Molecular dynamics simulation of diffusion of hydrogen in binary hydrogen–tetrahydrofuran hydrate

The binary structure II hydrogen–tetrahydrofuran (THF) hydrate was studied with molecular dynamics simulation. The simulations were carried out at 300, 310 K and 10.1 MPa, and with various contents of hydrogen and THF. The migrations of hydrogen molecules from cage to cage were observed. The migration process of hydrogen was also analysed, and the diffusion coefficients of hydrogen in the hydrate were calculated. The calculated diffusion coefficients qualitatively agreed with the experimental data. Double and quintet occupancies of hydrogen molecules were observed in the small and large cages, respectively, without changing the hydrate structure.     

The effect of drought stress on heterozygosity–fitness correlations in pedunculate oak (Quercus robur)

Background and Aims

The interaction between forest fragmentation and predicted climate change may pose a serious threat to tree populations. In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness through the expression of deleterious alleles. Climate change-induced drought stress may exacerbate these detrimental genetic consequences of forest fragmentation, as the fitness response to low levels of individual heterozygosity is generally thought to be stronger under environmental stress than under optimal conditions.

Methods

To test this hypothesis, a greenhouse experiment was performed in which various transpiration and growth traits of 6-month-old seedlings of Quercus robur differing in multilocus heterozygosity (MLH) were recorded for 3 months under a well-watered and a drought stress treatment. Heterozygosity–fitness correlations (HFC) were examined by correlating the recorded traits of individual seedlings to their MLH and by studying their response to drought stress.

Key Results

Weak, but significant, effects of MLH on several fitness traits were obtained, which were stronger for transpiration variables than for the recorded growth traits. High atmospheric stress (measured as vapour pressure deficit) influenced the strength of the HFCs of the transpiration variables, whereas only a limited effect of the irrigation treatment on the HFCs was observed.

Conclusions

Under ongoing climate change, increased atmospheric stress in the future may strengthen the negative fitness responses of trees to low MLH. This indicates the necessity to maximize individual multilocus heterozygosity in forest tree breeding programmes.     

Computer modelling study on the compatibility of PEO–PMMA block copolymers

The compatibility of six kinds of designed poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA) copolymers was studied at 270, 298 and 400 K by mesoscopic modelling. The values of order parameter depended on both the structures of block copolymers and the simulation temperatures, while the values of order parameter of the long chains were higher than those of the short ones; temperature showed a more obvious effect on long chains than on short ones. These plain copolymers doped with PEO or PMMA homopolymer showed different order parameter values. When the triblock copolymer was composed of the same component at both ends and was doped with a homopolymer with the same component as that in the middle or the end of triblock copolymer, the values of order parameter depended on the simulation temperature, such as A5B6A5 doped with B6 at 400 K and A5B6A5 doped with A5 at 270 K, it showed the highest order parameter values. The study of copolymers doped with nanoparticles showed that the mesoscopic phase was influenced by not only the properties of the nanoparticles, such as the size and density, but also the compositions of copolymers. Among them, increasing the size of doped nanoparticles was the most significant effect on changing the phase morphologies.     

Diatom–salinity relationships in wetlands: assessing the influence of salinity variability on the development of inference models

We determined in situ feeding rates of three co-occurring coastal mysid species using [methyl-³H]-thymidine-labelled algal detritus (Lessonia corrugata), NaH¹⁴CO₃-labelled phytoplankton (Isochrysis galbana) and zooplankton (Artemia sp. nauplii). All three species showed a wide and overlapping range of feeding rates on the three food types, suggesting they were broadly omnivorous. However, selectivity studies often showed a strong preference for animal prey. Although there was an overlap in the types of food the mysids ingested, some degree of feeding niche partitioning was demonstrated. Paramesopodopsis rufa tended to be more carnivorous, Tenagomysis tasmaniae fed least on zooplankton and phytoplankton, and largely on algal detritus, and Anisomysis mixta australis ingested few zooplankters, and moderate amounts of algal detritus and phytoplankton. Handling editor: P. Viaroli     

The influence of birth order on birth weight: does the sex of preceding siblings matter?

The purpose of this study was to investigate whether the well-established relationship between parity and birth weight is affected by the sex composition of siblings, especially for male newborns. Subjects were 856 male and 862 female newborns who weighed at least 2500 g at birth, who were born after 37 completed weeks of gestation, who obtained an Apgar score of 7 or higher, who had the same biological parents as all other children in the sibship, and who lived in the same household. Information on birth weight was collected from hospital records. Results showed that male newborns with older brothers weighed less than male newborns with older sisters. In contrast, the weight of female newborns with older brothers did not differ from the weight of female newborns with older sisters. One explanation of these results is that maternal immunoreactivity to some male-specific feature of the fetus affects prenatal development and consequently reduces birth weight in males. The relation between older brothers and birth weight may have theoretical significance for behavioural variables.     

