{"id":"https://openalex.org/W2290703973","doi":"https://doi.org/10.1186/s12918-016-0259-2","title":"Spatiotemporal modeling of microbial metabolism","display_name":"Spatiotemporal modeling of microbial metabolism","publication_year":2016,"publication_date":"2016-03-01","ids":{"openalex":"https://openalex.org/W2290703973","doi":"https://doi.org/10.1186/s12918-016-0259-2","mag":"2290703973","pmid":"https://pubmed.ncbi.nlm.nih.gov/26932448"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0259-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-016-0259-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-016-0259-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089564180","display_name":"Jin Chen","orcid":"https://orcid.org/0000-0002-6497-4141"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin Chen","raw_affiliation_strings":["Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. jchen3@umass.edu","Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. jchen3@umass.edu","institution_ids":["https://openalex.org/I24603500"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090706532","display_name":"Jose A. Gomez","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose A. Gomez","raw_affiliation_strings":["Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. jagomezr@mit.edu","Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. jagomezr@mit.edu","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071196531","display_name":"Kai H\u00f6ffner","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kai H\u00f6ffner","raw_affiliation_strings":["Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. hoeffner@mit.edu","Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. hoeffner@mit.edu","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072585177","display_name":"Poonam Phalak","orcid":null},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Poonam Phalak","raw_affiliation_strings":["Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. pphalak@umass.edu","Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. pphalak@umass.edu","institution_ids":["https://openalex.org/I24603500"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037278011","display_name":"Paul I. Barton","orcid":"https://orcid.org/0000-0003-2895-9443"},"institutions":[{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul I. Barton","raw_affiliation_strings":["Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. pib@mit.edu","Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. pib@mit.edu","institution_ids":["https://openalex.org/I63966007","https://openalex.org/I4210110987"]},{"raw_affiliation_string":"Department of Chemical Engineering, Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085032105","display_name":"Michael A. Henson","orcid":"https://orcid.org/0000-0003-1969-4906"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael A. Henson","raw_affiliation_strings":["Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. henson@ecs.umass.edu","Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA. henson@ecs.umass.edu","institution_ids":["https://openalex.org/I24603500"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Massachusetts, 240 Thatcher Way, Life Science Laboratories Building, Amherst, MA, 01003, USA","institution_ids":["https://openalex.org/I24603500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085032105"],"corresponding_institution_ids":["https://openalex.org/I24603500"],"apc_list":null,"apc_paid":null,"fwci":5.8092,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.96506834,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"21","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9121999740600586,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9121999740600586,"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/T10284","display_name":"Anaerobic Digestion and Biogas Production","score":0.05429999902844429,"subfield":{"id":"https://openalex.org/subfields/2215","display_name":"Building and Construction"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12688","display_name":"Microbial metabolism and enzyme function","score":0.012199999764561653,"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/flux-balance-analysis","display_name":"Flux balance analysis","score":0.805077075958252},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.6460171937942505},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5834937691688538},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.505174458026886},{"id":"https://openalex.org/keywords/discretization","display_name":"Discretization","score":0.5010561943054199},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4760308563709259},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.45512861013412476},{"id":"https://openalex.org/keywords/partial-differential-equation","display_name":"Partial differential equation","score":0.45236629247665405},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.32426759600639343},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3220664858818054},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.2566502094268799},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23175224661827087},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22858890891075134},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.18688488006591797},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.14305153489112854},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10447445511817932}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.805077075958252},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.6460171937942505},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5834937691688538},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.505174458026886},{"id":"https://openalex.org/C73000952","wikidata":"https://www.wikidata.org/wiki/Q17007827","display_name":"Discretization","level":2,"score":0.5010561943054199},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4760308563709259},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.45512861013412476},{"id":"https://openalex.org/C93779851","wikidata":"https://www.wikidata.org/wiki/Q271977","display_name":"Partial differential