MHD stability of a collisionless anisotropic plasma in a system with an internal conductor

A study is made of the MHD stability of a collisionless anisotropic-pressure plasma in a nonparaxial magnetic configuration with an internal conductor in cylindrical geometry. A stability criterion for flutelike modes is obtained, and the families of marginally stable profiles of the longitudinal and transverse plasma pressures are calculated by using the Chew-Goldberger-Low anisotropic MHD equations. Possible marginally stable plasma states are considered with allowance for the expected turbulent relaxation and self-organization processes, on the one hand, and isotropization processes, on the other. A stability criterion for Alfvén modes is also derived in the Chew-Goldberger-Low model.     

Self-consistent electron and ion motion in a high-current plasma channel

The problem of self-consistent motion of charged particles in a high-current plasma channel is solved using the kinetic model of a plasma with electron and ion beams whose motion is governed by the resulting electromagnetic field. It is shown that, in a high-density plasma, the ion motion makes the contribution of electrons to the current in the channel negative, in which case the ion current is higher than the net current and the plasma moves at a high speed as an electrically neutral axial stream whose direction coincides with the direction of the current in the channel.     

Excitation of low-frequency electrostatic oscillations in a collisionless plasma with an anisotropic ion distribution

The stability of an anisotropic ion distribution with unoccupied regions (holes) in velocity space is studied. Such distributions are expected to form near the neutral plane of the Earth's magnetotail. It is shown that, in such systems, electrostatic waves can be excited. The growth rate and propagation direction of these oscillations are determined by the parameters characterizing the ion hole, as well as by the relation between the electron and ion temperatures. The solution to the quasilinear equation for the waves propagating perpendicular to the current sheet is found, and the energy of the excited oscillations as a function of the parameters of the ion hole is evaluated.     

Colonization in metapopulations: a review of theory and observations

In metapopulation dynamics turnover of populations in isolated patches may be frequent. Regional survival of a species in such a system with frequent extinctions hinges on its colonization ability. Colonization is more than just dispersal; when a propagule reaches a new patch it faces higher extinction probabilities than does an established population. Extinction models as well as empirical data suggest that a large propagule with a potential for rapid increase in a varying environment, or with a low mortality rate in an environment perceived as constant, has a higher probability of successful colonization. Large variation in population size when it is still small increases the risk of failure. Factors introducing such variation are demographic stochasticity and environmental variation. It is hard to single out demographic traits that ensure good colonizing ability, since colonization can be achieved in many different ways, but generalists and species with self-fertilization seem to be superior.     

Empirical approaches to metacommunities: a review and comparison with theory

Metacommunity theory has advanced understanding of how spatial dynamics and local interactions shape community structure and biodiversity. Here, we review empirical approaches to metacommunities, both observational and experimental, pertaining to how well they relate to and test theoretical metacommunity paradigms and how well they capture the realities of natural ecosystems. First, we show that the species-sorting and mass-effects paradigms are the most commonly tested and supported paradigms. Second, the dynamics observed can often be ascribed to two or more of the four non-exclusive paradigms. Third, empirical approaches relate only weakly to the concise assumptions and predictions made by the paradigms. Consequently, we suggest major avenues of improvement for empirical metacommunity approaches, including the integration across theoretical approaches and the incorporation of evolutionary and meta-ecosystem dynamics. We hope for metacommunity ecology to thereby bridge existing gaps between empirical and theoretical work, thus becoming a more powerful framework to understand dynamics across ecosystems.     

Spectral analysis of the surface electromyogram as a tool for studying rate modulation: A comparison between theory,simulation, and experiment

Theoretical work suggests that if the interpulse intervals (IPIs) of motor unit action potential trains (MUAPTs) are independently and normally distributed, then spectral analysis of the electromyogram could be a useful tool for studying rate modulation by virtue of the presence of a peak in the power spectrum at the average firing frequency of all active motor units. It is shown in this paper that IPIs need not be normally distributed, specifically that the results are very much the same if the IPIs are distributed according to a Gamma probability density function (PDF). Simulation of the electromyogram based on this theory proved the applicability of the method. Experimental results obtained for the masseter, biceps brachii and first dorsal interosseus (FDI) muscles, however, were in disagreement with both theory and simulation except for the biceps muscle at force levels up to 20% of the maximal force and for the masseter and FDI muscles in 1 out of 5 subjects. This indicates that the models for MUAPTs hitherto used might not be generally correct. Apart from this discrepancy, our results reveal differences between masseter and FDI muscles on the one hand and the biceps brachii on the other, which indicate that motor unit synchronisation is much more pronounced in the latter muscle.     