Computer simulation of the motoneuron pool–muscle complex. I. Input system and motoneuron pool

 The aim of the present study was to simulate the input system and the motoneuron (MN) pool of the MN pool–muscle complex (MNPMC). Input fibers, which can originate from command centers in the central nervous system or from sensory organs, activate the MN pool. They generate sequences of action potentials, the frequency of which is proportional to a time-dependent activation factor (which is an input to the model). Different connection patterns between the input fibers and motor units (MUs) are allowed. For simplicity and since no precise experimental data are available, 70 input fibers and 4 boutons per fiber and MN are simulated (this corresponds approximately to the monosynaptic group-Ia input of the cat medial gastrocnemius muscle). Each bouton generates the same conductance change in the postsynaptic membrane. The MNs are modeled with a single compartment and a homogenous membrane. According to experimental data, the membrane leakage conductance and capacitance are MU dependent. Since the precise relation is unknown: (a) the computed relation between MU contraction force and the MN leakage conductance was taken from a steady-state MNPMC model, and (b) the capacitance was assumed to be proportional to the leakage conductance. The MN membrane includes time- and voltage-dependent ionic channels (fast and slow K⁺ and low- and high-threshold Ca²⁺ channels). The density and time constant of the slow K⁺ channels and the density of the Ca²⁺ channels were fitted to approximate afterhyperpolarization characteristics and frequency-injected current relations of type-identified cat MNs. If the membrane reaches a voltage threshold the MNs generate action potentials, which were simulated by voltage pulses. The activation of the MN pool of the human first dorsal interosseus muscle was simulated with injected and synaptic currents in order to illustrate the size principle, synaptic noise, and other features of muscle activation. It is concluded that the present model reproduces the main properties of the input–output relations of different MN types within a muscle. Together with the simulation of the muscle force and the surface EMG, which will be published in subsequent papers, it will be a powerful tool for reproducing experiments on the motor system and investigating functional mechanisms of motor control. Received: 17 April 2001 / Accepted in revised form: 6 November 2001     

IB–LBM simulation of the haemocyte dynamics in a stenotic capillary

To study the behaviour of a haemocyte when crossing a stenotic capillary, the immersed boundary–lattice Boltzmann method was used to establish a quantitative analysis model. The haemocyte was assumed to be spherical and to have an elastic cell membrane, which can be driven by blood flow to adopt a highly deformable character. In the stenotic capillary, the spherical blood cell was stressed both by the flow and the wall dimension, and the cell shape was forced to be stretched to cross the stenosis. Our simulation investigated the haemocyte crossing process in detail. The velocity and pressure were anatomised to obtain information on how blood flows through a capillary and to estimate the degree of cell damage caused by excessive pressure. Quantitative velocity analysis results demonstrated that a large haemocyte crossing a small stenosis would have a noticeable effect on blood flow, while quantitative pressure distribution analysis results indicated that the crossing process would produce a special pressure distribution in the cell interior and to some extent a sudden change between the cell interior and the surrounding plasma.     

On the influence of prenatal hypoxia on formation of the orexinergic system and sleep–wake cycle in early ontogenesis of rats

The role of orexin in the organization of the sleep–wake cycle (SWC) is well known. The aim of this study was to examine the timing of the orexinergic system formation in rat postnatal ontogenesis and to assess the role of orexin A in the SWC organization under normal conditions and after prenatal hypoxia undergone on days 14 and 19 of embryogenesis. The SWC was investigated in 30-day-old rats with electrodes implanted into the somatosensory and occipital cortex. Immunoreactivity within the orexigenic structures of the lateral hypothalamus was analyzed. It was shown that in control 14-day-old animals the orexinergic structures were in their formative stage, whereas in 30-day-old rats they were already as formed as in adults. In 14-day-old rats, prenatal hypoxia evoked retarded formation of the orexinergic system. In 30-day-old animals, hypoxia undergone in the prenatal period increased the activity of the orexinergic system, which was higher in animals exposed to hypoxia on day 19 than on day 14 of gestation. In 30-day-old rats, these changes were reflected in the SWC formation in the form of shorter slow-wave sleep, more fitful sleep and increased number of transitions from slow- to fast-wave sleep. The results obtained are discussed in the light of the adaptive-compensatory role of the orexigenic system in postnatal ontogenesis after prenatal damage to the central nervous system.     

