Nonequilibrium Population Research Articles

On the Utility of Linkage Disequilibrium as a Statistic for Identifying Targets of Positive Selection in Nonequilibrium Populations

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (omega(max)) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.

Controlling Nonequilibrium Phonon Populations in Single-Walled Carbon Nanotubes

We studied spatially isolated single-walled carbon nanotubes (SWNTs) immobilized in a quasi-planar optical lambda/2-microresonator using confocal microscopy and spectroscopy. The modified photonic mode density within the resonator is used to selectively enhance or inhibit different Raman transitions of SWNTs. Experimental spectra are presented that exhibit single Raman bands only. Calculations of the relative change in the Raman scattering cross sections underline the potential of our microresonator for the optical control of nonequilibrium phonon populations in SWNT.

Universal two-dimensional kinetics of the populations of Rydberg atoms in plasmas

Universal kinetics has been developed for calculating the two-dimensional populations (in the space of principal n and orbital l quantum numbers) of Rydberg atomic states in plasmas. It has been shown that the direct population of the atomic states by three-body and radiative recombination sources should be taken into account, because the radiative cascade is of quantum character. The subsequent two-dimensional radiation-collision cascade is constructed in the framework of the classical approach. The developed model makes it possible to obtain the populations in the form of universal functions of temperature and density. The numerical calculations of the populations of highly excited hydrogen states (n ∝ 100) in low-density plasmas (103–1013 cm−3) at moderate temperatures (1 eV) indicate a significantly nonequilibrium population both in n and in l, which is important for the diagnostics of astrophysical and laboratory plasmas.

Effects of high carrier densities on phonon and carrier lifetimes in Si by time-resolved anti-Stokes Raman scattering

The relaxation times T1 of nonequilibrium populations of elementary excitations in Si are studied by time-resolved Raman scattering using a subpicosecond pump-probe method. Incoherent anti-Stokes Raman scattering is used to monitor the decay of the nonequilibrium populations of holes and the generation and decay of zone-center longitudinal optical (LO) phonons. At lower levels of laser excitation, hole and LO phonon T1 lifetimes are less than 0.2ps and greater than 1.6ps, respectively. At higher laser intensities, the lifetime of holes increases and the lifetime of LO phonons decrease toward a common value of T1∼0.4ps.

Nonequilibrium population of charge carriers in structures with InGaN deep quantum dots

Electronic and optical properties of ensembles of quantum dots with various energies of activation from the ground-state level to the continuous-spectrum region were studied theoretically and experimentally with the InGaN quantum dots as an example. It is shown that, depending on the activation energy, both the quasi-equilibrium statistic of charge carriers at the levels of quantum dots and nonequilibrium statistic at room temperature are possible. In the latter case, the position of the maximum in the emission spectrum is governed by the value of the demarcation transition: the quantum dots with the transition energy higher than this value feature the quasi-equilibrium population of charge carriers, while the quantum dots with the transition energy lower than the demarcation-transition energy feature the nonequilibrium population. A model based on kinetic equations was used in the theoretical analysis. The key parameters determining the statistic are the parameters of thermal ejection of charge carriers; these parameters depend exponentially on the activation energy. It is shown experimentally that the use of stimulated phase decomposition makes it possible to appreciably increase the activation energy. In this case, the thermal-activation time is found to be much longer than the recombination time for an electron-hole pair, which suppresses the redistribution of charge carriers between the quantum dots and gives rise to the nonequilibrium population. The effect of nonequilibrium population on the luminescent properties of the structures with quantum dots is studied in detail.

Optimized Device Characteristics of Lateral Spin Valves

The lateral spin valve is a planar ferromagnet/nonmagnet/ferromagnet (F1/N/F2) structure with a resistance modulation DeltaR that derives from a nonequilibrium population of spin-polarized conduction electrons. This paper analyzes the characteristics of a future-generation all-metal device fabricated with minimum feature size f of 50 nm. Theoretical principles of operation are reviewed, and the rule is derived: Output resistance modulation varies inversely with the volume of the nonmagnetic material in the device. The thermodynamic formalism of Johnson and Silsbee is also used to study details of charge and spin transport at the F/N interface and to understand the limits of the fractional polarization of injected current. Experiments on lateral spin valves with N channels having widths of 150 nm are described. A high fractional polarization is observed for structures with low interface resistance. A survey of recent results on similar devices shows that inverse scaling is upheld over ten decades of sample volume. Using these experimentally observed parameters and extrapolating further to f = 50 nm, a spin-accumulation device that is fabricated to have an output impedance of 50 Omega and an output modulation of 50 Omega (DeltaR/R = 100%) is discussed

