Modelling Lipid Competition Dynamics in Heterogeneous Protocell Populations

Recent experimental work in the field of synthetic protocell biology has shown that prebiotic vesicles are able to 'steal' lipids from each other. This phenomenon is driven purely by asymmetries in the physical state or composition of the vesicle membranes, and, when lipid resource is limited, translates directly into competition amongst the vesicles. Such a scenario is interesting from an origins of life perspective because a rudimentary form of cell-level selection emerges. To sharpen intuition about possible mechanisms underlying this behaviour, experimental work must be complemented with theoretical modelling. The aim of this paper is to provide a coarse-grain mathematical model of protocell lipid competition. Our model is capable of reproducing, often quantitatively, results from core experimental papers that reported distinct types vesicle competition. Additionally, we make some predictions untested in the lab, and develop a general numerical method for quickly solving the equilibrium point of a model vesicle population.

Electric fishing survey of the gravel addition sites on the River Wyre, Grizedale Beck and Joshua's Beck.

Although geographically the River Wyre lies between two rivers containing major migrations of adult salmon and sea trout, its rod & line fisheries have for a number of years produced exceptionally low catches. In order to determine the causes of this the Wyre Salmon and Sea trout Restoration Group (WSSRG) was conceived in 1994 as a partnership between the then National Rivers Authority (now Environment Agency), local landowners, angling clubs and interested parties. Two studies of 1994 and 1995 stated that there is a shortage of useable spawning gravels on the river. This is compounded by Abbeystead Reservoir acting as a gravel trap, the siltation of gravels on several side becks and problems with access to available gravels by returning adults. There was also perceived to be a need for accurate fishery data from the river encompassing redd counts, catch data and surveys of fry populations. The 1995 report suggested a number of management proposals which might be adopted in order to improve and create available spawning habitat for migratory salmonids. Funding was made available to create three spawning gravels on each of two side becks (Grizedale Beck and Joshua's Beck) and the addition of gravels to a site oh the main river below Abbeystead Reservoir. Modifications were also made to the fish pass at Abbeystead to allow easier passage of fish. These improvements were made in the autumn of 1995. Salmonid spawning redd counting was undertaken on the whole Wyre catchment in 1995/1996 and specific surveys by electric fishing on the gravel enhancement sites in the summer of 1996. This report details the current state of the improvement works that were undertaken and presents the results of electric fishing surveys in September 1996. A number of lessons have been learnt which will be of great benefit to the Fisheries Function in other parts of the Wyre catchment and the Central Area in general.

Aspects of the biology and population dynamics of freshwater mussels in Lake Kariba and Lake McIlwaine

The essential aim of this study was to provide a broad foundation of biological knowledge upon which a programme of mussel utilization and management could be built. Results of the study are presented in three main sections. Part 1 describes the stock of Lake Kariba and Lake McIlwaine; part 2 describes various aspects of the breeding biology of the three species; and part 3 presents the results of morphological, biochemical and age analyses - aspects which are used for initial standing crop and production calculations. The final discussion concludes the thesis with a general examination in ecological terms of the factors which have influenced the development and nature of the mussel faunas of the two lakes under consideration.

Multiple grasp-specific representations of tool dynamics mediate skillful manipulation.

Skillful tool use requires knowledge of the dynamic properties of tools in order to specify the mapping between applied force and tool motion. Importantly, this mapping depends on the orientation of the tool in the hand. Here we investigate the representation of dynamics during skillful manipulation of a tool that can be grasped at different orientations. We ask whether the motor system uses a single general representation of dynamics for all grasp contexts or whether it uses multiple grasp-specific representations. Using a novel robotic interface, subjects rotated a virtual tool whose orientation relative to the hand could be varied. Subjects could immediately anticipate the force direction for each orientation of the tool based on its visual geometry, and, with experience, they learned to parameterize the force magnitude. Surprisingly, this parameterization of force magnitude showed limited generalization when the orientation of the tool changed. Had subjects parameterized a single general representation, full generalization would be expected. Thus, our results suggest that object dynamics are captured by multiple representations, each of which encodes the mapping associated with a specific grasp context. We suggest that the concept of grasp-specific representations may provide a unifying framework for interpreting previous results related to dynamics learning.

The effects of size-selective fisheries on the stock dynamics of and sperm limitation in sex-changing fish

