juice characteristics at different modes of PEF treatment are discussed. Three main consolidation phases were observed in a case of mechanical expression. A unified approach is proposed for liquid yield data analysis allowing to reduce the data scattering caused by differences in the quality of samples. Simultaneous application of pressure and PEF treatment allows to reveal a passive form of electrical damage. Pressure provokes the damage of defected cells, enhances diffusion migration of moisture in porous cellular material and depresses the cell resealing processes. PEF application at a moment when a sample specific electrical conductivity reaches minimum and pressure achieves its constant value seemed to be the most optimal.

physics.bio-ph↗
arXiv2001

Evolution: The Case of the Glyceraldehyde-3-Phosphate Dehydrogenase Gene

The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucose. The gene that produces the GAPDH is therefore present in a wide class of organisms. We show that for this gene the average value of the fluctuations in nucleotide distribution in the codons, normalized to strand bias, provides a reasonable measure of how the gene has evolved in time.

physics.bio-ph↗
arXiv2000

Noise Delays Bifurcation in a Positively Coupled Neural Circuit

We report a noise induced delay of bifurcation in a simple pulse-coupled neural circuit. We study the behavior of two neural oscillators, each individually governed by saddle-node dynamics, with reciprocal excitatory synaptic connections. In the deterministic circuit, the synaptic current amplitude acts as a control parameter to move the circuit from a mono-stable regime through a bifurcation into a bistable regime. In this regime stable sustained anti-phase oscillations in both neurons coexist with a stable rest state. We introduce a small amount of random current into both neurons to model possible randomly arriving synaptic inputs. We find that such random noise delays the onset of bistability, even though in decoupled neurons noise tends to advance bifurcations and the circuit has only excitatory coupling. We show that the delay is dependent on the level of noise and suggest that a curious stochastic ``anti-resonance'' is present.

physics.bio-ph↗
arXiv2001

A minimum principle in mRNA editing ?

mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of the crystal basis model of the genetic code introduced by the authors.

physics.bio-ph↗
arXiv2000

On Optimality in Auditory Information Processing

We study limits for the detection and estimation of weak sinusoidal signals in the primary part of the mammalian auditory system using a stochastic Fitzhugh-Nagumo (FHN) model and an action-reaction model for synaptic plasticity. Our overall model covers the chain from a hair cell to a point just after the synaptic connection with a cell in the cochlear nucleus. The information processing performance of the system is evaluated using so called phi-divergences from statistics which quantify a dissimilarity between probability measures and are intimately related to a number of fundamental limits in statistics and information theory (IT). We show that there exists a set of parameters that can optimize several important phi-divergences simultaneously and that this set corresponds to a constant quiescent firing rate (QFR) of the spiral ganglion neuron. The optimal value of the QFR is frequency dependent but is essentially independent of the amplitude of the signal (for small amplitudes). Consequently, optimal processing according to several standard IT criteria can be accomplished for this model if and only if the parameters are ``tuned'' to values that correspond to one and the same QFR. This offers a new explanation for the QFR and can provide new insight into the role played by several other parameters of the peripheral auditory system.

physics.bio-ph↗
arXiv2000

Compound Poisson Statistics and Models of Clustering of Radiation Induced DNA Double Strand Breaks

According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks (DSBs) which are formed when the breaks occur in both DNA strands and are directly opposite or separated by only a few base pairs. The paper discusses a model of clustered DSB formation viewed in terms of compound Poisson process along with the predictive assay of the formalism in application to experimental data.

physics.bio-ph↗
arXiv2000

Evolutionary conservation of the folding nucleus

In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: 1) grouping of amino acids into classes according to their physical-chemical properties and 2) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological ``signals'' from conservation profiles disappear.

physics.bio-ph↗
arXiv2000

Biology and Thermodynamics: Seemingly-Opposite Phenomena in Search of a Unified Paradigm

It is probably not a coincidence that two of the pioneers of thermodynamics, Helmholtz and Mayer, were physicians. Thermodynamics studies the transformations of energy, and such transformations ceaselessly take place in all living systems (probably with important differences between the states of health and disease). Moreover, thermodynamics studies the elusive notions of order and disorder, which are also, respectively, the very hallmarks of life and death. These similarities suggest that thermodynamics might provide a unifying paradigm for many life sciences, explaining the multitude of life's manifestations on the basis of a few basic physical principles. In this article we introduce some basic thermodynamic concepts and point out their usefulness for the biologist and the physician. We hope to show that thermodynamics enables looking at the riddles of life from a new perspective and asking some new fruitful questions.

physics.bio-ph↗