{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T22:01:08Z","timestamp":1743112868293,"version":"3.40.3"},"publisher-location":"Cham","reference-count":24,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030497774"},{"type":"electronic","value":"9783030497781"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-3-030-49778-1_16","type":"book-chapter","created":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T06:32:35Z","timestamp":1593585155000},"page":"200-211","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Application of Agent-Based Modelling to Simulate Ribosome Translation"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6740-3742","authenticated-orcid":false,"given":"Gael","family":"P\u00e9rez-Rodr\u00edguez","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4434-6989","authenticated-orcid":false,"given":"Beatriz T.","family":"Magalh\u00e3es","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5864-3250","authenticated-orcid":false,"given":"Nuno F.","family":"Azevedo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8401-5362","authenticated-orcid":false,"given":"An\u00e1lia","family":"Louren\u00e7o","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,15]]},"reference":[{"key":"16_CR1","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcdb.2015.07.001","author":"GW Brodland","year":"2015","unstructured":"Brodland, G.W.: How computational models can help unlock biological systems (2015). https:\/\/doi.org\/10.1016\/j.semcdb.2015.07.001","journal-title":"How computational models can help unlock biological systems"},{"key":"16_CR2","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-30440-3_13","volume-title":"Encyclopedia of Complexity and Systems Science","author":"F Castiglione","year":"2009","unstructured":"Castiglione, F.: Agent based modeling and simulation, introduction to. In: Meyers, R. (ed.) Encyclopedia of Complexity and Systems Science. Springer, New York (2009). https:\/\/doi.org\/10.1007\/978-0-387-30440-3_13"},{"key":"16_CR3","doi-asserted-by":"publisher","first-page":"40301","DOI":"10.1088\/1478-3975\/10\/4\/040301","volume":"10","author":"G Foffi","year":"2013","unstructured":"Foffi, G., Pastore, A., Piazza, F., Temussi, P.A.: Macromolecular crowding: chemistry and physics meet biology. Phys. Biol. 10, 40301 (2013). https:\/\/doi.org\/10.1088\/1478-3975\/10\/4\/040301. (Ascona, Switzerland, 10\u201314 June 2012)","journal-title":"Phys. Biol."},{"key":"16_CR4","series-title":"Advances in Intelligent Systems and Computing","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-319-19776-0_1","volume-title":"9th International Conference on Practical Applications of Computational Biology and Bioinformatics","author":"AP Garc\u00eda","year":"2015","unstructured":"Garc\u00eda, A.P., Rodr\u00edguez-Pat\u00f3n, A.: A preliminary assessment of three strategies for the agent-based modeling of bacterial conjugation. In: Overbeek, R., Rocha, M.P., Fdez-Riverola, F., De Paz, J.F. (eds.) 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. AISC, vol. 375, pp. 1\u20139. Springer, Cham (2015). https:\/\/doi.org\/10.1007\/978-3-319-19776-0_1"},{"key":"16_CR5","doi-asserted-by":"publisher","first-page":"3809","DOI":"10.1021\/acs.jpcb.5b12544","volume":"120","author":"G P\u00e9rez-Rodr\u00edguez","year":"2016","unstructured":"P\u00e9rez-Rodr\u00edguez, G., Gameiro, D., P\u00e9rez-P\u00e9rez, M., Louren\u00e7o, A., Azevedo, N.F.: Single molecule simulation of diffusion and enzyme kinetics. J. Phys. Chem. B. 120, 3809\u20133820 (2016). https:\/\/doi.org\/10.1021\/acs.jpcb.5b12544","journal-title":"J. Phys. Chem. B."