@article{GrimmBergerBastiansenetal.2006, author = {Grimm, Volker and Berger, Uta and Bastiansen, Finn and Eliassen, Sigrunn and Ginot, Vincent and Giske, Jarl and Goss-Custard, John and Grand, Tamara and Heinz, Simone K. and Huse, Geir and Huth, Andreas and Jepsen, Jane U. and Jorgensen, Christian and Mooij, Wolf M. and Mueller, Birgit and Piou, Cyril and Railsback, Steven Floyd and Robbins, Andrew M. and Robbins, Martha M. and Rossmanith, Eva and Rueger, Nadja and Strand, Espen and Souissi, Sami and Stillman, Richard A. and Vabo, Rune and Visser, Ute and DeAngelis, Donald L.}, title = {A standard protocol for describing individual-based and agent-based models}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {198}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2006.04.023}, pages = {115 -- 126}, year = {2006}, abstract = {Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved.}, language = {en} } @article{AbboudSendPashniaketal.2013, author = {Abboud, Ali and Send, Sebastian and Pashniak, N. and Leitenberger, Wolfram and Ihle, Sebastian and Huth, M. and Hartmann, Robert and Str{\"u}der, Lothar and Pietsch, Ullrich}, title = {Sub-pixel resolution of a pnCCD for X-ray white beam applications}, series = {Journal of instrumentation}, volume = {8}, journal = {Journal of instrumentation}, number = {3}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1748-0221}, doi = {10.1088/1748-0221/8/05/P05005}, pages = {17}, year = {2013}, abstract = {A new approach to achieve sub-pixel spatial resolution in a pnCCD detector with 75 x 75 mu m(2) pixel size is proposed for X-ray applications in single photon counting mode. The approach considers the energy dependence of the charge cloud created by a single photon and its split probabilities between neighboring pixels of the detector based on a rectangular model for the charge cloud density. For cases where the charge of this cloud becomes distributed over three or four pixels the center position of photon impact can be reconstructed with a precision better than 2 mu m. The predicted charge cloud sizes are tested at selected X-ray fluorescence lines emitting energies between 6.4 keV and 17.4 keV and forming charge clouds with size (rms) varying between 8 mu m and 10 mu m respectively. The 2 mu m enhanced spatial resolution of the pnCCD is verified by means of an x-ray transmission experiment throughout an optical grating.}, language = {en} } @article{SendAbboudHartmannetal.2013, author = {Send, Sebastian and Abboud, Ali and Hartmann, Robert and Huth, M. and Leitenberger, Wolfram and Pashniak, N. and Schmidt, J. and Str{\"u}der, Lothar and Pietsch, Ullrich}, title = {Characterization of a pnCCD for applications with synchrotron radiation}, series = {Nuclear instruments \& methods in physics research : a journal on accelerators, instrumentation and techniques applied to research in nuclear and atomic physics, materials science and related fields in physics ; A, Accelerators, spectrometers, detectors and associated equipment}, volume = {711}, journal = {Nuclear instruments \& methods in physics research : a journal on accelerators, instrumentation and techniques applied to research in nuclear and atomic physics, materials science and related fields in physics ; A, Accelerators, spectrometers, detectors and associated equipment}, number = {5}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0168-9002}, doi = {10.1016/j.nima.2013.01.044}, pages = {132 -- 142}, year = {2013}, abstract = {In this work we study the response of a pnCCD by means of X-ray spectroscopy in the energy range between 6 key and 20 key and by Laue diffraction techniques. The analyses include measurements of characteristic detector parameters like energy resolution, count rate capability and effects of different gain settings. The limit of a single photon counting operation in white beam X-ray diffraction experiments is discussed with regard to the occurrence of pile-up events, for which the energy information about individual photons is lost. In case of monochromatic illumination the pnCCD can be used as a fast conventional CCD with a charge handling capacity (CHC) of about 300,000 electrons per pixel. If the CHC is exceeded, any surplus charge will spill to neighboring pixels perpendicular to the transfer direction due to electrostatic repulsion. The possibilities of increasing the number of storable electrons are investigated for different voltage settings by exposing a single pixel with X-rays generated by a microfocus X-ray source. The pixel binning mode is tested as an alternative approach that enables a pnCCD operation with significantly shorter readout times.}, language = {en} } @article{JeltschBlaumBroseetal.2013, author = {Jeltsch, Florian and Blaum, Niels and Brose, Ulrich and Chipperfield, Joseph D. and Clough, Yann and Farwig, Nina and Geissler, Katja and Graham, Catherine H. and Grimm, Volker and Hickler, Thomas and Huth, Andreas and May, Felix and Meyer, Katrin M. and Pagel, J{\"o}rn and Reineking, Bj{\"o}rn and Rillig, Matthias C. and Shea, Katriona and Schurr, Frank Martin and Schroeder, Boris and Tielb{\"o}rger, Katja and Weiss, Lina and Wiegand, Kerstin and Wiegand, Thorsten and Wirth, Christian and Zurell, Damaris}, title = {How can we bring together empiricists and modellers in functional biodiversity research?}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {14}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {2}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2013.01.001}, pages = {93 -- 101}, year = {2013}, abstract = {Improving our understanding of biodiversity and ecosystem functioning and our capacity to inform ecosystem management requires an integrated framework for functional biodiversity research (FBR). However, adequate integration among empirical approaches (monitoring and experimental) and modelling has rarely been achieved in FBR. We offer an appraisal of the issues involved and chart a course towards enhanced integration. A major element of this path is the joint orientation towards the continuous refinement of a theoretical framework for FBR that links theory testing and generalization with applied research oriented towards the conservation of biodiversity and ecosystem functioning. We further emphasize existing decision-making frameworks as suitable instruments to practically merge these different aims of FBR and bring them into application. This integrated framework requires joint research planning, and should improve communication and stimulate collaboration between modellers and empiricists, thereby overcoming existing reservations and prejudices. The implementation of this integrative research agenda for FBR requires an adaptation in most national and international funding schemes in order to accommodate such joint teams and their more complex structures and data needs.}, language = {en} }