Fractional features in radiation-induced oscillations of the magnetoresistance of two-dimensional electron systems

The magnetoresistance of two-dimensional electron systems irradiated by microwave radiation is calculated. It exhibits oscillatory features at fractional values of the ratio ω/ωc of the circular frequency of microwave radiation to the cyclotron frequency. The calculation explains existing experimental data by nonequilibrium population of electron states that appears due to one-photon processes and predicts ω/ωc values near which the basic features in magnetoresistance are expected. In the framework of the mechanism under consideration, the fractional features can be observed only in the crossover from strongly overlapping to separate Landau levels and only at radiation frequencies below the threshold frequencies depending on a fractional value.

Electrical detection of spin transport in lateral ferromagnet–semiconductor devices

A longstanding goal of research in semiconductor spintronics is the ability to inject, modulate, and detect electron spin in a single device. A simple prototype consists of a lateral semiconductor channel with two ferromagnetic contacts, one of which serves as a source of spin-polarized electrons and the other as a detector. Based on work in analogous metallic systems, two important criteria have emerged for demonstrating electrical detection of spin transport. The first is the measurement of a non-equilibrium spin population using a non-local ferromagnetic detector through which no charge current flows. The potential at the detection electrode should be sensitive to the relative magnetizations of the detector and the source electrodes, a property referred to as the spin-valve effect. A second and more rigorous test is the existence of a Hanle effect, which is the modulation and suppression of the spin valve signal due to precession and dephasing in a transverse magnetic field. Here we report on the observation of both the spin valve and Hanle effects in lateral devices consisting of epitaxial Fe Schottky tunnel barrier contacts on an n-doped GaAs channel. The dependence on transverse magnetic field, temperature, and contact separation are in good agreement with a model incorporating spin drift and diffusion. Spin transport is detected for both directions of current flow through the source electrode. The sign of the electrical detection signal is found to vary with the injection current and is correlated with the spin polarization in the GaAs channel determined by optical measurements. These results therefore demonstrate a fully electrical scheme for spin injection, transport, and detection in a lateral semiconductor device.

Intra-miniband gain in a super-superlattice structure with alternating electric-field domains

A super-superlattice structure containing a conventional superlattice, a graded-gap superlattice, and a wide quantum well in its unit cell is analyzed. It is designed in such a way that alternating high- and low-electric-field domains appear due to the presence of positive and negative space charges. The positive space charge is formed by ionized donors, while electrons, which are trapped in the wide quantum well, provide the negative space charge. Since the low-field domain spans the conventional superlattice and the high-field domain is located in the graded-gap superlattice, the flatband condition can be simultaneously achieved for the two superlattices. The self-consistent solution of the Poisson and Schrödinger equations using a simplified scattering-rate approach demonstrates that the conventional superlattice exhibits an inversion of the intra-miniband population. Such structures may be useful for terahertz lasers, since the large dipole matrix element of the intra-miniband transitions allow for a rather low doping density and hence a reduction of scattering processes. Furthermore, they permit the study of superlattices under flatband conditions with a nonequilibrium population, which is achieved without optical excitation.

