trans gene regulation in adaptive evolution: A genetic algorithm model

This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate—“plastic”—loci, where a plastic locus had a finite probability in each generation of functioning (being switched “on”) or not functioning (being switched “off”). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation.

Does acoustic adaptation drive vertical stratification? A test in a tropical cricket assemblage

In species-rich assemblages, differential utilization of vertical space can be driven by resource availability. For animals that communicate acoustically over long distances under habitat-induced constraints, access to an effective transmission channel is a valuable resource. The acoustic adaptation hypothesis suggests that habitat acoustics imposes a selective pressure that drives the evolution of both signal structure and choice of calling sites by signalers. This predicts that species-specific signals transmit best in native habitats. In this study, we have tested the hypothesis that vertical stratification of calling heights of acoustically communicating species is driven by acoustic adaptation. This was tested in an assemblage of 12 coexisting species of crickets and katydids in a tropical wet evergreen forest. We carried out transmission experiments using natural calls at different heights from the forest floor to the canopy. We measured signal degradation using 3 different measures: total attenuation, signal-to-noise ratio (SNR), and envelope distortion. Different sets of species supported the hypothesis depending on which attribute of signal degradation was examined. The hypothesis was upheld by 5 species for attenuation and by 3 species each for SNR and envelope distortion. Only 1 species of 12 provided support for the hypothesis by all 3 measures of signal degradation. The results thus provided no overall support for acoustic adaptation as a driver of vertical stratification of coexisting cricket and katydid species.

EESM-Based Link Adaptation in Point-to-Point and Multi-Cell OFDM Systems: Modeling and Analysis

In contemporary wideband orthogonal frequency division multiplexing (OFDM) systems, such as Long Term Evolution (LTE) and WiMAX, different subcarriers over which a codeword is transmitted may experience different signal-to-noise-ratios (SNRs). Thus, adaptive modulation and coding (AMC) in these systems is driven by a vector of subcarrier SNRs experienced by the codeword, and is more involved. Exponential effective SNR mapping (EESM) simplifies the problem by mapping this vector into a single equivalent fiat-fading SNR. Analysis of AMC using EESM is challenging owing to its non-linear nature and its dependence on the modulation and coding scheme. We first propose a novel statistical model for the EESM, which is based on the Beta distribution. It is motivated by the central limit approximation for random variables with a finite support. It is simpler and as accurate as the more involved ad hoc models proposed earlier. Using it, we develop novel expressions for the throughput of a point-to-point OFDM link with multi-antenna diversity that uses EESM for AMC. We then analyze a general, multi-cell OFDM deployment with co-channel interference for various frequency-domain schedulers. Extensive results based on LTE and WiMAX are presented to verify the model and analysis, and gain new insights.

Bi-Domain Protein Tyrosine Phosphatases Reveal an Evolutionary Adaptation to Optimize Signal Transduction

Significance: The bi-domain protein tyrosine phosphatases (PTPs) exemplify functional evolution in signaling proteins for optimal spatiotemporal signal transduction. Bi-domain PTPs are products of gene duplication. The catalytic activity, however, is often localized to one PTP domain. The inactive PTP domain adopts multiple functional roles. These include modulation of catalytic activity, substrate specificity, and stability of the bi-domain enzyme. In some cases, the inactive PTP domain is a receptor for redox stimuli. Since multiple bi-domain PTPs are concurrently active in related cellular pathways, a stringent regulatory mechanism and selective cross-talk is essential to ensure fidelity in signal transduction. Recent Advances: The inactive PTP domain is an activator for the catalytic PTP domain in some cases, whereas it reduces catalytic activity in other bi-domain PTPs. The relative orientation of the two domains provides a conformational rationale for this regulatory mechanism. Recent structural and biochemical data reveal that these PTP domains participate in substrate recruitment. The inactive PTP domain has also been demonstrated to undergo substantial conformational rearrangement and oligomerization under oxidative stress. Critical Issues and Future Directions: The role of the inactive PTP domain in coupling environmental stimuli with catalytic activity needs to be further examined. Another aspect that merits attention is the role of this domain in substrate recruitment. These aspects have been poorly characterized in vivo. These lacunae currently restrict our understanding of neo-functionalization of the inactive PTP domain in the bi-domain enzyme. It appears likely that more data from these research themes could form the basis for understanding the fidelity in intracellular signal transduction.

