{"id":"https://openalex.org/W102033946","doi":"https://doi.org/10.1007/978-3-642-40708-6_6","title":"Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models","display_name":"Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W102033946","doi":"https://doi.org/10.1007/978-3-642-40708-6_6","mag":"102033946"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-642-40708-6_6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-40708-6_6","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-00872963","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032056161","display_name":"Michael Klann","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Michael Klann","raw_affiliation_strings":["BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067946028","display_name":"Lo\u00efc Paulev\u00e9","orcid":"https://orcid.org/0000-0002-7219-2027"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lo\u00efc Paulev\u00e9","raw_affiliation_strings":["BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091695783","display_name":"Tatjana Petrov","orcid":"https://orcid.org/0000-0002-9041-0905"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tatjana Petrov","raw_affiliation_strings":["BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070544702","display_name":"Heinz Koeppl","orcid":"https://orcid.org/0000-0002-8305-9379"},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Heinz Koeppl","raw_affiliation_strings":["BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland","IBM Research - Zurich, Rueschlikon, Switzerland"],"affiliations":[{"raw_affiliation_string":"BISON Group, Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"IBM Research - Zurich, Rueschlikon, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032056161"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":3.481,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.92466656,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"64","last_page":"77"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.6406533718109131},{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.6035991907119751},{"id":"https://openalex.org/keywords/scaffold-protein","display_name":"Scaffold protein","score":0.4946148097515106},{"id":"https://openalex.org/keywords/brownian-motion","display_name":"Brownian motion","score":0.4325043559074402},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.4236219525337219},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4225690960884094},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.3787873387336731},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.37581050395965576},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3717217743396759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36229342222213745},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3351684808731079},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.32801318168640137},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17971748113632202},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16325321793556213},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1288793385028839}],"concepts":[{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.6406533718109131},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.6035991907119751},{"id":"https://openalex.org/C53645450","wikidata":"https://www.wikidata.org/wiki/Q907093","display_name":"Scaffold protein","level":3,"score":0.4946148097515106},{"id":"https://openalex.org/C112401455","wikidata":"https://www.wikidata.org/wiki/Q178036","display_name":"Brownian motion","level":2,"score":0.4325043559074402},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.4236219525337219},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4225690960884094},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.3787873387336731},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37581050395965576},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3717217743396759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36229342222213745},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3351684808731079},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.32801318168640137},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17971748113632202},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16325321793556213},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1288793385028839},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-642-40708-6_6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-40708-6_6","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:HAL:hal-00872963v1","is_oa":true,"landing_page_url":"https://hal.science/hal-00872963","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"The 11th Conference on Computational Methods in Systems Biology (CMSB'13), Sep 2013, Klosterneuburg, Austria. pp.64-77, ⟨10.1007/978-3-642-40708-6_6⟩","raw_type":"Conference papers"},{"id":"pmh:oai:arts.units.it:11368/3070447","is_oa":false,"landing_page_url":"https://hdl.handle.net/11368/3070447","pdf_url":null,"source":{"id":"https://openalex.org/S4306400480","display_name":"ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142444530","host_organization_name":"University of Trieste","host_organization_lineage":["https://openalex.org/I142444530"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-00872963v1","is_oa":true,"landing_page_url":"https://hal.science/hal-00872963","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"The 11th Conference on Computational Methods in Systems Biology (CMSB'13), Sep 2013, Klosterneuburg, Austria. pp.64-77, ⟨10.1007/978-3-642-40708-6_6⟩","raw_type":"Conference papers"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1586735752","https://openalex.org/W1707438493","https://openalex.org/W1972738796","https://openalex.org/W1973109523","https://openalex.org/W1974765037","https://openalex.org/W1974974415","https://openalex.org/W1986649132","https://openalex.org/W1986789040","https://openalex.org/W2002452115","https://openalex.org/W2002930675","https://openalex.org/W2030125944","https://openalex.org/W2038956038","https://openalex.org/W2040860090","https://openalex.org/W2047331390","https://openalex.org/W2097711273","https://openalex.org/W2099015579","https://openalex.org/W2101765772","https://openalex.org/W2102936861","https://openalex.org/W2112947723","https://openalex.org/W2120926795","https://openalex.org/W2126852846","https://openalex.org/W2169193349","https://openalex.org/W2175715045","https://openalex.org/W2796564118","https://openalex.org/W2951346023","https://openalex.org/W3098223981","https://openalex.org/W4255279538"],"related_works":["https://openalex.org/W2153719181","https://openalex.org/W1971748923","https://openalex.org/W2060986072","https://openalex.org/W1566155057","https://openalex.org/W2052574922","https://openalex.org/W2065045110","https://openalex.org/W64588465","https://openalex.org/W3120641340","https://openalex.org/W2793731703","https://openalex.org/W2967052024"],"abstract_inverted_index":null,"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}