How does a β-hairpin fold/unfold? Competition between topology and heterogeneity in a solvable model

We study the competition between topological effects and sequence inhomogeneities in determining the thermodynamics and the un/folding kinetics of a β-hairpin. Our work utilizes a new exactly solvable model that allows for arbitrary configurations of native contacts. In general, the competition between heterogeneity and topology results in a crossover of the dominant transition state. Interestingly, near this crossover, the single reaction coordinate picture can be seriously misleading. Our results also suggest that inferring the folding pathway from unfolding simulations is not always justified.

A model of self-thinning through local competition.

Explanations of self-thinning in plant populations have focused on plant shape and packing. A dynamic model based on the structure of local interactions successfully reproduces the pattern and can be approximated to identify key parameters and relationships. The approach generates testable new explanations for differences between species and populations, unifies self-thinning with other patterns in plant population dynamics, and indicates why organisms other than plants can follow the law.

Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model

One of the simplest models of adaptation to a new environment is Fisher's Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations-mutation cohorts-along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation-FGM.

Testes de desempenho aeróbio relacionados a intensidades de corrida em treinamento e competição para fundistas de alto rendimento = : Aerobic performance tests related to training and competition running intensities for high performance distance runners

Universidade Estadual de Campinas . Faculdade de Educação Física

Particle competition for complex network community detection

In many real situations, randomness is considered to be uncertainty or even confusion which impedes human beings from making a correct decision. Here we study the combined role of randomness and determinism in particle dynamics for complex network community detection. In the proposed model, particles walk in the network and compete with each other in such a way that each of them tries to possess as many nodes as possible. Moreover, we introduce a rule to adjust the level of randomness of particle walking in the network, and we have found that a portion of randomness can largely improve the community detection rate. Computer simulations show that the model has good community detection performance and at the same time presents low computational complexity. (C) 2008 American Institute of Physics.

Dynamic transitions in a two dimensional associating lattice gas model

Using Monte Carlo simulations we investigate some new aspects of the phase diagram and the behavior of the diffusion coefficient in an associating lattice gas (ALG) model on different regions of the phase diagram. The ALG model combines a two dimensional lattice gas where particles interact through a soft core potential and orientational degrees of freedom. The competition between soft core potential and directional attractive forces results in a high density liquid phase, a low density liquid phase, and a gas phase. Besides anomalies in the behavior of the density with the temperature at constant pressure and of the diffusion coefficient with density at constant temperature are also found. The two liquid phases are separated by a coexistence line that ends in a bicritical point. The low density liquid phase is separated from the gas phase by a coexistence line that ends in tricritical point. The bicritical and tricritical points are linked by a critical lambda-line. The high density liquid phase and the fluid phases are separated by a second critical tau-line. We then investigate how the diffusion coefficient behaves on different regions of the chemical potential-temperature phase diagram. We find that diffusivity undergoes two types of dynamic transitions: a fragile-to-strong transition when the critical lambda-line is crossed by decreasing the temperature at a constant chemical potential; and a strong-to-strong transition when the critical tau-line is crossed by decreasing the temperature at a constant chemical potential.

A PHASE TRANSITION FOR COMPETITION INTERFACES

We study the competition interface between two growing clusters in a growth model associated to last-passage percolation. When the initial unoccupied set is approximately a cone, we show that this interface has an asymptotic direction with probability 1. The behavior of this direction depends on the angle theta of the cone: for theta >= 180 degrees, the direction is deterministic, while for theta < 180 degrees, it is random, and its distribution can be given explicitly in certain cases. We also obtain partial results on the fluctuations of the interface around its asymptotic direction. The evolution of the competition interface in the growth model can be mapped onto the path of a second-class particle in the totally asymmetric simple exclusion process; from the existence of the limiting direction for the interface, we obtain a new and rather natural proof of the strong law of large numbers (with perhaps a random limit) for the position of the second-class particle at large times.

Grazers and diggers: Exploitation competition and coexistence among foragers with different feeding strategies on a single resource

A mathematical model is presented that describes a system where two consumer species compete exploitatively for a single renewable resource. The resource is distributed in a patchy but homogeneous environment; that is, all patches are intrinsically identical. The two consumer species are referred to as diggers and grazers, where diggers deplete the resource within a patch to lower densities than grazers. We show that the two distinct feeding strategies can produce a heterogeneous resource distribution that enables their coexistence. Coexistence requires that grazers must either move faster than diggers between patches or convert the resources to population growth much more efficiently than diggers. The model shows that the functional form of resource renewal within a patch is also important for coexistence. These results contrast with theory that considers exploitation competition for a single resource when the resource is assumed to be well mixed throughout the system.

Modeling the Competition Between Viruses in a Complex Plant-Pathogen System

In this article, we propose a mathematical model that describes the competition between two plant virus strains (MAV and PAV) for both the host plant (oat) and their aphid vectors. We found that although PAV is transmitted by two aphids and MAV by only one, this fact, by itself, does not explain the complete replacement of MAV by PAV in New York State during the period from 1961 through 1976; an interpretation that is in agreement with the theories of A. G. Power. Also, although MAV wins the competition within aphids, we assumed that, in 1961, PAV mutated into a new variant such that this new variant was able to overcome MAV within the plants during a latent period. As shown below, this is sufficient to explain the swap of strains; that is, the dominant MAV was replaced by PAV, also in agreement with Power`s expectations.

