Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Dirac electrons in graphene-based quantum wires and quantum dots

In this paper we analyse the electronic properties of Dirac electrons in finite-size ribbons and in circular and hexagonal quantum dots made of graphene.Comment: Contribution for J. Phys.: Cond. Mat. special issue on graphene physic

Using argument notation to engineer biological simulations with increased confidence

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions

The supply chain of violence

Every year, more people are killed defending the environment than are soldiers from the United Kingdom and Australia on overseas deployments in war zones combined. During the last 15 years, the number of both deaths of environmental defenders, and the countries where they occur, have increased. Recorded deaths have increased from two per week to four per week over this period. These deaths are primarily related to conflict over natural resources, across a range of sectors. Of 683 total deaths, >230 were related to mining and agribusiness between 2014 and 2017. We find that rule of law and corruption indices are closely linked to patterns of killings. Using spatial data, we investigate the drivers of these conflicts and violence and seek to identify who may be most at risk and why. We argue that businesses, investors and national governments at both ends of the chain of violence need to be more accountable

Watershed Management on Range and Forest Lands Proceedings of the Fifth Workshop of the United States/Australia Rangelands Panel

Preface: The U.S.-Australia Cooperative Rangeland Science Program In October 1968 the governments of the United States and Australia entered into an agreement for the purpose of facilitating close cooperative activities between the scientific communities of the two countries. The joint communique issued at that time designated the U.S. National Science Foundation and the Australian Commonwealth Department of Education and Science as the coordinating agencies. Both countries were to encourage binational teamwork in research, interchanges of scientists, joint seminars, and exchanges of information. A United States-Australia Rangeland Panel was established in December 1969 to further cooperation between the two countries in the rangeland sciences. The present panel includes the following

The Impact of HAART on the Respiratory Complications of HIV Infection: Longitudinal Trends in the MACS and WIHS Cohorts

Objective: To review the incidence of respiratory conditions and their effect on mortality in HIV-infected and uninfected individuals prior to and during the era of highly active antiretroviral therapy (HAART). Design: Two large observational cohorts of HIV-infected and HIV-uninfected men (Multicenter AIDS Cohort Study [MACS]) and women (Women's Interagency HIV Study [WIHS]), followed since 1984 and 1994, respectively. Methods: Adjusted odds or hazards ratios for incident respiratory infections or non-infectious respiratory diagnoses, respectively, in HIV-infected compared to HIV-uninfected individuals in both the pre-HAART (MACS only) and HAART eras; and adjusted Cox proportional hazard ratios for mortality in HIV-infected persons with lung disease during the HAART era. Results: Compared to HIV-uninfected participants, HIV-infected individuals had more incident respiratory infections both pre-HAART (MACS, odds ratio [adjusted-OR], 2.4; 95% confidence interval [CI], 2.2-2.7; p<0.001) and after HAART availability (MACS, adjusted-OR, 1.5; 95%CI 1.3-1.7; p<0.001; WIHS adjusted-OR, 2.2; 95%CI 1.8-2.7; p<0.001). Chronic obstructive pulmonary disease was more common in MACS HIV-infected vs. HIV-uninfected participants pre-HAART (hazard ratio [adjusted-HR] 2.9; 95%CI, 1.02-8.4; p = 0.046). After HAART availability, non-infectious lung diseases were not significantly more common in HIV-infected participants in either MACS or WIHS participants. HIV-infected participants in the HAART era with respiratory infections had an increased risk of death compared to those without infections (MACS adjusted-HR, 1.5; 95%CI, 1.3-1.7; p<0.001; WIHS adjusted-HR, 1.9; 95%CI, 1.5-2.4; p<0.001). Conclusion: HIV infection remained a significant risk for infectious respiratory diseases after the introduction of HAART, and infectious respiratory diseases were associated with an increased risk of mortality. © 2013 Gingo et al

China’s Dam Builders: their role in transboundary river management in Southeast Asia

This article investigates China’s role as the world’s largest builder of and investor in large dams, focussing on the Greater Mekong Sub-Region in South-East Asia. It addresses the role Chinese actors play in dam-building as well as the environmental, social, economic and political implications by drawing on case studies from Cambodia and Vietnam. The article finds that China’s dam-building is perceived very differently in different countries of South-East Asia. In Cambodia, the dams in the Greater Mekong Sub-Region are considered instruments of economic growth and development, whereas downstream in Vietnam the dams are seen as potentially undermining national growth, development and security

Crew Dispatch for Commercial and Technical Services in an Electric Power Distribution Company Using ACO Technique

The aim of this paper is to describe the application of ACO optimization method for dispatch of road crews for commercial and supply restoration services in an electric power distribution company. The proposed methodology takes as input a large amount of different service orders (commercial and supply restoration), ranked by importance. Thus, it is able to create routes to be taken by each road crew, to select the sequence in which the requests will be met on the current day and the ones that will be met on another day in order to better achieve the company’s targets. The methodology presented in this paper is of great relevance for electricity utilities because it optimizes the use of the potential capacity of the available road crews, increasing its efficiency and reducing costs. A computer program – named as ANTECOM – has been developed to apply this method and the results were compared with the ones from the current methodology used by CEMAR (and from other available on the literature), providing better results. Also, it is more suitable for real time applications

The anthropology of extraction: critical perspectives on the resource curse

Attempts to address the resource curse remain focussed on revenue management, seeking technical solutions to political problems over examinations of relations of power. In this paper, we provide a review of the contribution anthropological research has made over the past decade to understanding the dynamic interplay of social relations, economic interests and struggles over power at stake in the political economy of extraction. In doing so, we show how the constellation of subaltern and elite agency at work within processes of resource extraction is vital in order to confront the complexities, incompatibilities, and inequities in the exploitation of mineral resources