Unusually high zinc concentrations in snake plasma, with observations on plasma zinc concentrations in lizards, turtles and alligators

We provide evidence that normal plasma zinc levels in snakes are in the same range as the elevated zinc levels associated with haemolytic anaemia and fatal zinc toxicosis in dogs, and with weight loss and anorexia in crocodiles that had ingested coins with high zinc content. Blood plasma samples from large representative groups of snakes, lizards, turtles and alligators were analysed for zinc content by atomic absorption spectrophotometry. Plasma zinc levels in all snake species were five to 50-fold greater than levels reported in mammals. Plasma zinc levels in lizards and turtles were also higher than those of mammals, but significantly lower than those of snakes. Plasma zinc levels in alligators were in the same range as mammals and birds. After prolonged dialysis of snake plasma, 76% of the zinc remains in the retentate, suggesting the presence of a plasma protein with a strong affinity for the metal. Zinc levels vary significantly among the taxonomic groups, emphasizing the common evolutionary origin of crocodiles and birds and their divergence from the other reptiles.     

Pore disappearance in a cell after electroporation: theoretical simulation and comparison with experiments.

The process of pore disappearance after cell electroporation is analyzed theoretically. On the basis of the kinetic model, in which the formation and annihilation of a metastable hydrophilic pore are considered as random one-step processes, a distribution function of cell resealing times, Fr(t), is derived. Two cases are studied: 1) the rate of pore resealing, k(r), is significantly greater than the rate of pore formation, k(f); and 2) the rate of pore formation, k(f), is comparable with k(r). It is determined that the shape of the distribution function depends on the initial number of pores in a cell, n(i). If in the absence of an external electric field the rate of pore formation, k(f), is significantly less than the rate of pore resealing, k(r) (case 1), pores disappear completely, whereas when k(f) approximately k(r) (case 2), the cell achieves a steady state in which the number of pores is equal to k(f)/k(r). In case 1, when n(i) = 1, the distribution function Fr(t) is exponential. The developed theory is compared with experimental data available in the literature. Increasing the time of incubation at elevated temperature increases the fraction of resealed cells. This indicates that the time necessary for the resealing varies from cell to cell. Although the shape of experimental relationships depends on the electroporation conditions they can be described by theoretical curves quite well. Thus it can be concluded that the disappearance of pores in the cell membrane after electroporation is a random process. It is shown that from the comparison of presented theory with experiments, the following parameters can be estimated: the average number of pores, n(i), that appeared in a cell during an electric pulse; the rate of pore disappearance, k(r); the ratio k(f)/k(r); and the energy barrier to pore disappearance deltaWr(0). Estimated numerical values of the parameters show that increasing the amplitude of an electric pulse increases either the apparent number of pores created during the pulse (the rate of pore resealing remains the same) or the rate of pore resealing (the average number of pores remains the same).     

Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution

Neuroglobin (Ngb) is a monomeric protein that, despite the small sequence similarity with other globins, displays the typical globin fold. In the absence of exogenous ligands, the ferric and the ferrous forms of Ngb are both hexacoordinated to the distal and proximal histidines. In the ferrous form, oxygen, nitric oxide or carbon monoxide can displace the distal histidine, yielding a reversible adduct. Crystallographic data show that the binding of an exogenous ligand is associated to structural changes involving heme sliding and a topological reorganization of the internal cavities. Molecular dynamics (MD) simulations in solution show that the heme oscillates between two positions, much as the ones observed in the crystal structure, although the occupancy is different. The simulations also suggest that ligand binding in solution can affect the flexibility and conformation of residues connecting the C and D helices, referred to as the CD corner, which is coupled to the configuration adopted by the distal histidine. In this study, we report the results of 30 ns MD simulations of CO-bound Ngb in the crystal. Our goal was to compare the protein dynamical behavior in the crystal with the results supplied by the previous MD simulation of CO-bound Ngb in solution and the x-ray experimental data. The results show that the different environments (crystal or solution) affect the dynamics of the heme group and of the CD corner.     