},{"key":"16_CR6","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1080\/08927014.2018.1440392","volume":"34","author":"G P\u00e9rez-Rodr\u00edguez","year":"2018","unstructured":"P\u00e9rez-Rodr\u00edguez, G., Dias, S., P\u00e9rez-P\u00e9rez, M., Fdez-Riverola, F., Azevedo, N.F., Louren\u00e7o, A.: Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans. Biofouling 34, 335\u2013345 (2018). https:\/\/doi.org\/10.1080\/08927014.2018.1440392","journal-title":"Biofouling"},{"key":"16_CR7","series-title":"Lecture Notes in Computer Science (Lecture Notes in Artificial Intelligence)","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1007\/978-3-319-94580-4_6","volume-title":"Advances in practical applications of agents, multi-agent systems, and complexity: the PAAMS collection","author":"H Arduin","year":"2018","unstructured":"Arduin, H., Opatowski, L.: SimFI: a transmission agent-based model of two interacting pathogens. In: Demazeau, Y., An, B., Bajo, J., Fern\u00e1ndez-Caballero, A. (eds.) PAAMS 2018. LNCS (LNAI), vol. 10978, pp. 72\u201383. Springer, Cham (2018). https:\/\/doi.org\/10.1007\/978-3-319-94580-4_6"},{"key":"16_CR8","doi-asserted-by":"publisher","unstructured":"Maia, P., P\u00e9rez-Rodr\u00edguez, G., P\u00e9rez-P\u00e9rez, M., Fdez-Riverola, F., Louren\u00e7o, A., Azevedo, N.F.: Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Comput. Biol. Med. (2019). https:\/\/doi.org\/10.1016\/J.COMPBIOMED.2019.02.020","DOI":"10.1016\/J.COMPBIOMED.2019.02.020"},{"key":"16_CR9","doi-asserted-by":"publisher","DOI":"10.1385\/MB:31:3:245","author":"D Porro","year":"2005","unstructured":"Porro, D., Sauer, M., Branduardi, P., Mattanovich, D.: Recombinant protein production in yeasts (2005). https:\/\/doi.org\/10.1385\/MB:31:3:245","journal-title":"Recombinant protein production in yeasts"},{"key":"16_CR10","doi-asserted-by":"publisher","unstructured":"Magalh\u00e3es, T.B., Louren\u00e7o, A., Azevedo, N.F.: Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. Brief. Bioinform. (2019). https:\/\/doi.org\/10.1093\/bib\/bbz149","DOI":"10.1093\/bib\/bbz149"},{"key":"16_CR11","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1016\/j.jmb.2003.11.025","volume":"335","author":"LD Kapp","year":"2004","unstructured":"Kapp, L.D., Lorsch, J.R.: GTP-dependent recognition of the methionine moiety on initiator tRNA by translation factor eIF2. J. Mol. Biol. 335, 923\u2013936 (2004). https:\/\/doi.org\/10.1016\/j.jmb.2003.11.025","journal-title":"J. Mol. Biol."},{"key":"16_CR12","doi-asserted-by":"publisher","first-page":"e1005951","DOI":"10.1371\/journal.pcbi.1005951","volume":"14","author":"A Diament","year":"2018","unstructured":"Diament, A., Feldman, A., Schochet, E., Kupiec, M., Arava, Y., Tuller, T.: The extent of ribosome queuing in budding yeast. PLoS Comput. Biol. 14, e1005951 (2018). https:\/\/doi.org\/10.1371\/journal.pcbi.1005951","journal-title":"PLoS Comput. Biol."},{"key":"16_CR13","doi-asserted-by":"publisher","first-page":"2760","DOI":"10.1016\/j.ecolmodel.2010.08.019","volume":"221","author":"V Grimm","year":"2010","unstructured":"Grimm, V., Berger, U., DeAngelis, D.L., Polhill, J.G., Giske, J., Railsback, S.F.: The ODD protocol: a review and first update. Ecol. Modell. 221, 2760\u20132768 (2010). https:\/\/doi.org\/10.1016\/j.ecolmodel.2010.08.019","journal-title":"Ecol. Modell."},{"key":"16_CR14","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.ecolmodel.2006.04.023","volume":"198","author":"V Grimm","year":"2006","unstructured":"Grimm, V., et al.: A standard protocol for describing individual-based and agent-based models. Ecol. Modell. 198, 115\u2013126 (2006). https:\/\/doi.org\/10.1016\/j.ecolmodel.2006.04.023","journal-title":"Ecol. Modell."},{"key":"16_CR15","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1177\/0037549705058073","volume":"82","author":"S Luke","year":"2005","unstructured":"Luke, S., Cioffi-Revilla, C., Panait, L., Sullivan, K., Balan, G.: MASON: a multiagent simulation environment. Simul. Trans. Soc. Model. Simul. Int. 82, 517\u2013527 (2005). https:\/\/doi.org\/10.1177\/0037549705058073","journal-title":"Simul. Trans. Soc. Model. Simul. Int."