Application of spatial analysis techniques to adjust for fertility trends and identify interplot competition in early stage sugarcane selection trials

Most sugarcane breeding programs in Australia use large unreplicated trials to evaluate clones in the early stages of selection. Commercial varieties that are replicated provide a method of local control of soil fertility. Although such methods may be useful in detecting broad trends in the field, variation often occurs on a much smaller scale. Methods such as spatial analysis adjust a plot for variability by using information from immediate neighbours. These techniques are routinely used to analyse cereal data in Australia and have resulted in increased accuracy and precision in the estimates of variety effects. In this paper, spatial analyses in which the variability is decomposed into local, natural, and extraneous components are applied to early selection trials in sugarcane. Interplot competition in cane yield and trend in sugar content were substantial in many of the trials and there were often large differences in the selections between the spatial and current method used by the Bureau of Sugar Experiment Stations. A joint modelling approach for tonnes sugar per hectare in response to fertility trends and interplot competition is recommended.

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges. (C) 2003 Wiley Periodicals, Inc.

SPAnDX: a process-based population dynamics model to explore management and climate change impacts on an invasive alien plant, Acacia nilotica

This paper describes a process-based metapopulation dynamics and phenology model of prickly acacia, Acacia nilotica, an invasive alien species in Australia. The model, SPAnDX, describes the interactions between riparian and upland sub-populations of A. nilotica within livestock paddocks, including the effects of extrinsic factors such as temperature, soil moisture availability and atmospheric concentrations of carbon dioxide. The model includes the effects of management events such as changing the livestock species or stocking rate, applying fire, and herbicide application. The predicted population behaviour of A. nilotica was sensitive to climate. Using 35 years daily weather datasets for five representative sites spanning the range of conditions that A. nilotica is found in Australia, the model predicted biomass levels that closely accord with expected values at each site. SPAnDX can be used as a decision-support tool in integrated weed management, and to explore the sensitivity of cultural management practices to climate change throughout the range of A. nilotica. The cohort-based DYMEX modelling package used to build and run SPAnDX provided several advantages over more traditional population modelling approaches (e.g. an appropriate specific formalism (discrete time, cohort-based, process-oriented), user-friendly graphical environment, extensible library of reusable components, and useful and flexible input/output support framework). (C) 2003 Published by Elsevier Science B.V.

Market power analysis in the Iberian electricity market using a conjectural variations model

In the last years the electricity industry has faced a restructuring process. Among the aims of this process was the increase in competition, especially in the generation activity where firms would have an incentive to become more efficient. However, the competitive behavior of generating firms might jeopardize the expected benefits of the electricity industry liberalization. The present paper proposes a conjectural variations model to study the competitive behavior of generating firms acting in liberalized electricity markets. The model computes a parameter that represents the degree of competition of each generating firm in each trading period. In this regard, the proposed model provides a powerful methodology for regulatory and competition authorities to monitor the competitive behavior of generating firms. As an application of the model, a study of the day-ahead Iberian electricity market (MIBEL) was conducted to analyze the impact of the integration of the Portuguese and Spanish electricity markets on the behavior of generating firms taking into account the hourly results of the months of June and July of 2007. The advantages of the proposed methodology over other methodologies used to address market power, namely Residual Supply index and Lerner index are highlighted. (C) 2014 Elsevier Ltd. All rights reserved.

Three-dimensial patchy lattice model: Ring formation and phase separation

We investigate the structural and thermodynamic properties of a model of particles with 2 patches of type A and 10 patches of type B. Particles are placed on the sites of a face centered cubic lattice with the patches oriented along the nearest neighbor directions. The competition between the self- assembly of chains, rings, and networks on the phase diagram is investigated by carrying out a systematic investigation of this class of models, using an extension ofWertheim's theory for associating fluids and Monte Carlo numerical simulations. We varied the ratio r epsilon(AB)/epsilon(AA) of the interaction between patches A and B, epsilon(AB), and between A patches, epsilon(AA) (epsilon(BB) is set to theta) as well as the relative position of the A patches, i.e., the angle. between the (lattice) directions of the A patches. We found that both r and theta (60 degrees, 90 degrees, or 120 degrees) have a profound effect on the phase diagram. In the empty fluid regime (r < 1/2) the phase diagram is reentrant with a closed miscibility loop. The region around the lower critical point exhibits unusual structural and thermodynamic behavior determined by the presence of relatively short rings. The agreement between the results of theory and simulation is excellent for theta = 120 degrees but deteriorates as. decreases, revealing the need for new theoretical approaches to describe the structure and thermodynamics of systems dominated by small rings. (C) 2014 AIP Publishing LLC.

Quantity-setting competition with differentiated goods under uncertain demand

We consider a quantity-setting duopoly model, and we study the decision to move first or second, by assuming that the firms produce differentiated goods and that there is some demand uncertainty. The competitive phase consists of two periods, and in either period, the firms can make a production decision that is irreversible. As far as the firms are allowed to choose (non-cooperatively) the period they make the decision, we study the circumstances that favour sequential rather than simultaneous decisions.