Relevance of metal ions for lipase stability: Structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion

We have studied the accessibility of the structural calcium ion in the Burkholderia glumae lipase and the consequences of its removal on the protein conformation by different biophysical techniques (circular dichroism, fluorimetry, and mass spectrometry) and by molecular-dynamics simulations. We show that, in the native protein, calcium is not accessible unless specific flexible loops are displaced, for example, by a temperature increase. Such movements concern the whole calcium-binding pocket and particularly the environment of the coordinating aspartate residue 241. As a consequence of metal depletion the protein unfolds irreversibly and undergoes aggregation. The removal of the metal ion causes major structural transitions and leads to an increase in β-structure, in particular in protein regions that are largely unstructured in the native protein and encompass the calcium coordination residues.     

Stokes–Einstein violation and fragility in calcium aluminosilicate glass formers: a molecular dynamics study

A series of classical molecular dynamics simulations of calcium aluminosilicate (CAS) (CaO–Al₂O₃)_1–x(SiO₂)_x melts with varying silica content x, along the CaO/Al₂O₃ concentration ratio R = 1, have been performed for the purpose of studying (i) the evolution of fragility with silica content and (ii) the temperature and composition evolution of self-diffusion coefficients, viscosity and α-relaxation times. Our results indicate a decrease in the fragility of the CAS systems along R = 1 from calcium aluminate to pure silica. It is found that upon cooling, the Stokes–Einstein relation breaks down at a temperature significantly higher than the critical temperature of the mode-coupling theory T_C for all compositions and also above the melting point.     

Nonorthogonal tight-binding model with H–C–N–O parameterisation

A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info.     

Allee effects and extinction in a lattice model

In the interest of conservation, the importance of having a large habitat available for a species is widely known. Here, we introduce a lattice-based model for a population and look at the importance of fluctuations as well as that of the population density, particularly with respect to Allee effects. We examine the model analytically and by Monte Carlo simulations and find that, while the size of the habitat is important, there exists a critical population density below which the probability of extinction is greatly increased. This has large consequences with respect to conservation, especially in the design of habitats and for populations whose density has become small. In particular, we find that the probability of survival for small populations can be increased by a reduction in the size of the habitat and show that there exists an optimal size reduction.     

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Analysis of linkage disequilibrium (=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N _e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N _e based on for unlinked, diallelic gene loci are sharply biased downwards ( in some cases) if sample size (S) is less than true N _e. The bias is shown to arise from inaccuracies in published formula for when S and/or N _e are small. Empirically derived modifications to for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in % in most cases). The modified method also performs well in estimating N _e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect , but if N has recently increased from a bottleneck can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N _e in natural populations. However, a comprehensive assessment of performance of with highly polymorphic markers such as microsatellites is needed.The US Governmentȁ9s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

The effects of metamaterial on electromagnetic fields absorption characteristics of human eye tissues

The interaction of a dipole antenna with a human eye model in the presence of a metamaterial is investigated in this paper. The finite difference time domain (FDTD) method with convolutional perfectly matched layer (CPML) formulation have been used. A three-dimensional anatomical model of the human eye with resolution of 1.25 mm × 1.25 mm × 1.25 mm was used in this study. The dipole antenna was driven by modulated Gaussian pulse and the numerical study is performed with dipole operating at 900 MHz. The analysis has been done by varying the size and value of electric permittivity of the metamaterial. By normalizing the peak SAR (1 g and 10 g) to 1 W for all examined cases, we observed how the SAR values are not affected by the different permittivity values with the size of the metamaterial kept fixed.     