The influence of exogenous peptide on β2–microglobulin exchange in the HLA complex: analysis in real-time

 We used an optical biosensor to determine the relative binding affinity of peptides to purified HLA class I molecules. In this assay we monitor β₂–microglobulin (β₂m) exchange within the HLA-A2 molecule, whereby native β₂m in the complex is replaced by β₂m immobilized at the surface of the biosensor. Quantitative kinetic measurements permit us to obtain association rate (k_ass), dissociation rate (k_diss) and affinity constants (K_A) for the β₂m exchange reaction, alone, (control) and in the presence of exogenous peptide. We tested a panel of six peptides which had been designed and synthesized with an HLA-A2 binding motif, and had also been tested by the T2-cell binding assay, along with control peptides. The biosensor results demonstrate that exogenous peptide influences the dynamics of β₂m exchange in a sequence-specific manner. Five of six peptides increased the association rate, decreased the dissociation rate, and significantly increased the affinity (K_A=1.55–1.88×10⁹ M^–1) of HLA-A2 for immobilized β₂m compared with the control (K_A =1.14±0.04×10⁹ M^–1), demonstrating stabilization of the complex. One peptide was unable to stabilize the complex, as also shown in the T2 binding assay. However, analysis of peptide sequences demonstrated that the HLA-A2 secondary motif as well as primary motif residues are required for HLA-A2 stabilization. Further experiments demonstrated that β₂m exchange alone cannot stabilize the HLA class I complex at the cell surface until a peptide of sufficient binding affinity is bound. Hence kinetics equal to or below the control values in our biosensor assay probably represent an unstable complex in vivo. Unlike other methods described for the analysis of peptide stabilization, this approach is significantly faster, provides full kinetic analysis, and is simpler, since it requires no labeling of peptides. Furthermore, this may have important implications in the assessment of peptide vaccines. Received: 9 October 1997 / Revised: 20 January 1998     

The influence of changes to river hydrology on freshwater fish in regulated rivers of the Murray–Darling basin

Freshwater fish are often used as an indicator of the response of the ecosystem to the restoration of river flows or the provision of environmental flows. The ability to model the biological response of fish depends on the capacity to establish clear relationships between changes in river hydrology and the fish assemblages in a river. The fish assemblage structure and the abundances of individual fish species were examined in relation to a hydrological index that described hydrological change in six regulated rivers in the Murray–Darling Basin. The hydrological index explained only a small amount of variation in fish assemblage structure. In addition, the abundances of individual fish species were only weakly correlated with the index of flow deviation. It is suggested that these results make the modelling of responses of fish assemblages to environmental water allocations unfeasible at a large scale and that future studies should concentrate on potentially more simple responses, such as the relationships of fish spawning and recruitment to specific aspects of river hydrology.     

A molecular dynamics simulation study of the effect of water–graphene interaction on the properties of confined water

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsive r^?12 potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r^?12 potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential.     

The influence of ion concentrations on the dynamic behavior of the Hodgkin–Huxley model-based cortical network

Action potentials (APs) in the form of very short pulses arise when the cell is excited by any internal or external stimulus exceeding the critical threshold of the membrane. During AP generation, the membrane potential completes its natural cycle through typical phases that can be formatted by ion channels, gates and ion concentrations, as well as the synaptic excitation rate. On the basis of the Hodgkin–Huxley cell model, a cortical network consistent with the real anatomic structure is realized with randomly interrelated small population of neurons to simulate a cerebral cortex segment. Using this model, we investigated the effects of Na⁺ and K⁺ ion concentrations on the outcome of this network in terms of regularity, phase locking, and synchronization. The results suggested that Na⁺ concentration does slightly affect the amplitude but not considerably affects the other parameters specified by depolarization and repolarization. K⁺ concentration significantly influences the form, regularity, and synchrony of the network-generated APs. No previous study dealing directly with the effects of both Na⁺ and K⁺ ion concentrations on regularity and synchronization of the simulated cortical network-generated APs, allowing for the comparison of results obtained using our methods, was encountered in the literature. The results, however, were consistent with those obtained through studies concerning resonance and synchronization from another perspective and with the information revealed through physiological and pharmacological experiments concerning changing ion concentrations or blocking ion channels. Our results demonstrated that the regularity and reliability of brain functions have a strong relationship with cellular ion concentrations, and suggested the management of the dynamic behavior of the cellular network with ion concentrations.     