Characterizing the Impact of Feedback Delays on Wideband Rate Adaptation

In contemporary orthogonal frequency division multiplexing (OFDM) systems, such as Long Term Evolution (LTE), LTE-Advanced, and WiMAX, a codeword is transmitted over a group of subcarriers. Since different subcarriers see different channel gains in frequency-selective channels, the modulation and coding scheme (MCS) of the codeword must be selected based on the vector of signal-to-noise-ratios (SNRs) of these subcarriers. Exponential effective SNR mapping (EESM) maps the vector of SNRs into an equivalent flat-fading SNR, and is widely used to simplify this problem. We develop a new analytical framework to characterize the throughput of EESM-based rate adaptation in such wideband channels in the presence of feedback delays. We derive a novel accurate approximation for the throughput as a function of feedback delay. We also propose a novel bivariate gamma distribution to model the time evolution of EESM between the times of estimation and data transmission, which facilitates the analysis. These are then generalized to a multi-cell, multi-user scenario with various frequency-domain schedulers. Unlike prior work, most of which is simulation-based, our framework encompasses both correlated and independent subcarriers and various multiple antenna diversity modes; it is accurate over a wide range of delays.

Evolution of multivariant microstructures with anisotropic misfit: A phase field study

We study, in two dimensions, the effect of misfit anisotropy on microstructural evolution during precipitation of an ordered beta phase from a disordered alpha matrix; these phases have, respectively, 2- and 6-fold rotation symmetries. Thus, precipitation produces three orientational variants of beta phase particles, and they have an anisotropic (and crystallographically equivalent) misfit strain with the matrix. The anisotropy in misfit is characterized using a parameter t = epsilon(yy)/epsilon(xx), where epsilon(xx) and epsilon(yy) are the principal components of the misfit strain tensor. Our phase field, simulations show that the morphology of beta phase particles is significantly influenced by 1, the level of misfit anisotropy. Particles are circular in systems with dilatational misfit (t = 1), elongated along the direction of lower principal misfit when 0 < t < 1 and elongated along the invariant direction when - 1 <= t <= 0. In the special case of a pure shear misfit strain (t = - 1), the microstructure exhibits star, wedge and checkerboard patterns; these microstructural features are in agreement with those in Ti-Al-Nb alloys.

Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Evolution of electronic structure with dimensionality in divalent nickelates

We investigate the evolution of electronic structure with dimensionality (d) of Ni-O-Ni connectivity in divalent nickelates, NiO (3-d), La2NiO4, Pr2NiO4 (2-d), Y2BaNiO5 (1-d) and Lu2BaNi5 (0-d), by analyzing the valence band and the Ni 2p core-level photoemission spectra in conjunction with detailed many-body calculations including full multiplet interactions. Experimental results exhibit a reduction in the intensity of correlation-induced satellite features with decreasing dimensionality. The calculations based on the cluster model, but evaluating both Ni 3d and O 2p related photoemission processes on the same footing, provide a consistent description of both valence-band and core-level spectra in terms of various interaction strengths. While the correlation-induced satellite features in NiO is dominated by poorly screened d(8) states as described in the existing literature, we find that the satellite features in the nickelates with lower dimensional Ni-O-Ni connectivity are in fact dominated by the over-screened d(10)L(2) states. It is found that the changing electronic structure with the dimensionality is primarily driven by two factors: (i) a suppression of the nonlocal contribution to screening; and (ii) a systematic decrease of the charge-transfer energy Delta driven by changes in the Madelung potential. [S0163-1829(99)09619-8].

Finite volume evolution Galerkin method for hyperbolic conservation laws with spatially varying flux functions

We present a generalization of the finite volume evolution Galerkin scheme [M. Lukacova-Medvid'ova,J. Saibertov'a, G. Warnecke, Finite volume evolution Galerkin methods for nonlinear hyperbolic systems, J. Comp. Phys. (2002) 183 533-562; M. Luacova-Medvid'ova, K.W. Morton, G. Warnecke, Finite volume evolution Galerkin (FVEG) methods for hyperbolic problems, SIAM J. Sci. Comput. (2004) 26 1-30] for hyperbolic systems with spatially varying flux functions. Our goal is to develop a genuinely multi-dimensional numerical scheme for wave propagation problems in a heterogeneous media. We illustrate our methodology for acoustic waves in a heterogeneous medium but the results can be generalized to more complex systems. The finite volume evolution Galerkin (FVEG) method is a predictor-corrector method combining the finite volume corrector step with the evolutionary predictor step. In order to evolve fluxes along the cell interfaces we use multi-dimensional approximate evolution operator. The latter is constructed using the theory of bicharacteristics under the assumption of spatially dependent wave speeds. To approximate heterogeneous medium a staggered grid approach is used. Several numerical experiments for wave propagation with continuous as well as discontinuous wave speeds confirm the robustness and reliability of the new FVEG scheme.