Heat dissipation and non-equilibrium phonon distributions in molecular devices

Using a density functional approach we compute vibrations of molecules adsorbed on metal and semiconducting substrates and the electronphonon coupling of these modes. A non-equilibrium Green’s function approach is used to compute the partially coherent transmission in molecular junctions due to electron-vibration scattering [1], [2]. The electronic power dissipated into molecular vibrations allows to set a rate equation for the phonon population in the vibrational degrees of freedom of the molecule. The rate equation includes the phonon emission rate and phonon decay due to absorption, electron-hole pair production and dissipation into the contacting leads, which are assumed to behave as reservoirs. The rate of phonon decay is computed using a microscopic approach which includes a first-principle calculation of the coupling of the molecular modes with the vibrations of the contacts. In turn, the calculated phonon lifetime is used to correct the phonon propagator. As the power dissipated in the molecular junction depends nontrivially on the phonon populations, the equilibrium distribution under bias condition is a complex issue. A self consitent loop allows to compute the steady state non-equilibrium phonon population of the molecular junction under bias condition. We find that the resulting average population is far from the equilibrium thermal distribution, frequently assumed in such calculations, which allows to obtain a mean temperature of the junction. As expected the deviations increase with applied bias. As molecular electronics is moving to semiconducting substrates, it is relevant to explore and understand thermal issues. Metallic substrates have in fact a very efficient channel of phonon damping into electron-hole pairs, while vibrational coupling to the substrate may not be very efficient due to ionic mass mismatch and a weaker bond. On the other hand the the electron-hole generation is prevented on semiconducting substrates, where instead vibrational coupling is stronger.We compare thermal behavior of organic molecules adsorbed on Si with molecules adsorbed on metallic substrates (Au or Cu) and determine the molecular temperature as a function of applied bias and for different temperatures of the termostats.

Demographic spatial genetic structure of the Neotropical tree, Jacaranda copaia

We used genotypes from six microsatellite loci and demographic data from a large mapped forest plot to study changes in spatial genetic structure across demographic stages, from seed rain to seedlings, juveniles, and adult diameter classes in the Neotropical tree, Jacaranda copaia. In pairwise comparisons of genetic differentiation among demographic classes, only seedlings were significantly differentiated from the other diameter classes; F(ST) values ranged from 0.006 to 0.009. Furthermore, only seedlings showed homozygote excess suggesting biparental inbreeding in the large diameter reproductive adults. We found very low levels of relatedness in the first distance class of trees, 1-26 cm diameter (F(ij) = 0.011). However, there was a 5- to 10-fold rise in relatedness in the smallest distance class, from the smallest to the largest tree diameter classes (F(ij) = 0.110 for individuals > 56 cm diameter). A variety of non-mutually exclusive mechanisms have been invoked perviously to explain such a pattern, including natural selection, history, or nonequilibrium population dynamics. The long-term demographic data available for this species allow us to evaluate these mechanisms. Jacaranda is a fast-growing, light-demanding species with low recruitment rates and high mortality rates in the smaller diameter classes. It successfully regenerates only in large light gaps, which occur infrequently and stochastically in space and time. These factors contribute to the nonequilibrium population dynamics and observed low genetic structure in the small size classes. We conclude that the pattern of spatial genetic transitions in Jacaranda is consistent with overlapping related generations and strong but infrequent periods of high recruitment, followed by long periods of population decline.

Modeling Extent and Distribution of Zygotic Disequilibrium: Implications for a Multigenerational Canine Pedigree

Unlike gametic linkage disequilibrium defined for a random-mating population, zygotic disequilibrium describes the nonrandom association between different loci in a nonequilibrium population that deviates from Hardy-Weinberg equilibrium. Zygotic disequilibrium specifies five different types of disequilibria simultaneously that are (1) Hardy-Weinberg disequilibria at each locus, (2) gametic disequilibrium (including two alleles in the same gamete, each from a different locus), (3) nongametic disequilibrium (including two alleles in different gametes, each from a different locus), (4) trigenic disequilibrium (including a zygote at one locus and an allele at the other), and (5) quadrigenic disequilibrium (including two zygotes each from a different locus). However, because of the uncertainty on the phase of the double heterozygote, gametic and nongametic disequilibria need to be combined into a composite digenic disequilibrium and further define a composite quadrigenic disequilibrium together with the quadrigenic disequilibrium. To investigate the extent and distribution of zygotic disequilibrium across the canine genome, a total of 148 dogs were genotyped at 247 microsatellite markers located on 39 pairs of chromosomes for an outbred multigenerational pedigree, initiated with a limited number of unrelated founders. A major portion of zygotic disequilibrium was contributed by the composite digenic and quadrigenic disequilibrium whose values and numbers of significant marker pairs are both greater than those of trigenic disequilibrium. All types of disequilibrium are extensive in the canine genome, although their values tend to decrease with extended map distances, but with a greater slope for trigenic disequilibrium than for the other types of disequilibrium. Considerable variation in the pattern of disequilibrium reduction was observed among different chromosomes. The results from this study provide scientific guidance about the determination of the number of markers used for whole-genome association studies.

