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PubMed2006

Adsorption of phenylacetylene on Si(100)-2 x 1: kinetics and structure of the adlayer.

Direct adsorption of phenylacetylene on clean silicon surface Si(100)-2 x 1 is studied in ultrahigh vacuum (UHV). The combination of scanning tunnel microscopy (STM) and surface differential reflectance spectroscopy (SDRS) with Monte Carlo calculations are put together to draw a realistic kinetic model of the evolution of the surface coverage as a function of the molecular exposure. STM images of weakly covered surfaces provide evidence of two very distinct adsorption geometries for phenylacetylene, with slightly different initial sticking probabilities. One configuration is detected with STM as a bright spot that occupies two dangling bonds of a single dimer, whereas the other configuration occupies three dangling bonds of adjacent dimers. These data are used to implement a Monte Carlo model which further serves to design an accurate kinetic model. The resulting evolution toward saturation is compared to the optical data from surface differential reflectance spectroscopy (SDRS). SDRS is an in situ technique that monitors the exact proportion of affected adsorption sites and therefore gives access to the surface coverage which is evaluated at 0.65. We investigate the effect of surface temperature on this adsorption mechanism and show that it has no major effect either on kinetics or on structure, unless it passes the threshold of dissociation measured at ca. 200 degrees C. This offers a comprehensive image of the whole adsorption process of phenylacetylene from initial up to complete saturation.

Journal Article↗

PubMed1980

Regulatory gene adaptation: an evolutionary model.

There is increasing support for the notion that changes in regulatory loci have played a major role in eukaryotic evolution. Assuming a model of genetic regulation based upon presently accepted views of the organisation of the eukaryotic genome and basic models of evolutionary genetics, one can provide a context for speculation about the advantages and disadvantages of adaptation via regulatory genes. As additional information is obtained on particular regulatory systems, the evolutionary genetic model can be modified and expanded.

Adaptation, Biological↗

PubMed2004

Microsatellite mutation models: insights from a comparison of humans and chimpanzees.

Using genomic data from homologous microsatellite loci of pure AC repeats in humans and chimpanzees, several models of microsatellite evolution are tested and compared using likelihood-ratio tests and the Akaike information criterion. A proportional-rate, linear-biased, one-phase model emerges as the best model. A focal length toward which the mutational and/or substitutional process is linearly biased is a crucial feature of microsatellite evolution. We find that two-phase models do not lead to a significantly better fit than their one-phase counterparts. The performance of models based on the fit of their stationary distributions to the empirical distribution of microsatellite lengths in the human genome is consistent with that based on the human-chimp comparison. Microsatellites interrupted by even a single point mutation exhibit a twofold decrease in their mutation rate when compared to pure AC repeats. In general, models that allow chimps to have a larger per-repeat unit slippage rate and/or a shorter focal length compared to humans give a better fit to the human-chimp data as well as the human genomic data.

Animals↗

PubMed1996

The evolution of degrees of cooperation.

The Prisoner's Dilemma has been widely studied as a model for the evolution of cooperation, and most of this work has dealt with agents who either cooperate or not. In this paper we look at the consequences of allowing agents to have intermediate levels of cooperation, and to update these levels over time. The familiar strategy of "tit for tat" emerges as a robust mode of behaviour, yet there are important differences between this case and that of "all or nothing" cooperation.

Animals↗

PubMed1993

Ubiquitins revisited: further examples of within- and between-locus concerted evolution.

Ubiquitin genes provide a model for studying the effects of concerted evolution on the evolution of a family of short repeated sequences. Previous work has demonstrated the occurrence of within-locus concerted evolution and raised the question of the effectiveness of between-locus concerted evolution for ubiquitin repeats. In this study comparative analysis of additional nucleotide sequences of ubiquitin tandem repeats provides further details of within-locus concerted evolution. Moreover, the availability of multiple polyubiquitin loci and ubiquitin fusion loci within a species makes possible the detection of between-locus concerted evolution. These data indicate that concerted evolution is an effective force for homogenizing repeats between, as well as within, loci.