Managing visitor access to seabird colonies: a spatial simulation and empirical observations

Managers of wildlife reserves have a range of tools available to them when considering the best way to provide visitor access while avoiding as many of the negative effects of human disturbance as possible. However, managers lack guidelines as to whether conservation interests are best met by spreading visitors thinly throughout a reserve or by aggregating them in a small area. Here I describe how relationships between disturbance impact and disturbance pressure (the dose–response curve) can be used to address this issue. I generate a spatial simulation of two different models of visitor distribution (one more aggregated than the other) and explicitly model disturbance impact for a variety of dose–response curves. I show that the optimal visitor distribution is likely to depend on the sensitivity of the species and the overall visitor pressure. Importantly, I find that in certain circumstances optimal management can shift from one management option to the other if visitor numbers cross a certain threshold. I use published relationships predicting nesting success of Common Guillemots Uria aalge and Black-legged Kittiwakes Rissa tridactyla to assess optimal management at three nature reserves in Scotland. Optimal management for Guillemots depends on the number of people and the distance between the people and the birds. At sites with high disturbance pressures, management should aim to aggregate visitors in as small an area as possible, whereas at sites with lower disturbance pressure, an even distribution of visitors is favoured. Kittiwake models were not generally accurate, and consequently only site-specific guidelines could be generated, where an even distribution was favoured.     

Chemical competition in target radical reactions: numerical simulation of the theory and comparison with measured oxygen effect on DNA damage in cells

An intracellular radiation-chemical reaction scheme is tested in which solute and solvent radicals R. react with non-target molecules Sa (scavengers) or with target molecules (presumed to be DNA) to produce target radicals T., which may also be produced by direct ionization of DNA. The rate of target radical decomposition to become 'uncommitted damage' that the cell may repair is affected by the concentration of oxygen (O2), thiols (S) and electronaffinic sensitizers (F), which compete with one another to form, respectively, target products TO2, TS and TF. This uncommitted damage is then subject to biochemical modification, including molecular repair, by the cell. The rate equations for this competing reaction scheme were written and programmed for computer simulations of changes in oxygen, thiol and electronaffinic sensitizer concentrations. A reaction scheme that also includes some non-radical target damage was also simulated. Simulations were made using available experimental data concerning intranuclear concentrations and reaction rate constants, respectively, ko, ks and k1 for the reactions T. + O2----TO2, T. + S----TS and T. + F----TF, which produce uncommitted chemical damage. Experimental data on strand-break induction in glutathione-proficient and glutathione-deficient cells, in cells treated with thiol active agents, and in cells treated with hypoxic sensitizers, along with the computer simulations, generally agree that thiol molecules can react with target radicals to reverse T. in competition with O2 and/or electronaffinic sensitizers. Forward reaction rate constants ko, ks (dithiothreitol), ks (glutathione) and k1 (misonidazole) in the approximate ratio 10:0.3:0.02:0.4 satisfied the above reaction scheme, and approximately 5 per cent non-radical target molecule damage could be included with satisfactory agreement with experimental data.     

The extended phenotype(s): a comparison with niche construction theory

While niche construction theory locates animal artefacts in their constructors’ environment, hence treating them as capable of exerting selective pressure on both the constructors and their descendants, the extended phenotype concept assimilates artefacts with their constructors’ genes. Analogous contrasts apply in the case of endoparasite and brood parasite genes influencing host behaviour. The explanatory power of these competing approaches are assessed by re-examining the core chapters of Richard Dawkins’ The Extended Phenotype. Because animal artefacts (chapter 11) have multiple evolutionary consequences for their constructors, the extra-body effects of a gene seemingly include feedback effects on multiple other genes, a result which is more consistent with niche construction theory than with selfish gene theory. In the case of endoparasite genes influencing host behaviour (chapter 12), Dawkins’ argument leaves out what appears to be the key explanatory component, namely the role of the host’s own bodily systems in making it possible for such genes to exist. For action at a distance (chapter 13), it is unclear whether the key genes have extended effects because they sit in the body of the manipulating organism, or alternatively do not have such effects because they sit in the body of its victim. It is argued that niche construction theory offers a superior explanation in all three cases, regardless of whether the extended phenotype concept is interpreted in selfish gene or selfish organism terms.     

Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations

Using inbreeding theory as applied to neutral alleles inherited maternally, we generate expected probability distributions of times to identity by descent for random pairs of mitochondrial genotypes within a population or within an entire species characterized by high gene flow. For comparisons with these expectations, empirical distributions of times to most recent common ancestry were calculated (by conventional mtDNA clock calibrations) from mtDNA haplotype distances observed within each of three vertebrate species--American eels, hardhead catfish, and redwinged blackbirds. These species were chosen for analysis because census population size in each is currently large and because both genetic and life-history data are consistent with the postulate that historical gene flow within these species has been high. The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size. Several considerations point to the latter possibility as most likely. The genetic structure of any species is greatly influenced by historical demography; even for species that are currently abundant, mtDNA gene lineages appear to have been channeled through fairly small numbers of ancestors.      