Effect of arsenic–phosphorus interaction on arsenic-induced oxidative stress in chickpea plants

Arsenic-induced oxidative stress in chickpea was investigated under glasshouse conditions in response to application of arsenic and phosphorus. Three levels of arsenic (0, 30 and 60 mg kg^?1) and four levels of P (50, 100, 200, and 400 mg kg^?1) were applied to soil-grown plants. Increasing levels of both arsenic and P significantly increased arsenic concentrations in the plants. Shoot growth was reduced with increased arsenic supply regardless of applied P levels. Applied arsenic induced oxidative stress in the plants, and the concentrations of H₂O₂ and lipid peroxidation were increased. Activity of superoxide dismutase (SOD) and concentrations of non-enzymatic antioxidants decreased in these plants, but activities of catalase (CAT) and ascorbate peroxidase (APX) were significantly increased under arsenic phytotoxicity. Increased supply of P decreased activities of CAT and APX, and decreased concentrations of non-enzymatic antioxidants, but the high-P plants had lowered lipid peroxidation. It can be concluded that P increased uptake of arsenic from the soil, probably by making it more available, but although plant growth was inhibited by arsenic the P may have partially protected the membranes from arsenic-induced oxidative stress.     

The influence of the reference electrode location on the M−wave characteristics in the quadriceps

IntroductionIn the compound muscle action potential (M wave) recorded using the belly-tendon configuration, the contribution of the tendon electrode is assumed to be negligible compared to the belly electrode. We tested this assumption by placing the reference electrode at a distant (contralateral) site, which allowed separate recording of the belly and tendon contributions.MethodsM waves were recorded at multiple selected sites over the right quadriceps heads and lower leg using two different locations for the reference electrode: the ipsilateral (right) and contralateral (left) patellar tendon. The general parameters of the M wave (amplitude, area, duration, latency, and frequency) were measured.Results(1) The tendon potential had a small amplitude (<30%) compared to the belly potential; (2) Changing the reference electrode from the ipsilateral to the contralateral patella produced moderate changes in the M wave recorded over the innervation zone, these changes affecting significantly the amplitude of the M−wave second phase (p = 0.006); (3) Using the contralateral reference system allowed recording of short-latency components occurring immediately after the stimulus artefact, which had the same latency and amplitude (p = 0.18 and 0.25, respectively) at all recording sites over the leg.ConclusionsThe potential recorded at the “tendon” site after femoral nerve stimulation is small (compared to the belly potential), but not negligible, and makes a significant contribution to the second phase of belly-tendon M wave. Adopting a distant (contralateral) reference allowed recording of far-field components that may aid in the understanding of the electrical formation of the M wave.     

Impacts of grazing on the alkalinized–salinized meadow steppe ecosystem in the Songnen Plain,China – A simulation study

A process-based model was built to describe the ecological processes of an alkalinized–salinized meadow steppe ecosystem, including the hydrological and alkalization–salinization processes in the soil, as well as the succession and growth dynamics of the grassland communities. A numerical integration model and a water and salt balance model were integrated into a physically-based model, describing the dynamics of soil moisture, salt concentration, exchangeable sodium percentage (ESP) and pH. Meteorological variables and soil characteristics were the main environmental factors used to estimate the growth dynamics of three herbaceous communities that were dominated by Aneurolepidium chinense, Chloris virgata, and Suaeda glauca, respectively. Model validation showed good agreement between the simulated results and the observed data. Simulation studies were conducted to evaluate the potential changes in hydrological and alkalization–salinization processes, succession and growth dynamics from 1991 to 1998, under five grazing intensities, namely 0%, 25%, 50%, 75% and 90% above-ground biomass removal (AGBR). The simulations show that soil moisture decreased markedly under the 50%, 75% and 90% AGBR, but increased slightly under the 25% AGBR. The de-alkalization and de-salinization processes would be predominant under the 0% AGBR, and the processes became a little slower under the 25% AGBR. In contrast, the 50%, 75% and 90% AGBR accelerated the degradation of soil properties. The grassland was dominated by A. chinense under the 0% AGBR, and by A. chinense and C. virgata under the 25% AGBR. C. virgata could grow on slightly alkalinized–salinized soil and became a dominant species after three years of 50% AGBR. The soil degraded quickly and only S. glauca could grow on the severe alkalinized–salinized soil if the grassland received 75% or 90% AGBR. The grassland grew well under the 0% AGBR, and the biomass stayed at moderate level under 25% AGBR. The 50%, 75% and 90% AGBR decreased the grassland growth greatly. After accumulating the grazed biomass for each year, the 25% AGBR would provide the highest production, and the grassland production would decrease sharply with the increasing of grazing intensities. The simulation results indicate that 25% AGBR is significant for preserving the soil from degradation, and maintaining high grassland production.     

