Energy-scales convergence for optimal and robust quantum transport in photosynthetic complexes

Underlying physical principles for the high efficiency of excitation energy transfer in light-harvesting complexes are not fully understood. Notably, the degree of robustness of these systems for transporting energy is not known considering their realistic interactions with vibrational and radiative environments within the surrounding solvent and scaffold proteins. In this work, we employ an efficient technique to estimate energy transfer efficiency of such complex excitonic systems. We observe that the dynamics of the Fenna-Matthews-Olson (FMO) complex leads to optimal and robust energy transport due to a convergence of energy scales among all important internal and external parameters. In particular, we show that the FMO energy transfer efficiency is optimum and stable with respect to the relevant parameters of environmental interactions and Frenkel-exciton Hamiltonian including reorganization energy $\lambda$, bath frequency cutoff $\gamma$, temperature $T$, bath spatial correlations, initial excitations, dissipation rate, trapping rate, disorders, and dipole moments orientations. We identify the ratio of \lambda T/\gamma\*g as a single key parameter governing quantum transport efficiency, where g is the average excitonic energy gap.Comment: minor revisions, removing some figures, 19 pages, 19 figure

Where should livestock graze? Integrated modeling and optimization to guide grazing management in the Cañete basin, Peru

Integrated watershed management allows decision-makers to balance competing objectives, for example agricultural production and protection of water resources. Here, we developed a spatially-explicit approach to support such management in the Cañete watershed, Peru. We modeled the effect of grazing management on three services – livestock production, erosion control, and baseflow provision – and used an optimization routine to simulate landscapes providing the highest level of services. Over the entire watershed, there was a trade-off between livestock productivity and hydrologic services and we identified locations that minimized this trade-off for a given set of preferences. Given the knowledge gaps in ecohydrology and practical constraints not represented in the optimizer, we assessed the robustness of spatial recommendations, i.e. revealing areas most often selected by the optimizer. We conclude with a discussion of the practical decisions involved in using optimization frameworks to inform watershed management programs, and the research needs to better inform the design of such programs

Potential landscape-scale pollinator networks across Great Britain: structure, stability and influence of agricultural land cover

Understanding spatial variation in the structure and stability of plant-pollinator networks, and their relationship with anthropogenic drivers, is key to maintaining pollination services and mitigating declines. Constructing sufficient networks to examine patterns over large spatial scales remains challenging. Using biological records (citizen science), we constructed potential plant-pollinator networks at 10km resolution across Great Britain, comprising all potential interactions inferred from recorded floral visitation and species co-occurrence. We calculated network metrics (species richness, connectance, pollinator and plant generality) and adapted existing methods to assess robustness to sequences of simulated plant extinctions across multiple networks. We found positive relationships between agricultural land cover and both pollinator generality and robustness to extinctions under several extinction scenarios. Increased robustness was attributable to changes in plant community composition (fewer extinction-prone species) and network structure (increased pollinator generality). Thus, traits enabling persistence in highly agricultural landscapes can confer robustness to potential future perturbations on plant-pollinator networks

Tools for Assessing Climate Impacts on Fish and Wildlife

Climate change is already affecting many fish and wildlife populations. Managing these populations requires an understanding of the nature, magnitude, and distribution of current and future climate impacts. Scientists and managers have at their disposal a wide array of models for projecting climate impacts that can be used to build such an understanding. Here, we provide a broad overview of the types of models available for forecasting the effects of climate change on key processes that affect fish and wildlife habitat (hydrology, fire, and vegetation), as well as on individual species distributions and populations. We present a framework for how climate-impacts modeling can be used to address management concerns, providing examples of model-based assessments of climate impacts on salmon populations in the Pacific Northwest, fire regimes in the boreal region of Canada, prairies and savannas in the Willamette Valley-Puget Sound Trough-Georgia Basin ecoregion, and marten Martes americana populations in the northeastern United States and southeastern Canada. We also highlight some key limitations of these models and discuss how such limitations should be managed. We conclude with a general discussion of how these models can be integrated into fish and wildlife management

