Linking the coevolutionary and population dynamics of host-parasitoid interactions

The interplay between coevolutionary and population or community dynamics is currently the focus of much empirical and theoretical consideration. Here, we develop a simulation model to study the coevolutionary and population dynamics of a hypothetical host-parasitoid interaction. In the model, host resistance and parasitoid virulence are allowed to coevolve. We investigate how trade-offs associated with these traits modify the system's coevolutionary and population dynamics. The most important influence on these dynamics comes from the incorporation of density-dependent costs of resistance ability. We find three main outcomes. First, if the costs of resistance are high, then one or both of the players go extinct. Second, when the costs of resistance are intermediate to low, cycling population and coevolutionary dynamics are found, with slower evolutionary changes observed when the costs of virulence are also low. Third, when the costs associated with resistance and virulence are both high, the hosts trade-off resistance against fecundity and invest little in resistance. However, the parasitoids continue to invest in virulence, leading to stable host and parasitoid population sizes. These results support the hypothesis that costs associated with resistance and virulence will maintain the heritable variation in these traits found in natural populations and that the nature of these trade-offs will greatly influence the population dynamics of the interacting species.

Dynamics of shear-induced orientation transitions in block copolymers

This review discusses liquid crystal phase formation by biopolymers in solution. Lyotropic mesophases have been observed for several classes of biopolymer including DNA, peptides, polymer/peptide conjugates, glycopolymers and proteoglycans. Nematic or chiral nematic (cholesteric) phases are the most commonly observed mesophases, in which the rod-like fibrils have only orientational order. Hexagonal columnar phases are observed for several systems (DNA, PBLG, polymer/peptide hybrids) at higher concentration. Lamellar (smectic) phases are reported less often, although there are examples such as the layer arrangement of amylopectin side chains in starch. Possible explanations for the observed structures are discussed. The biological role of liquid crystal phases for several of these systems is outlined. Commonly, they may serve as a template to align fibrils for defined structural roles when the biopolymer is extruded and dried, for instance in the production of silk by spiders or silkworms, or of chitin in arthropod shells. In other cases, liquid crystal phase formation may occur in vivo simply as a consequence of high concentration, for instance the high packing density of DNA within cell nuclei.

Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Dynamics of brand competition: Effects of unobserved social networks

Brand competition is modelled using an agent based approach in order to examine the long run dynamics of market structure and brand characteristics. A repeated game is designed where myopic firms choose strategies based on beliefs about their rivals and consumers. Consumers are heterogeneous and can observe neighbour behaviour through social networks. Although firms do not observe them, the social networks have a significant impact on the emerging market structure. Presence of networks tends to polarize market share and leads to higher volatility in brands. Yet convergence in brand characteristics usually happens whenever the market reaches a steady state. Scale-free networks accentuate the polarization and volatility more than small world or random networks. Unilateral innovations are less frequent under social networks.

Remarkable dynamics of nanoparticles in the urban atmosphere

Nanoparticles emitted from road traffic are the largest source of respiratory exposure for the general public living in urban areas. It has been suggested that the adverse health effects of airborne particles may scale with the airborne particle number, which if correct, focuses attention on the nanoparticle (less than 100 nm) size range which dominates the number count in urban areas. Urban measurements of particle size distributions have tended to show a broadly similar pattern dominated by a mode centred on 20–30 nm diameter particles emitted by diesel engine exhaust. In this paper we report the results of measurements of particle number concentration and size distribution made in a major London park as well as on the BT Tower, 160 m high. These measurements taken during the REPARTEE project (Regents Park and BT Tower experiment) show a remarkable shift in particle size distributions with major losses of the smallest particle class as particles are advected away from the traffic source. In the Park, the traffic related mode at 20–30 nm diameter is much reduced with a new mode at <10 nm. Size distribution measurements also revealed higher number concentrations of sub-50 nm particles at the BT Tower during days affected by higher turbulence as determined by Doppler Lidar measurements and indicate a loss of nanoparticles from air aged during less turbulent conditions. These results suggest that nanoparticles are lost by evaporation, rather than coagulation processes. The results have major implications for understanding the impacts of traffic-generated particulate matter on human health.