Animals↗

PubMedDate not supplied

Classical and quantum dynamics on p-adic trees of ideas.

We propose mathematical models of information processes of unconscious and conscious thinking (based on p-adic number representation of mental spaces). Unconscious thinking is described by classical cognitive mechanics (which generalizes Newton's mechanics). Conscious thinking is described by quantum cognitive mechanics (which generalizes the pilot wave model of quantum mechanics). The information state and motivation of a conscious cognitive system evolve under the action of classical information forces and a new quantum information force, namely, conscious force. Our model might provide mathematical foundations for some cognitive and psychological phenomena: collective conscious behavior, connection between physiological and mental processes in a biological organism, Freud's psychoanalysis, hypnotism, homeopathy. It may be used as the basis of a model of conscious evolution of life.

Cognition↗

PubMed2004

Imprint of evolution on protein structures.

We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence duplication and subsequent point mutations. A new gene's ability to fold into a stable and unique structure is tested each time through direct kinetic folding simulations. Where possible, the algorithm accepts the new sequence and structure and thus a "new protein structure" is born. During the course of each run, this model evolutionary algorithm provides several thousand new proteins with diverse structures. Analysis of evolved structures shows that later evolved structures are more designable than seed structures as judged by recently developed structural determinant of protein designability, as well as direct estimate of designability for selected structures by thermodynamic sampling of their sequence space. We test the significance of this trend predicted on lattice models on real proteins and show that protein domains that are found in eukaryotic organisms only feature statistically significant higher designability than their prokaryotic counterparts. These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.

Algorithms↗

PubMed2007

Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.

Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.

Aspergillus nidulans↗

PubMed1998

The forces driving molecular evolution.

Competitive replication among RNA or DNA molecules at linear and non-linear rates of propagation has been reviewed from the perspective of a recent physicochemical model of molecular evolution and the findings are applied to pre-replication, prebiotic and biological evolution. A system of competitively replicating molecules was seen to follow a path of least action on both its thermodynamic and kinetic branch, in evolving toward steady state kinetics and equilibrium for the nucleotide condensation reaction. Stable and unstable states of coexistence, between competing molecular species, arise at nonlinear rates of propagation, and they derive from an equilibrium between kinetic forces. The de novo formation of self-replicating RNA molecules involves damping of these scalar forces, error tolerance and RNA driven strand separation. Increases in sequence complexity in the transition to self-replication does not exceed the free energy dissipated in RNA synthesis. Retrodiction of metabolic pathways and phylogenetic evidence point to the occurrence of three pre-replication metabolic systems, driven by autocatalytic C-fixation cycles. Thermodynamic and kinetic factors led to the replication take over. Biological evolution was found to involve resource capture, in addition to competition for a shared resource.

Archaea↗

PubMed2004

Strong altruism can evolve in randomly formed groups.

Although the conditions under which altruistic behaviors evolve continue to be vigorously debated, there is general agreement that altruistic traits involving an absolute cost to altruists (strong altruism) cannot evolve when populations are structured with randomly formed groups. This conclusion implies that the evolution of such traits depends upon special environmental conditions or additional organismic capabilities that enable altruists to interact with each other more than would be expected with random grouping. Here we show, using both analytic and simulation results, that the positive assortment necessary for strong altruism to evolve does not require these additional mechanisms, but merely that randomly formed groups exist for more than one generation. Conditions favoring the selection of altruists, which are absent when random groups initially form, can naturally arise even after a single generation within groups-and even as the proportion of altruists simultaneously decreases. The gains made by altruists in a second generation within groups can more than compensate for the losses suffered in the first and in this way altruism can ratchet up to high levels. This is true even if altruism is initially rare, migration between groups allowed, homogeneous altruist groups prohibited, population growth restricted, or kin selection precluded. Until now random group formation models have neglected the significance of multigenerational groups-even though such groups are a central feature of classic "haystack" models of the evolution of altruism. We also explore the important role that stochasticity (effectively absent in the original infinite models) plays in the evolution of altruism. The fact that strong altruism can increase when groups are periodically and randomly formed suggests that altruism may evolve more readily and in simpler organisms than is generally appreciated.