Experimental field test of the influence of generalist stingless bees (Meliponini) on the topology of a bee–flower mutualistic network in the tropics

1. Generalists are assumed to play a key role in structuring and stabilising animal–plant mutualistic networks. Until now, analyses on the effects of generalists have been based on empirical field data or simulations. The present natural field experiment manipulated the abundance of a generalist and abundant stingless bee [Melipona (Eomelipona) marginata] to determine the effects on the mutualistic network. 2. Networks were generated, and associated metrics were used for comparing replicate plots with and without the insertion of stingless bee nests. 3. Unweighted metrics and the basic qualitative structural pattern of networks (high nestedness, very low modularity and specialisation) was not affected by experimental variation in stingless bee abundance because they exert strong basal effects on the plant–pollinator community under natural conditions of abundance. Still, increased abundance caused significant variation in weighted nestedness and modularity and community-level specialisation. 4. Supporting predictions of neutral models, increased abundance of the stingless bee led to an increase in most of its specific metrics, expressing the expansion of its realised trophic niche. 5. During this process, specialist and other generalist bees were affected in different ways. More plant species became even more dependent on this stingless bee (increased asymmetry). 6. Long-term effects could not be inferred directly from instantaneous values of network metrics. Nonetheless, the increased abundance of the generalist stingless bee may both reduce the local level of ecological specialisation in the short term and affect the spatial distribution of less abundant and/or specialist bee species and plants in the long term.     

The influence of space dimension on the large-time behavior in a reaction–diffusion system modeling diallelic selection

We study a mathematical model from population genetics, describing a single-locus diallelic (A/a) selection–migration process. The model consists of a coupled system of three reaction–diffusion equations, one for the density of each genotype, posed in the whole space \mathbb Rⁿ{\mathbb R^n}. The genotype AA is advantageous, due to a smaller death rate, and we consider the fully recessive case where the other two genotypes aa and Aa have the same (higher) death rate. In the nondiffusive (spatially homogeneous) case, the disadvantageous gene a is always eliminated in the large time limit. In the presence of diffusion, when the birth rate exceeds a certain threshold value, we prove that this conclusion is still true for dimensions n ≤ 2, whereas for n ≥ 3 there exist initial distributions for which the advantageous gene A ultimately disappears. This is the first rigorous result of this type for the full system, and it solves a problem which seems to have been open since the celebrated work of Aronson and Weinberger (Lecture notes in mathematics, vol 446, Springer, New York, pp 5–49, 1975; Adv Math 30, 33–76, 1977), where similar results had been obtained for a simplified scalar model, that they derived as an approximation of the full system. Interestingly, we moreover show that, at the threshold value of the birth rate, the cut-off dimension shifts from n = 2 to n = 6.     

Interactive influence of biotic and abiotic cues on the plasticity of preferred body temperatures in a predator–prey system

The ability to modify phenotypes in response to heterogeneity of the thermal environment represents an important component of an ectotherm's non-genetic adaptive capacity. Despite considerable attention being dedicated to the study of thermally-induced developmental plasticity, whether or not interspecific interactions shape the plastic response in both a predator and its prey remains unknown. We tested several predictions about the joint influence of predator/prey scents and thermal conditions on the plasticity of preferred body temperatures (T (p)) in both actors of this interaction, using a dragonfly nymphs-newt larvae system. Dragonfly nymphs (Aeshna cyanea) and newt eggs (Ichthyosaura alpestris) were subjected to fluctuating cold and warm thermal regimes (7-12 and 12-22°C, respectively) and the presence/absence of a predator or prey chemical cues. Preferred body temperatures were measured in an aquatic thermal gradient (5-33°C) over a 24-h period. Newt T (p) increased with developmental temperature irrespective of the presence/absence of predator cues. In dragonflies, thermal reaction norms for T (p) were affected by the interaction between temperature and prey cues. Specifically, the presence of newt scents in cold regime lowered dragonfly T (p). We concluded that predator-prey interactions influenced thermally-induced plasticity of T (p) but not in a reciprocal fashion. The occurrence of frequency-dependent thermal plasticity may have broad implications for predator-prey population dynamics, the evolution of thermal biology traits, and the consequences of sustaining climate change within ecological communities.