Microstructural evolution and mechanical characteristics in nanocrystalline nickel with a bimodal grain-size distribution

An attractive microstructural possibility for enhancing the ductility of high-strength nanocrystals is to develop a bimodal grain-size distribution, in which the fine grains provide strength, and the coarser grains enable strain hardening. Annealing of nanocrystalline Ni over a range of temperatures and times led to microstructures with varying volume fractions of coarse grains and a change in texture. Tensile tests revealed a drastic reduction in ductility with increasing volume fraction of coarse grains. The reduction in ductility may be related to the segregation of sulphur to grain boundaries.

Study of texture evolution in metastable beta-Ti alloy as a function of strain path and its effect on alpha transformation texture

Texture evolution in a low cost beta titanium alloy was studied for different modes of rolling and heat treatments. The alloy was cold rolled by unidirectional and multi-step cross rolling. The cold rolled material was either aged directly or recrystallized and then aged. The evolution of texture in alpha and beta phases were studied. The rolling texture of beta phase that is characterized by the gamma fiber is stronger for MSCR than UDR; while the trend is reversed on recrystallization. The mode of rolling affects alpha transformation texture on aging with smaller alpha lath size and stronger alpha texture in UDR than in MSCR. The defect structure in beta phase influences the evolution of a texture on aging. A stronger defect structure in beta phase leads to variant selection with the rolled samples showing fewer variants than the recrystallized samples.

Oded Schramm and the Schramm-Loewner evolution: In memoriam

Oded Schramm, the inventor of the stochastic Loewner evolution (SLE), died on 1 September 2008 in a tragic hiking accident in the Cascades Mountains. He was forty-six. He is survived by his wife and two children.

Effects of the filling process on the evolution of the mushy zone and macrosegregation in alloy casting

A numerical model of the entire casting process starting from the mould filling stage to complete solidification is presented. The model takes into consideration any phase change taking place during the filling process. A volume of fluid method is used for tracking the metal–air interface during filling and an enthalpy based macro-scale solidification model is used for the phase change process. The model is demonstrated for the case of filling and solidification of Pb–15 wt%Sn alloy in a side-cooled two-dimensional rectangular cavity, and the resulting evolution of a mushy region and macrosegregation are studied. The effects of process parameters related to filling, namely degree of melt superheat and filling velocity on macrosegregation in the cavity, are also investigated. Results show significant differences in the progress of the mushy zone and macrosegregation pattern between this analysis and conventional analysis without the filling effect.

Cultural-Evolution of Ecological Prudence

Animals often behave in a profligate fashion and decimate the populations of plants and animals they depend upon. They may, however, evolve prudent behaviour under special conditions, namely when such prudence greatly enhances the success of populations that are not too prone to invasions by profligate individuals. Cultural evolution in human societies can also lead to the adoption of prudent practices under similar conditions. These are more likely to be realized in stable environments in which the human populations tend to grow close to the carrying capacity, when the human groups are closed, and when the technology is stagnant. These conditions probably prevailed in the hunter—gatherer societies of the tropics and subtropics, and led to the adoption of a number of socially imposed restraints on the use of plant and animal resources. Such practices were rationalized in the form of Nature-worship. The Indian caste society became so organized as to fulfill these conditions, and gave rise to two religions, Buddhism and Jainism, which emphasize compassion towards all forms of life. The pastoral nomads of the middle east, on the other hand, lived in an environment which militated against prudence, and these societies gave rise to religions like Christianity, which declared war on nature. As the ruling elite and state have grown in power, they have tried to wrest control of natural resources from the local communities. This has sometimes resulted in conservation and prudent use under guidance from the state, but has often led to conflicts with local populations to the detriment of prudent behaviour. Modern technological progress has also often removed the need for conservation, as when availability of coal permitted the deforestation of England. While modern scientific understanding has led to a better appreciation of the need for prudence, the prevailing social and economic conditions often militate against any implementation of the understanding, as is seen from the history of whaling. However, the imperative for survival of the poor from the Third-World countries may finally bring about conditions in which ecological prudence may once again come to dominate human cultures as it might once have done with stable societies of hunter—gatherers.