Understanding the persistence of measles: reconciling theory, simulation and observation

Ever since the pattern of localized extinction associated with measles was discovered by Bartlett in 1957, many models have been developed in an attempt to reproduce this phenomenon. Recently, the use of constant infectious and incubation periods, rather than the more convenient exponential forms, has been presented as a simple means of obtaining realistic persistence levels. However, this result appears at odds with rigorous mathematical theory; here we reconcile these differences. Using a deterministic approach, we parameterize a variety of models to fit the observed biennial attractor, thus determining the level of seasonality by the choice of model. We can then compare fairly the persistence of the stochastic versions of these models, using the 'best-fit' parameters. Finally, we consider the differences between the observed fade-out pattern and the more theoretically appealing 'first passage time'.     

Modelling competition for water in intercrops: theory and comparison with field experiments

A knowledge of plant interactions above and below ground with respect to water is essential to understand the performance of intercrop systems. In this study, a physically based framework is proposed to analyse the competition for soil water in the case of intercropped plants. A radiative transfer model, associated with a transpiration-partitioning model based on a modified form of the Penman-Monteith equation, was used to estimate the evaporative demand of maize (Zea mays L.) and sorghum ( Sorghum vulgare R.) intercrops. In order to model soil–root water transport, the root water potential of each species was calculated so as to minimise the difference between the evaporative demand and the amount of water taken up by each species. A characterisation of the micrometeorological conditions (net radiation, photosynthetically active radiation, air temperature and humidity, rain), plant water relations (leaf area index, leaf water potential, stomatal conductance, sap flow measurements), as well as the two-component root systems and water balance (soil–root impacts, soil evaporation) was carried out during a 7-day experiment with densities of about 4.2 plant m-2 for both maize and sorghum. Comparison of the measured and calculated transpiration values shows that the slopes of the measured versus predicted regression lines for hourly transpiration were 0.823 and 0.778 for maize and sorghum, respectively. Overall trends in the variation of volumetric water content profiles are also reasonably well described. This model could be useful for analysing competition where several root systems are present under various environmental conditions.     

Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles

Domain formation is modeled on the surface of giant unilamellar vesicles using a Landau field theory model for phase coexistence coupled to elastic deformation mechanics (e.g., membrane curvature). Smooth particle applied mechanics, a form of smoothed particle continuum mechanics, is used to solve either the time-dependent Landau-Ginzburg or Cahn-Hilliard free-energy models for the composition dynamics. At the same time, the underlying elastic membrane is modeled using smooth particle applied mechanics, resulting in a unified computational scheme capable of treating the response of the composition fields to arbitrary deformations of the vesicle and vice versa. The results indicate that curvature coupling, along with the field theory model for composition free energy, gives domain formations that are correlated with surface defects on the vesicle. In the case that external deformations are included, the domain structures are seen to respond to such deformations. The present simulation capability provides a significant step forward toward the simulation of realistic cellular membrane processes.     

Incoherent neutron scattering of copper azurin: a comparison with molecular dynamics simulation results

The low-frequency dynamics of copper azurin has been studied at different temperatures for a dry and deuterium hydrated sample by incoherent neutron scattering and the experimental results have been compared with molecular dynamics (MD) simulations carried out in the same temperature range. Experimental Debye-Waller factors are consistent with a dynamical transition at approximately 200 K which appears partially suppressed in the dry sample. Inelastic and quasielastic scattering indicate that hydration water modulates both vibrational and diffusive motions. The low-temperature experimental dynamical structure factor of the hydrated protein shows an excess of inelastic scattering peaking at about 3 meV and whose position is slightly shifted downwards in the dry sample. Such an excess is reminiscent of the “boson peak” observed in glass-like materials. This vibrational peak is quite well reproduced by MD simulations, although at a lower energy. The experimental quasielastic scattering of the two samples at 300 K shows a two-step relaxation behaviour with similar characteristic times, while the corresponding intensities differ only by a scale factor. Also, MD simulations confirm the two-step diffusive trend, but the slow process seems to be characterized by a decay faster than the experimental one. Comparison with incoherent neutron scattering studies carried out on proteins having different structure indicates that globular proteins display common elastic, quasielastic and inelastic features, with an almost similar hydration dependence, irrespective of their secondary and tertiary structure. Received: 12 October 1998 / Revised version: 19 February 1999 / Accepted: 1 March 1999     

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.