Fisheries models have traditionally focused on patterns of growth, fecundity, and survival of fish. However, reproductive rates are the outcome of a variety of interconnected factors such as life-history strategies, mating patterns, population sex ratio, social interactions, and individual fecundity and fertility. Behaviorally appropriate models are necessary to understand stock dynamics and predict the success of management strategies. Protogynous sex-changing fish present a challenge for management because size-selective fisheries can drastically reduce reproductive rates. We present a general framework using an individual-based simulation model to determine the effect of life-history pattern, sperm production, mating system, and management strategy on stock dynamics. We apply this general approach to the specific question of how size-selective fisheries that remove mainly males will impact the stock dynamics of a protogynous population with fixed sex change compared to an otherwise identical dioecious population. In this dioecious population, we kept all aspects of the stock constant except for the pattern of sex determination (i.e. whether the species changes sex or is dioecious). Protogynous stocks with fixed sex change are predicted to be very sensitive to the size-selective fishing pattern. If all male size classes are fished, protogynous populations are predicted to crash even at relatively low fishing mortality. When some male size classes escape fishing, we predict that the mean population size of sex-changing stocks will decrease proportionally less than the mean population size of dioecious species experiencing the same fishing mortality. For protogynous species, spawning-per-recruit measures that ignore fertilization rates are not good indicators of the impact of fishing on the population. Decreased mating aggregation size is predicted to lead to an increased effect of sperm limitation at constant fishing mortality and effort. Marine protected areas have the potential to mitigate some effects of fishing on sperm limitation in sex-changing populations.

Fishery dynamics of the California market squid (Loligo opalescens), as measured by satellite remote sensing

Novel data on the spatial and temporal distribution of fishing effort and population abundance are presented for the market squid fishery (Loligo opalescens) in the Southern California Bight, 1992−2000. Fishing effort was measured by the detection of boat lights by the Defense Meteorological Satellite Program (DMSP) Operational Linescan System (OLS). Visual confirmation of fishing vessels by nocturnal aerial surveys indicated that lights detected by satellites are reliable indicators of fishing effort. Overall, fishing activity was concentrated off the following Channel Islands: Santa Rosa, Santa Cruz, Anacapa, and Santa Catalina. Fishing activity occurred at depths of 100 m or less. Landings, effort, and squid abundance (measured as landings per unit of effort, LPUE) markedly declined during the 1997−98 El Niño; landings and LPUE increased afterwards. Within a fishing season, the location of fishing activity shifted from the northern shores of Santa Rosa and Santa Cruz Islands in October, the typical starting date for squid fishing in the Bight, to the southern shores by March, the typical end of the squid season. Light detection by satellites offers a source of fine-scale spatial and temporal data on fishing effort for the market squid fishery off California, and these data can be integrated with environmental data and fishing logbook data in the development of a management plan.

A general framework for integrating environmental time series into stock assessment models: model description, simulation testing, and example

We present a method to integrate environmental time series into stock assessment models and to test the significance of correlations between population processes and the environmental time series. Parameters that relate the environmental time series to population processes are included in the stock assessment model, and likelihood ratio tests are used to determine if the parameters improve the fit to the data significantly. Two approaches are considered to integrate the environmental relationship. In the environmental model, the population dynamics process (e.g. recruitment) is proportional to the environmental variable, whereas in the environmental model with process error it is proportional to the environmental variable, but the model allows an additional temporal variation (process error) constrained by a log-normal distribution. The methods are tested by using simulation analysis and compared to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. In the traditional method, the estimates of recruitment were provided by a model that allowed the recruitment only to have a temporal variation constrained by a log-normal distribution. We illustrate the methods by applying them to test the statistical significance of the correlation between sea-surface temperature (SST) and recruitment to the snapper (Pagrus auratus) stock in the Hauraki Gulf–Bay of Plenty, New Zealand. Simulation analyses indicated that the integrated approach with additional process error is superior to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. The results suggest that, for the snapper stock, recruitment is positively correlated with SST at the time of spawning.

Decadal climate variability over the North Pacific and North America: dynamics and predictability [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): The dynamics and predictability of decadal climate variability over the North Pacific and North America are investigated by analyzing various observational datasets and the output of a state-of-the-art coupled ocean-atmosphere general circulation model, which was integrated for 120 years.

Towards identification of a general model of damping

Characterization of damping forces in a vibrating structure has long been an active area of research in structural dynamics. In spite of a large amount of research, understanding of damping mechanisms is not well developed. A major reason for this is that unlike inertia and stiffness forces it is not in general clear what are the state variables that govern the damping forces. The most common approach is to use `viscous damping' where the instantaneous generalized velocities are the only relevant state variables. However, viscous damping by no means the only damping model within the scope of linear analysis. Any model which makes the energy dissipation functional non-negative is a possible candidate for a valid damping model. This paper is devoted to develop methodologies for identification of such general damping models responsible for energy dissipation in a vibrating structure. The method uses experimentally identified complex modes and complex natural frequencies and does not a-priori assume any fixed damping model (eg., viscous damping) but seeks to determine parameters of a general damping model described by the so called `relaxation function'. The proposed method and several related issues are discussed by considering a numerical example of a linear array of damped spring-mass oscillators.

90° domain dynamics and relaxation in thin ferroelectric/ferroelastic films

We investigated the dynamics and relaxation of 90° domains in 60-nm-thick lead-zirconium titanate (PbZr0.3 T0.7 O3) films, with enhanced piezoresponse force microscopy. We show that under opposite electric fie ld, ferroelectric domains are reversibly switched while ferroelastic domains reorganize in a nonreversible way. Moreover, we show that the relaxation-time constant of 90° domains is two orders of magnitude shorter than for the previously reported 180° domains relaxation. Furthermore, we demonstrate the influence of geometry and scale on the relaxation process. Finally, we propose a relaxation mechanism for ferroelastic-ferroelectric systems, with implications for devices based on these materials. © 2010 The American Physical Society.

