@misc{WeberBeckerKoeppenetal., author = {Weber, Marcus and Becker, Roland and K{\"o}ppen, Robert and Durmaz, Vedat}, title = {Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane}, organization = {Zuse-Institut Berlin}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10308}, number = {07-31}, abstract = {In this paper, we investigate the interconversion processes of the major flame retardant -- 1,2,5,6,9,10-hexabromocyclododecane (HBCD) -- by the means of statistical thermodynamics based on classical force-fields. Three ideas will be presented. First, the application of classical hybrid Monte-Carlo simulations for quantum mechanical processes will be justified. Second, the problem of insufficient convergence properties of hybrid Monte-Carlo methods for the generation of low temperature canonical ensembles will be solved by an interpolation approach. Furthermore, it will be shown how free energy differences can be used for a rate matrix computation. The results of our numerical simulations will be compared to experimental results.}, language = {en} } @article{DurmazWeberBecker2012, author = {Durmaz, Vedat and Weber, Marcus and Becker, Roland}, title = {How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers}, series = {Journal of Molecular Modeling}, volume = {18}, journal = {Journal of Molecular Modeling}, doi = {10.1007/s00894-011-1239-5}, pages = {2399 -- 2408}, year = {2012}, language = {en} } @article{KoeppenBeckerWeberetal.2009, author = {K{\"o}ppen, Robert and Becker, Roland and Weber, Marcus and Durmaz, Vedat and Nehls, Irene}, title = {HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota}, series = {Organohalogen Compounds}, volume = {70}, journal = {Organohalogen Compounds}, pages = {910 -- 913}, year = {2009}, language = {en} } @article{WeberDurmazBeckeretal.2009, author = {Weber, Marcus and Durmaz, Vedat and Becker, Roland and Esslinger, Susanne}, title = {Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR}, series = {Organohalogen Compounds}, volume = {71}, journal = {Organohalogen Compounds}, pages = {247 -- 252}, year = {2009}, language = {en} } @article{ScharkoiEsslingerBeckeretal., author = {Scharkoi, Olga and Esslinger, Susanne and Becker, Roland and Weber, Marcus and Nehls, Irene}, title = {Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane}, series = {Molecular Simulation}, journal = {Molecular Simulation}, doi = {10.1080/08927022.2014.898845}, language = {en} } @article{WeberBeckerKoeppenetal.2008, author = {Weber, Marcus and Becker, Roland and K{\"o}ppen, Robert and Durmaz, Vedat}, title = {Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane}, series = {Journal of Molecular Simulation}, volume = {34}, journal = {Journal of Molecular Simulation}, number = {7}, pages = {727 -- 736}, year = {2008}, language = {en} } @misc{BeckerBertelmannCeynowaetal., author = {Becker, Pascal-Nicolas and Bertelmann, Roland and Ceynowa, Klaus and Christof, J{\"u}rgen and Dierkes, Thomas and Goltz-Fellgiebel, Julia Alexandra and Groß, Matthias and Heidrich, Regina and H{\"o}hnow, Tobias and Kassube, Michael and Koch, Thorsten and Kuberek, Monika and Landes, Lilian and Pampel, Heinz and Putnings, Markus and Rusch, Beate and Sch{\"a}ffler, Hildegard and Schobert, Dagmar and Schwab, Oliver and Schwidder, Jens and S{\"o}llner, Konstanze and Stoyanova, Tonka and Vierkant, Paul}, title = {DeepGreen - Metadata Schema for the exchange of publications between publishers and open access repositories. Version 1.1. June 2016}, issn = {1438-0064}, doi = {10.12752/3.dg.1.0}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59580}, abstract = {In 2011, important priorities were set to realize green publications in the open access movement in Germany. With financial support from the German Research Foundation (DFG), libraries negotiated Alliance licenses with publishers that guarantee extensive open access rights. Authors of institutions, that have therewith access to licensed journals, can freely publish their articles immediately or after a short embargo period in a repository of their choice. However, authors hesitantly use these open access rights. Also libraries - as managers of institutional and subject based repositories and thus legitimated representatives for the authors - only rarely make use of these rights. The aim of DeepGreen is to make the majority of those publications available online. Together with publishers of the Alliance licenses, the project consortium wants to develop a nearly fully automated workflow that covers both the delivery of data, including the full texts, of the publishers, as well as the data transformation to the necessary import formats and the loading process into the repositories. An intermediate "publication router" will serve as a distribution platform. The DeepGreen metadata schema contains metadata properties describing a wide range of deliverable bibliographic metadata from the Alliance license publishers (most common standards are JATS and CrossRef XML) as well as its compliance with technical, quality and metadata standards of the repositories. The schema includes required metadata elements and optional properties providing additional information.The metadata schema is aligned to the OCLC repository best practices ("Best Practices for CONTENTdm and other OAI-PMH compliant repositories: creating sharable metadata", URL: http://www.oclc.org/content/dam/support/wcdigitalcollectiongateway/MetadataBestPractices.pdf). The current version of the schema is subject to changes as the functional requirements and workflow practices are evolving during the project experiences and prototype production.}, language = {en} } @misc{BeckerBertelmannCeynowaetal., author = {Becker, Pascal-Nicolas and Bertelmann, Roland and Ceynowa, Klaus and Christof, J{\"u}rgen and Dierkes, Thomas and Goltz-Fellgiebel, Julia Alexandra and Groß, Matthias and Heidrich, Regina and H{\"o}hnow, Tobias and Kassube, Michael and Koch, Thorsten and Kuberek, Monika and Landes, Lilian and Pampel, Heinz and Putnings, Markus and Rusch, Beate and Sch{\"a}ffler, Hildegard and Schobert, Dagmar and Schwab, Oliver and Schwidder, Jens and S{\"o}llner, Konstanze and Stoyanova, Tonka and Vierkant, Paul}, title = {Questionnaire for effective exchange of bibliographic metadata - current status of publishing houses}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60419}, abstract = {The project DeepGreen aims to realise better usage of green open access publication rights with regard to Alliance Licenses in Germany (https://www.nationallizenzen.de/open-access). Together with publishers who offer Alliance Licenses and authorized libraries, the project group intends to develop a prototype of a nearly fully automated workflow that covers the delivery of data from the publishers, including the article full texts, as well as the process of loading data into the institutional repositories of licensees. Further information about the project can be found within ZIB-Report 15-58, urn:nbn:de:0297-zib-56799. In order to become acquainted with publishers' processes for exchanging documents and metadata, the project group developed a questionnaire for an online survey. The publishing of this questionnaire is intended to demonstrate relevant aspects of the issue (e. g. methods of data exchange, protocols and interfaces) and to foster reuse of valuable questionnaire elements. The XML-file can be reused as a template, the PDF-file reproduces the original survey layout.}, subject = {Open Access}, language = {en} }