Noise control and utility: From regulatory network to spatial patterning

Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major mystery. Regulatory network configurations, such as their topology and timescale, are shown to be critical in attenuating noise, and noise is also found to facilitate cell fate decision. Here we review major recent findings on noise attenuation through regulatory control, the benefit of noise via noise-induced cellular plasticity during developmental patterning, and summarize key principles underlying noise control

Half a billion simulations: evolutionary algorithms and distributed computing for calibrating the SimpopLocal geographical model

Multi-agent geographical models integrate very large numbers of spatial interactions. In order to validate those models large amount of computing is necessary for their simulation and calibration. Here a new data processing chain including an automated calibration procedure is experimented on a computational grid using evolutionary algorithms. This is applied for the first time to a geographical model designed to simulate the evolution of an early urban settlement system. The method enables us to reduce the computing time and provides robust results. Using this method, we identify several parameter settings that minimise three objective functions that quantify how closely the model results match a reference pattern. As the values of each parameter in different settings are very close, this estimation considerably reduces the initial possible domain of variation of the parameters. The model is thus a useful tool for further multiple applications on empirical historical situations

Doing evolution in economic geography

Evolutionary approaches in economic geography face questions about the relationships between their concepts, theories, methods, politics, and policy implications. Amidst the growing but unsettled consensus that evolutionary approaches should employ plural methodologies, the aims here are, first, to identify some of the difficult issues confronting those working with different frameworks. The concerns comprise specifying and connecting research objects, subjects, and levels; handling agency and context; engaging and integrating the quantitative and the qualitative; comparing cases; and, considering politics, policy, and praxis. Second, the purpose is to articulate a distinctive geographical political economy approach, methods, and illustrative examples in addressing these issues. Bringing different views of evolution in economic geography into dialogue and disagreement renders methodological pluralism a means toward improved understanding and explanation rather than an end in itself. Confronting such thorny matters needs to be embedded in our research practices and supported by greater openness; more and better substantiation of our conceptual, theoretical, and empirical claims; enhanced critical reflection; and deeper engagement with politics, policy, and praxis

Force-imitated particle swarm optimization using the near-neighbor effect for locating multiple optima

Copyright @ Elsevier Inc. All rights reserved.Multimodal optimization problems pose a great challenge of locating multiple optima simultaneously in the search space to the particle swarm optimization (PSO) community. In this paper, the motion principle of particles in PSO is extended by using the near-neighbor effect in mechanical theory, which is a universal phenomenon in nature and society. In the proposed near-neighbor effect based force-imitated PSO (NN-FPSO) algorithm, each particle explores the promising regions where it resides under the composite forces produced by the “near-neighbor attractor” and “near-neighbor repeller”, which are selected from the set of memorized personal best positions and the current swarm based on the principles of “superior-and-nearer” and “inferior-and-nearer”, respectively. These two forces pull and push a particle to search for the nearby optimum. Hence, particles can simultaneously locate multiple optima quickly and precisely. Experiments are carried out to investigate the performance of NN-FPSO in comparison with a number of state-of-the-art PSO algorithms for locating multiple optima over a series of multimodal benchmark test functions. The experimental results indicate that the proposed NN-FPSO algorithm can efficiently locate multiple optima in multimodal fitness landscapes.This work was supported in part by the Key Program of National Natural Science Foundation (NNSF) of China under Grant 70931001, Grant 70771021, and Grant 70721001, the National Natural Science Foundation (NNSF) of China for Youth under Grant 61004121, Grant 70771021, the Science Fund for Creative Research Group of NNSF of China under Grant 60821063, the PhD Programs Foundation of Ministry of Education of China under Grant 200801450008, and in part by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1 and Grant EP/E060722/2