Altruism↗

PubMed1999

Mathematical models of diffusion-limited gas bubble dynamics in tissue.

Mathematical models of bubble evolution in tissue have recently been incorporated into risk functions for predicting the incidence of decompression sickness (DCS) in human subjects after diving and/or flying exposures. Bubble dynamics models suitable for these applications assume the bubble to be either contained in an unstirred tissue (two-region model) or surrounded by a boundary layer within a well-stirred tissue (three-region model). The contrasting premises regarding the bubble-tissue system lead to different expressions for bubble dynamics described in terms of ordinary differential equations. However, the expressions are shown to be structurally similar with differences only in the definitions of certain parameters that can be transformed to make the models equivalent at large tissue volumes. It is also shown that the two-region model is applicable only to bubble evolution in tissues of infinite extent and cannot be readily applied to bubble evolution in finite tissue volumes to simulate how such evolution is influenced by interactions among multiple bubbles in a given tissue. Two-region models that are incorrectly applied in such cases yield results that may be reinterpreted in terms of their three-region model equivalents but only if the parameters in the two-region model transform into consistent values in the three-region model. When such transforms yield inconsistent parameter values for the three-region model, results may be qualitatively correct but are in substantial quantitative error. Obviation of these errors through appropriate use of the different models may improve performance of probabilistic models of DCS occurrence that express DCS risk in terms of simulated in vivo gas and bubble dynamics.

Air Pressure↗

PubMedDate not supplied

Mathematical model for the AIDS epidemic's evolution in Romania.

The individuals are distributed in 9 risk groups (adults and children), in which an HIV transmission way is predominant. Taking into account a simplified graph of the HIV infection evolution, kinetic equations for the number of individuals from each risk group--situated in various stages of HIV infection--are written. The approximative solutions of these equations give us: the characteristic exponents of the temporal evolutions of the main and secondary local epidemics; the ratios Ci/Bi and Di/Bi of asymptomatically contaminated and dead (as consequence of AIDS)--versus symptomatically contaminated; the onset of local epidemics in various risk groups; the relative amplitude of the secondary local epidemics versus the main local ones.

Acquired Immunodeficiency Syndrome↗

PubMed1998

Changes in matrix metalloproteinases during the evolution of interstitial renal fibrosis in a rat experimental model.

The aim of the present study was to analyze the matrix metalloproteinase (MMP) activity during the evolution of interstitial renal fibrosis in a rat experimental model of unilateral ureteral obstruction. The interstitial type I collagenase and the gelatinolytic activities were analyzed by radiolabeled substrate degradation. Interstitial collagenase activity was low at all times while gelatinolytic activity increased on day 6 of evolution, with a decrease in activity from this point. The use of organomercurials revealed the presence of latent enzyme in all cases. Normal kidney samples contained MMP-9 in both active and proenzyme forms as revealed by zymography. On day 3 MMP-9 dimers appeared, and increased activity was observed until day 6. A decrease in the gelatinolytic activity was detected from days 9-15 of evolution. This observation was confirmed by Western blot analysis that revealed the presence of proMMP-9 mainly from days 6-12. Tissue inhibitor of metalloproteinase-1 (TIMP-1) was also detected alone and in combination with proMMP-1 and MMP-1, particularly from days 6-15 of evolution. The presence of MMP-9 and MMP-1 was detected in the cytoplasm of cortical tubular cells by immunohistochemistry, with no difference between the experimental and the normal kidneys. There was also an increase in collagen concentration from day 3 after surgery that increased during the entire evolution of the experimental model. This work reveals that the decrease in the MMP-9 and MMP-1 enzymatic activity, due to their interaction with TIMP-1 and to the lack of activation of the latent forms, may participate in the excessive collagen deposit during the evolution of experimental interstitial renal fibrosis.