equation","level":2,"score":0.45236629247665405},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.32426759600639343},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3220664858818054},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.2566502094268799},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23175224661827087},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22858890891075134},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.18688488006591797},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.14305153489112854},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10447445511817932},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003013","descriptor_name":"Clostridium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005110","descriptor_name":"Extracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005110","descriptor_name":"Extracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005110","descriptor_name":"Extracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005110","descriptor_name":"Extracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0259-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-016-0259-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:26932448","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26932448","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3748540","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4774267","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0259-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-016-0259-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1129846750","display_name":"GOALI:   Development of Spatiotemporal Metabolic Models for Syngas Fermentation in Industrial Bubble Column Reactors","funder_award_id":"1511346","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1994748996","display_name":null,"funder_award_id":"Award U01EB019416","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2615353771","display_name":null,"funder_award_id":"CBET 1511346","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"id":"https://openalex.org/G4560130676","display_name":null,"funder_award_id":"CBET 1511346","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5542443046","display_name":null,"funder_award_id":"U01 EB019416","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G5826989766","display_name":null,"funder_award_id":"T32 GM108556","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6019509955","display_name":null,"funder_award_id":"U01EB019416","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7041702592","display_name":null,"funder_award_id":"1511346","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"id":"https://openalex.org/G940242144","display_name":null,"funder_award_id":"U01EB019416","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2290703973.pdf","grobid_xml":"https://content.openalex.org/works/W2290703973.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W19461444","https://openalex.org/W1497457526","https://openalex.org/W1529898704","https://openalex.org/W1540113021","https://openalex.org/W1601882703","https://openalex.org/W1603494243","https://openalex.org/W1914699547","https://openalex.org/W1968787701","https://openalex.org/W1973808917","https://openalex.org/W1987300339","https://openalex.org/W1995770577","https://openalex.org/W2014294355","https://openalex.org/W2019347117","https://openalex.org/W2022391021","https://openalex.org/W2028985317","https://openalex.org/W2038304602","https://openalex.org/W2041663932","https://openalex.org/W2046468613","https://openalex.org/W2047168839","https://openalex.org/W2047228180","https://openalex.org/W2048596643","https://openalex.org/W2079485359","https://openalex.org/W2081572309","https://openalex.org/W2091651320","https://openalex.org/W2094741398","https://openalex.org/W2101981035","https://openalex.org/W2102961219","https://openalex.org/W2110055456","https://openalex.org/W2110585362","https://openalex.org/W2113186567","https://openalex.org/W2115801514","https://openalex.org/W2117486132","https://openalex.org/W2118343646","https://openalex.org/W2122093325","https://openalex.org/W2122836009","https://openalex.org/W2125029961","https://openalex.org/W2136004458","https://openalex.org/W2143861551","https://openalex.org/W2149792405","https://openalex.org/W2150900885","https://openalex.org/W2153448274","https://openalex.org/W2156054854","https://openalex.org/W2162237022","https://openalex.org/W2165158499","https://openalex.org/W2398660690","https://openalex.org/W2461320403","https://openalex.org/W4210598977","https://openalex.org/W4256259619"],"related_works":["https://openalex.org/W3082668976","https://openalex.org/W2517973022","https://openalex.org/W1543121148","https://openalex.org/W1580703421","https://openalex.org/W2996841952","https://openalex.org/W2618518959","https://openalex.org/W2231364979","https://openalex.org/W4295745414","https://openalex.org/W4382202915","https://openalex.org/W2489516236"],"abstract_inverted_index":{"BACKGROUND:":[0],"Microbial":[1],"systems":[2,137],"in":[3,16,19,79],"which":[4,173],"the":[5,23,42,73,92,102,148,161,167,170,187],"extracellular":[6],"environment":[7],"varies":[8],"both":[9,212],"spatially":[10,82],"and":[11,18,35,81,121,154,179,193,206,214,217,223],"temporally":[12],"are":[13,40],"very":[14],"common":[15],"nature":[17],"engineering":[20],"applications.":[21],"While":[22],"use":[24],"of":[25,44,91,101,105,138,169,175],"genome-scale":[26,65,208],"metabolic":[27,46,60,133,209],"reconstructions":[28,66],"for":[29,37,58,135,204],"steady-state":[30],"flux":[31],"balance":[32],"analysis":[33],"(FBA)":[34],"extensions":[36],"dynamic":[38,123],"FBA":[39,124],"common,":[41],"development":[43],"spatiotemporal":[45,59,132],"models":[47,134,172,210],"has":[48,218],"received":[49],"little":[50],"attention.":[51],"RESULTS:":[52],"We":[53,126],"present":[54],"a":[55,115,143,156,201],"general":[56],"methodology":[57,129],"modeling":[61],"based":[62],"on":[63],"combining":[64],"with":[67,109,147,160,211],"fundamental":[68],"transport":[69],"equations":[70,108],"that":[71,118,186],"govern":[72],"relevant":[74],"convective":[75],"and/or":[76],"diffusional":[77],"processes":[78],"time":[80,213],"varying":[83],"environments.":[84],"Our":[85,198],"solution":[86],"procedure":[87],"involves":[88],"spatial":[89,215],"discretization":[90],"partial":[93],"differential":[94,107],"equation":[95],"model":[96,195],"followed":[97],"by":[98,130],"numerical":[99],"integration":[100],"resulting":[103],"system":[104],"ordinary":[106],"embedded":[110],"linear":[111],"programs":[112],"using":[113],"DFBAlab,":[114],"MATLAB":[116],"code":[117],"performs":[119],"reliable":[120],"efficient":[122,192],"simulations.":[125],"demonstrate":[127],"our":[128],"solving":[131,207],"two":[136],"considerable":[139],"practical":[140],"interest:":[141],"(1)":[142],"bubble":[144],"column":[145],"reactor":[146],"syngas":[149],"fermenting":[150],"bacterium":[151],"Clostridium":[152],"ljungdahlii;":[153],"(2)":[155],"chronic":[157],"wound":[158],"biofilm":[159],"human":[162],"pathogen":[163],"Pseudomonas":[164],"aeruginosa.":[165],"Despite":[166],"complexity":[168],"discretized":[171],"consist":[174],"900":[176],"ODEs/600":[177],"LPs":[178],"250":[180],"ODEs/250":[181],"LPs,":[182],"respectively,":[183],"we":[184],"show":[185],"proposed":[188],"computational":[189],"framework":[190],"allows":[191],"robust":[194],"solution.":[196],"CONCLUSIONS:":[197],"study":[199],"establishes":[200],"new":[202],"paradigm":[203],"formulating":[205],"variations":[216],"wide":[219],"applicability":[220],"to":[221],"natural":[222],"engineered":[224],"microbial":[225],"systems.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}