Hot-electron energy-loss rate via PO-phonon scattering in CdZnSe/ZnSe quantum wire

The hot-electron energy-loss rate conditioned by confined and interface polar-optical phonons for a Cd 0.35Zn 0.65Se quantum wire embedded in ZnSe medium is investigated theoretically. It is shown that the inclusion of the polar-optical phonon confinement effects is crucial for accurate calculation of the energy-loss rate in quantum wire. Taking into account the nonequilibrium phonon populations, the hot-electron energy-loss rate is derived by a model, which includes the lowest subband occupation and the phonon confinement effects. The contribution of intersubband transitions to electron energy-loss rate as well as the relaxation time of the electron temperature with and without hot-phonon bottleneck effect is estimated.

Divergence With Gene Flow in Anopheles funestus From the Sudan Savanna of Burkina Faso, West Africa

Anopheles funestus is a major vector of malaria across Africa. Understanding its complex and nonequilibrium population genetic structure is an important challenge that must be overcome before vector populations can be successfully perturbed for malaria control. Here we examine the role of chromosomal inversions in structuring genetic variation and facilitating divergence in Burkina Faso, West Africa, where two incipient species (chromosomal forms) of A. funestus, defined principally by rearrangements of chromosome 3R, have been hypothesized. Sampling across an approximately 300-km east-west transect largely contained within the Sudan-Savanna ecoclimatic zone, we analyzed chromosomal inversions, 16 microsatellite loci distributed genomewide, and 834 bp of the mtDNA ND5 gene. Both molecular markers revealed high genetic diversity, nearly all of which was accounted for by within-population differences among individuals, owing to recent population expansion. Across the study area there was no correlation between genetic and geographic distance. Significant genetic differentiation found between chromosomal forms on the basis of microsatellites was not genomewide but could be explained by chromosome 3R alone on the basis of loci inside and near inversions. These data are not compatible with complete reproductive isolation but are consistent with differential introgression and sympatric divergence between the chromosomal forms, facilitated by chromosome 3R inversions.

Nonequilibrium radiative heat flux modeling for the Huygens entry probe

An electronic collisional‐radiative model is proposed to predict the nonequilibrium populations and the radiation of the excited electronic states CN(A, B) and N2(A, B, C) during the entry of the Huygens probe into the atmosphere of Titan. The model is loosely coupled with flow solvers using a Lagrangian method. First, the model was tested against measurements obtained with the shock‐tube of NASA Ames Research Center. Then, the model was applied to the simulation of Huygen's entry. Our simulations predict that the population of the CN(B) state is lower than the Boltzmann population by a factor 40 at trajectory time t = 165 s and by a factor 2 at t = 187 s and that the population of the CN(A) state remains close to the Boltzmann population for both trajectory points. The radiative heat fluxes, driven by the CN(A, B) states, are lower than predictions based on the Boltzmann populations by a factor 15 at t = 165 s and a factor 2 at t = 187 s.

Cosmological production of H2 before the formation of the first galaxies

Previous calculations of the pre-galactic chemistry have found that a small amount of H 2 , x[H 2 ] ≡ n[H 2 ]/n[H] ≈ 2.6 x 10 -6 , is produced catalytically through the H-, H 2 + and HeH + mechanisms. We revisit this standard calculation taking into account the effects of the non-thermal radiation background produced by cosmic hydrogen recombination, which is particularly effective at destroying H - via photodetachment. We also take into consideration the non-equilibrium level populations of H + 2 , which occur since transitions among the rotational-vibrational levels are slow compared to photodissociation. The new calculation predicts a final H 2 abundance of x[H 2 ] ≈ 6 x 10 -7 for the standard cosmology. This production is due almost entirely to the H - mechanism, with ∼ 1 per cent coming from HeH + and ∼0.004 per cent from H 2 + . We evaluate the heating of the diffuse pre-galactic gas from the chemical reactions that produce H 2 and from rotational transitions in H 2 , and find them to be negligible.