Mobility unevenness in rock–paper–scissors models

We investigate a tritrophic system whose cyclic dominance is modelled by the rock–paper–scissors game. We consider that organisms of one or two species are affected by movement limitations, which unbalances the cyclic spatial game. Performing stochastic simulations, we show that mobility unevenness controls the population dynamics. In the case of one slow species, the predominant species depends on the level of mobility restriction, with the slow species being preponderant if the mobility limitations are substantial. If two species face mobility limitations, our outcomes show that being higher dispersive does not constitute an advantage in terms of population growth. On the contrary, if organisms move with higher mobility, they expose themselves to enemies more frequently, being more vulnerable to being eliminated. Finally, our findings show that biodiversity benefits in regions where species are slowed. Biodiversity loss for high mobility organisms, common to cyclic systems, may be avoided with coexistence probability being higher for robust mobility limitations. Our results may help biologists understand the dynamics of unbalanced spatial systems where organisms’ dispersal is fundamental to biodiversity conservation.     

Molecular simulations in metal–organic frameworks for diverse potential applications

As a new class of intriguing nanoporous materials, metal–organic frameworks (MOFs) have been considered for diverse potential applications. The number of MOFs synthesised to date is extremely large; thus, experimental testing alone is economically expensive and practically formidable. With rapidly growing computational resources, molecular simulation has become an indispensable tool to characterise, screen and design MOFs. Our research group has conducted comprehensive simulation studies in MOFs for carbon capture, hydrocarbon separation, alcohol adsorption and biofuel purification, water treatment, bio- and chiral separation and drug loading; furthermore, mechanical moduli, structural transition and thermal conductivity have also been examined. These systematic simulation studies are summarised in this review to demonstrate that simulation at a molecular level can secure the quantitative interpretation of experimental observation, provide the microscopic insight from bottom-up and facilitate the development of new MOFs.     

Strategy selection in structured populations

Evolutionary game theory studies frequency dependent selection. The fitness of a strategy is not constant, but depends on the relative frequencies of strategies in the population. This type of evolutionary dynamics occurs in many settings of ecology, infectious disease dynamics, animal behavior and social interactions of humans. Traditionally evolutionary game dynamics are studied in well-mixed populations, where the interaction between any two individuals is equally likely. There have also been several approaches to study evolutionary games in structured populations. In this paper we present a simple result that holds for a large variety of population structures. We consider the game between two strategies, A and B, described by the payoff matrix . We study a mutation and selection process. For weak selection strategy A is favored over B if and only if σa+b>c+σd. This means the effect of population structure on strategy selection can be described by a single parameter, σ. We present the values of σ for various examples including the well-mixed population, games on graphs, games in phenotype space and games on sets. We give a proof for the existence of such a σ, which holds for all population structures and update rules that have certain (natural) properties. We assume weak selection, but allow any mutation rate. We discuss the relationship between σ and the critical benefit to cost ratio for the evolution of cooperation. The single parameter, σ, allows us to quantify the ability of a population structure to promote the evolution of cooperation or to choose efficient equilibria in coordination games.     

Food-supplementing parents reduces their sons' song repertoire size

Food-supplemented parents typically produce more offspring, as numerous experiments on vertebrate populations have shown. ‘Propagule’ (egg or neonate) size and parental care may also be affected, with implications concerning the adult quality of offspring, although few experiments have addressed whether food-supplementing one generation affects adult quality in the next. We conducted a food supplementation experiment on song sparrows (Melospiza melodia) and tested whether song repertoire size, a demonstrated indicator of male quality, differed between the adult sons of fed (food-supplemented) and unfed (non-food-supplemented) parents. Counterintuitively, fed parents produced sons with smaller adult song repertoires, who may thus be expected to contribute fewer offspring, and fewer grand-offspring, to the population. Fed and unfed parents invested equally in the total biomass of their clutches and broods, and average nestling condition was comparable, but because fed parents produced more offspring, average egg and nestling sizes were reduced. Fed and unfed parents apportioned care differently within their broods, and we suggest compensatory growth of offspring emerging from light eggs, or egg size itself, may have affected adult repertoire size. Conceivably, the conservation benefits of food-supplementing populations could attenuate over time if fed parents produce offspring of poorer quality than themselves.