Scalable robustness for consensus protocols with heterogeneous dynamics

It is shown in the paper how robustness can be guaranteed for consensus protocols with heterogeneous dynamics in a scalable and decentralized way i.e. by each agent satisfying a test that does not require knowledge of the entire network. Random graph examples illustrate that the proposed certificates are not conservative for classes of large scale networks, despite the heterogeneity of the dynamics, which is a distinctive feature of this work. The conditions hold for symmetric protocols and more conservative stability conditions are given for general nonsymmetric interconnections. Nonlinear extensions in an IQC framework are finally discussed. Copyright © 2005 IFAC.

Dynamics of parasite population and its histopathological and histophysiological effects in the stomach of a freshwater fish

The caryophyllaeid cestode Lytocestoides fossilis infects the freshwater catfish Heteropneustes fossilis. The study was conducted for two consecutive years (2004-06) to record the bio-statistical data of the parasite. The incidence, intensity, density and index of infection of the parasite have been recorded. The infection was more during June to September, moderate during February to May and low during October to January. The parasite brought about severe histopathological changes in the stomach of infected fish. The changes observed in the stomach of fish included structural damage of the villi, inflammation, and fibrosis associated with hyperplasia and metaplasia. The hypertrophy of mucous layer led to vacuolation and necrosis. Histochemical changes were noticed with enhanced carbohydrate, protein and lipid contents. The enhanced substrate content in the infected organ might be due to the disfunctioning of the digestive tract, which results in the accumulation of various metabolites. Mucus secretion was triggered as a protective interaction against parasitic invasion. The parasitic infection affects the general metabolic state of the host and as the result, the fish becomes sluggish and moribund.

Assessment of computational fluid dynamics and experimental data for shock boundary-layer interactions

A workshop on the computational fluid dynamics (CFD) prediction of shock boundary-layer interactions (SBLIs) was held at the 48th AIAA Aerospace Sciences Meeting. As part of the workshop, numerous CFD analysts submitted solutions to four experimentally measured SBLIs. This paper describes the assessment of the CFD predictions. The assessment includes an uncertainty analysis of the experimental data, the definition of an error metric, and the application of that metric to the CFD solutions. The CFD solutions provided very similar levels of error and, in general, it was difficult to discern clear trends in the data. For the Reynolds-averaged Navier-Stokes (RANS) methods, the choice of turbulence model appeared to be the largest factor in solution accuracy. Scale-resolving methods, such as large-eddy simulation (LES), hybrid RANS/LES, and direct numerical simulation, produced error levels similar to RANS methods but provided superior predictions of normal stresses. Copyright © 2012 by Daniella E. Raveh and Michael Iovnovich.

Combustion rumble prediction with integrated computational-fluid-dynamics/ low-order-model methods

The pressure oscillation within combustion chambers of aeroengines and industrial gas turbines is a major technical challenge to the development of high-performance and low-emission propulsion systems. In this paper, an approach integrating computational fluid dynamics and one-dimensional linear stability analysis is developed to predict the modes of oscillation in a combustor and their frequencies and growth rates. Linear acoustic theory was used to describe the acoustic waves propagating upstream and downstream of the combustion zone, which enables the computational fluid dynamics calculation to be efficiently concentrated on the combustion zone. A combustion oscillation was found to occur with its predicted frequency in agreement with experimental measurements. Furthermore, results from the computational fluid dynamics calculation provide the flame transfer function to describe unsteady heat release rate. Departures from ideal one-dimensional flows are described by shape factors. Combined with this information, low-order models can work out the possible oscillation modes and their initial growth rates. The approach developed here can be used in more general situations for the analysis of combustion oscillations. Copyright © 2012 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Quantification of the effects of antibodies on the extra- and intracellular dynamics of Salmonella enterica.

Antibodies are known to be essential in controlling Salmonella infection, but their exact role remains elusive. We recently developed an in vitro model to investigate the relative efficiency of four different human immunoglobulin G (IgG) subclasses in modulating the interaction of the bacteria with human phagocytes. Our results indicated that different IgG subclasses affect the efficacy of Salmonella uptake by human phagocytes. In this study, we aim to quantify the effects of IgG on intracellular dynamics of infection by combining distributions of bacterial numbers per phagocyte observed by fluorescence microscopy with a mathematical model that simulates the in vitro dynamics. We then use maximum likelihood to estimate the model parameters and compare them across IgG subclasses. The analysis reveals heterogeneity in the division rates of the bacteria, strongly suggesting that a subpopulation of intracellular Salmonella, while visible under the microscope, is not dividing. Clear differences in the observed distributions among the four IgG subclasses are best explained by variations in phagocytosis and intracellular dynamics. We propose and compare potential factors affecting the replication and death of bacteria within phagocytes, and we discuss these results in the light of recent findings on dormancy of Salmonella.