Transfer of CIDNP among coupled spins at low magnetic field

Coherent polarization transfer among groups of dynamically polarized spins is explored and applied to field cycling experiments where spin evolution proceeds at low magnetic field while observation is performed at high field. The case of two nonequivalent spins-1/2 with scalar spin coupling is considered theoretically in detail for the cases of sudden and adiabatic field change. The criterion for efficient polarization transfer is derived theoretically and consistently confirmed experimentally for three photochemical reactions, involving spin systems of increasing complexity that exhibit chemically induced dynamic nuclear polarization: (1) the two polarized protons of the purine base of adenosine monophosphate; (2) four coupled indole protons of tryptophan; and (3) long-range polarization transfer among the aliphatic protons of cycloundecanone. The importance of polarization transfer in other cases with non-equilibrium population of the nuclear spin levels and the possibility of its utilization in field cycling NMR studies are discussed.

Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography.

Work carried out over the last 30 years unveiled the role of structural dynamics in controlling protein function. Cavity networks modulate structural dynamics trajectories and are functionally relevant; in globins they have been assigned a role in ligand migration and docking. These findings raised renewed interest for time-resolved structural investigations of myoglobin (Mb), a simple heme protein displaying a photosensitive iron-ligand bond. Photodissociation of MbCO generates a nonequilibrium population of protein structures relaxing over a time range extending from picoseconds to milliseconds. This process triggers ligand migration to matrix cavities with clear-cut effects on the rate and yield of geminate rebinding. Here, we report subnanosecond time-resolved Laue diffraction data on the triple mutant YQR-Mb [Leu-29(B10)Tyr, His-64(E7)Gln, Thr-67(E10)Arg] that depict the sequence of structural events associated with heme and protein relaxation from 100 ps to 316 ns and above. The photodissociated ligand rapidly (<0.1 ns) populates the Xe-binding cavity distal to the heme. Moreover, the heme relaxation toward the deoxy configuration is heterogeneous, with a slower phase ( approximately ns) evident in these experiments. Damping of the heme response appears to result from a strain exerted by the E-helix via the CD-turn; Phe-43(CD1), in close contact with heme, opposes tilt until the strain is relieved. A comparison with crystallographic data on wild-type Mb and mutants Leu(29)Phe or Leu(29)Trp suggests that the internal structure controls the rate and amplitude of the relaxation events. A correlation between structural dynamics as unveiled by Laue crystallography and functional properties of Mb is presented.

Mathematical simulation of the spectrum of a nonequilibrium laser plasma

A method is proposed for calculating the spectrum of a nonequilibrium plasma, which is based on a nonequilibrium collision—radiation model including all common line broadening mechanisms (natural, pressure, Doppler, and quadratic Stark effect broadening) and supplemented with the energy balance equations for electrons and ions. The nonequilibrium populations of the ground and excited states of neutral atoms and ions for an arbitrary instant of time are found by solving kinetic equations. The shape of each spectral line is determined by its central core calculated in the collision approximation up to the frequency boundary of its applicability, where the central core is 'joined' with the line wings calculated in the quasi-static approximation. The validity of this theoretical model is confirmed by simulations of a number of experimental studies of emission spectra under the conditions of a local thermodynamic equilibrium. It is shown that the calculated and experimental data obtained for the ground-state lines of the first carbon ion and neutral helium and argon atoms are in good agreement. The nonequilibrium spectrum of the optical breakdown in argon is calculated. Mathematical simulations showed that the intensities of nonequilibrium line spectra can be noticeably (by several times) lower than those of equilibrium spectra.

Direct Demonstration of Decoupling of Spin and Charge Currents in Nanostructures

The notion of decoupling of spin and charge currents is one of the basic principles underlying the rapidly expanding field of spintronics. However, no direct demonstration of the phenomenon exists. We report a novel measurement in which a nonequilibrium spin population is created by a pointlike injection of current from a ferromagnet across a tunnel barrier into a one-dimensional spin channel and detected differentially by a pair of ferromagnetic electrodes placed symmetrically about the injection point. We demonstrate that the spin current is strictly isotropic about the injection point and, therefore, completely decoupled from the unidirectional charge current.