Animals↗

PubMed2004

Evaluating alternative hypotheses for the origin of eusociality in corbiculate bees.

We use a likelihood-based statistical test to evaluate the extent to which the available molecular data sets can be used to falsify alternative phylogenetic hypotheses describing the inter-relationship among corbiculate bee tribes. Based on the results of this test, we explore three alternative models of behavioural character state evolution and evaluate the support each model has for single-origin versus dual-origin hypotheses for 'highly' eusocial behaviour. We show that only one of four data sets could statistically reject any of the 15 possible outgroup-rooted phylogenetic hypotheses. However, a cytochrome b data set rejected all but three alternative topologies. Using this information, a simple model of behavioural character state evolution, in which transitions between solitary/communal, 'primitively' eusocial, and 'highly' eusocial are unconstrained, supports single-origin hypotheses for 'highly' eusocial behaviour, in spite of phylogenetic uncertainty. By contrast, an ordered model, in which 'highly' eusocial is constrained to be an evolutionarily terminal state, supports a dual-origins hypothesis. Our results show that the molecular phylogenetic evidence favouring a dual-origins hypothesis for 'highly' eusocial behaviour is, at present, conditional on information from one gene (cyt b) and on specific, though likely realistic, assumptions regarding the nature of eusocial evolution.

Animals↗

PubMed1998

The application of model-based complexity inference method to molecular evolution analysis.

In this study, a new method based on the concept of complexity in inductive inference is proposed for reconstructing molecular phylogenetic tree. This method describes the complexity of molecular phylogenetic tree by three terms, which are related to tree topology, the branch lengths and fitness between the model and data measured by likelihood function. The computer simulation is used to investigate the efficiency of this method. The results suggest that this method is superior to the traditional methods because it avoids excess-complexity in the tree model estimation available from DNA sequence.

Base Sequence↗

PubMed2002

Variable selection by an evolution algorithm using modified Cp based on MLR and PLS modeling: QSAR studies of carcinogenicity of aromatic amines.

The variable selection in QSAR studies by MLR and PLS modeling has been performed using the evolution algorithm (EA). The Cp statistic has been modified and used as the objective function in the EA search for different combinations of molecular descriptors. For MLR modeling a few information-rich descriptors are selected for model formulation. In PLS modeling, the proposed procedure selects a relatively large number of information-containing descriptors, and a PLS model is formulated based on a few latent variables, which are linear combinations of the selected descriptors. The proposed procedures were used for the prediction of carcinogenicity of aromatic amines.

Algorithms↗

PubMed2001

An evolutionary model for the origin of non-randomness, long-range order and fractality in the genome.

We present a model for genome evolution, comprising biologically plausible events such as transpositions inside the genome and insertions of exogenous sequences. This model attempts to formulate a minimal proposition accounting for key statistical properties of genomes, avoiding, as far as possible, unsupportable hypotheses for the remote evolutionary past. The statistical properties that are observed in genomic sequences and are reproduced by the proposed model are: (i) deviations from randomness at different length scales, measured by suitable algorithms, (ii) a special form of size distribution (power law distribution) characterising different levels of genome organisation in the non-coding, and (iii) extensive resemblance in the alternation of coding and non-coding regions at several length scales (self-similarity) in long genomic sequences of higher eukaryotes.

DNA↗

PubMed1998

Reconstructing the Evolution of Viviparity and Placentation.

A recent paper in J. theor. Biol. has challenged the proposed application of punctuated equilibrium models to the evolution of reptilian viviparity and placentation. While clarifying some aspects of the models, the paper's criticisms reflect misinterpretations of the literature and an unnecessary reluctance to apply punctuationist concepts to extant taxa. The punctuated equilibrium model retains potential for clarification of the patterns of stasis and episodic change that may well have characterized squamate reproductive history.Copyright 1998 Academic Press Limited

Journal Article↗