},{"key":"16_CR16","unstructured":"PMP1 - Plasma membrane ATPase proteolipid 1 precursor - Saccharomyces cerevisiae (strain ATCC 204508\/S288c) (Baker\u2019s yeast) - PMP1 gene & protein. https:\/\/www.uniprot.org\/uniprot\/P32903. Accessed 09 Jan 2020"},{"key":"16_CR17","unstructured":"PMP1 Protein|SGD. https:\/\/www.yeastgenome.org\/locus\/S000000619\/protein. Accessed 15 Jan 2020"},{"key":"16_CR18","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1002\/yea.3365","volume":"36","author":"M Palmgren","year":"2019","unstructured":"Palmgren, M., Morsomme, P.: The plasma membrane H+\u2009-ATPase, a simple polypeptide with a long history. Yeast 36, 201\u2013210 (2019). https:\/\/doi.org\/10.1002\/yea.3365","journal-title":"Yeast"},{"key":"16_CR19","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1093\/jmicro\/dfr052","volume":"60","author":"M Yamaguchi","year":"2011","unstructured":"Yamaguchi, M., Namiki, Y., et al.: Structome of Saccharomyces cerevisiae determined by freeze-substitution and serial ultrathin-sectioning electron microscopy. J. Electron. Microsc. (Tokyo) 60, 321\u2013335 (2011). https:\/\/doi.org\/10.1093\/jmicro\/dfr052","journal-title":"J. Electron. Microsc. (Tokyo)"},{"key":"16_CR20","doi-asserted-by":"publisher","DOI":"10.1201\/b13170","volume-title":"Game Physics Engine Development: How to Build a Robust Commercial-Grade Physics Engine for your Game","author":"I Millington","year":"2010","unstructured":"Millington, I.: Game Physics Engine Development: How to Build a Robust Commercial-Grade Physics Engine for your Game. CRC Press, Boca Raton (2010)"},{"key":"16_CR21","doi-asserted-by":"publisher","unstructured":"Palmer, G.: Physics for Game Programmers. Apress (2005). https:\/\/doi.org\/10.1007\/978-1-59059-472-8","DOI":"10.1007\/978-1-59059-472-8"},{"key":"16_CR22","doi-asserted-by":"publisher","unstructured":"Cecconi, F., Cencini, M., Falcioni, M., Vulpiani, A.: Brownian motion and diffusion: from stochastic processes to chaos and beyond. Chaos. 15 (2005). https:\/\/doi.org\/10.1063\/1.1832773","DOI":"10.1063\/1.1832773"},{"key":"16_CR23","doi-asserted-by":"publisher","first-page":"e1000865","DOI":"10.1371\/journal.pcbi.1000865","volume":"6","author":"M Siwiak","year":"2010","unstructured":"Siwiak, M., Zielenkiewicz, P.: A comprehensive, quantitative, and genome-wide model of translation. PLoS Comput. Biol. 6, e1000865 (2010). https:\/\/doi.org\/10.1371\/journal.pcbi.1000865","journal-title":"PLoS Comput. Biol."},{"key":"16_CR24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku646","author":"A Dana","year":"2014","unstructured":"Dana, A., Tuller, T.: The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res. (2014). https:\/\/doi.org\/10.1093\/nar\/gku646","journal-title":"Nucleic Acids Res."}],"container-title":["Lecture Notes in Computer Science","Advances in Practical Applications of Agents, Multi-Agent Systems, and Trustworthiness. The PAAMS Collection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-49778-1_16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T15:21:13Z","timestamp":1710256873000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-49778-1_16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9783030497774","9783030497781"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-49778-1_16","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"15 June 2020","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"PAAMS","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Practical Applications of Agents and Multi-Agent Systems","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"L\u2019Aquila","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Italy","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2020","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"7 October 2020","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"9 October 2020","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"18","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"paams2020","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/www.paams.net\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Double-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"64","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"29","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"17","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"45% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}