{"id":"https://openalex.org/W1968029714","doi":"https://doi.org/10.3390/computation2020023","title":"A 3-D Model of a Perennial Ryegrass Primary Cell Wall and Its Enzymatic Degradation","display_name":"A 3-D Model of a Perennial Ryegrass Primary Cell Wall and Its Enzymatic Degradation","publication_year":2014,"publication_date":"2014-05-05","ids":{"openalex":"https://openalex.org/W1968029714","doi":"https://doi.org/10.3390/computation2020023","mag":"1968029714"},"language":"en","primary_location":{"id":"doi:10.3390/computation2020023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2020023","pdf_url":"https://www.mdpi.com/2079-3197/2/2/23/pdf?version=1399281075","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/2/2/23/pdf?version=1399281075","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031725361","display_name":"I. Vetharaniam","orcid":"https://orcid.org/0000-0003-3726-0802"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Indrakumar Vetharaniam","raw_affiliation_strings":["AgResearch Limited, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AgResearch Limited, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086062238","display_name":"William J. Kelly","orcid":"https://orcid.org/0000-0001-8982-066X"},"institutions":[{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"William Kelly","raw_affiliation_strings":["AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand","institution_ids":["https://openalex.org/I41125697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004324173","display_name":"Graeme T. Attwood","orcid":"https://orcid.org/0000-0002-6443-8760"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]},{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Graeme Attwood","raw_affiliation_strings":["AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand","University of AUCKLAND"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand","institution_ids":["https://openalex.org/I41125697"]},{"raw_affiliation_string":"University of AUCKLAND","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089621714","display_name":"Philip J. Harris","orcid":"https://orcid.org/0000-0003-1807-8079"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]},{"id":"https://openalex.org/I41125697","display_name":"AgResearch","ror":"https://ror.org/0124gwh94","country_code":"NZ","type":"government","lineage":["https://openalex.org/I41125697","https://openalex.org/I4405260297"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Philip Harris","raw_affiliation_strings":["School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand","AgResearch"],"raw_orcid":"https://orcid.org/0000-0003-1807-8079","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"AgResearch","institution_ids":["https://openalex.org/I41125697"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031725361"],"corresponding_institution_ids":["https://openalex.org/I41125697"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.4656,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.73943118,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2","issue":"2","first_page":"23","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10869","display_name":"Polysaccharides and Plant Cell Walls","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10869","display_name":"Polysaccharides and Plant Cell Walls","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10171","display_name":"Biofuel production and bioconversion","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"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/T10750","display_name":"Fermentation and Sensory Analysis","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cell-wall","display_name":"Cell wall","score":0.9357688426971436},{"id":"https://openalex.org/keywords/cellulose","display_name":"Cellulose","score":0.7157940864562988},{"id":"https://openalex.org/keywords/steric-effects","display_name":"Steric effects","score":0.6590970754623413},{"id":"https://openalex.org/keywords/pectin","display_name":"Pectin","score":0.6449429988861084},{"id":"https://openalex.org/keywords/secondary-cell-wall","display_name":"Secondary cell wall","score":0.6213223934173584},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.596938967704773},{"id":"https://openalex.org/keywords/polysaccharide","display_name":"Polysaccharide","score":0.5914660692214966},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.5607267618179321},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5015981197357178},{"id":"https://openalex.org/keywords/trichoderma-reesei","display_name":"Trichoderma reesei","score":0.41707417368888855},{"id":"https://openalex.org/keywords/xyloglucan","display_name":"Xyloglucan","score":0.4155576527118683},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4106099605560303},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3555629253387451},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.19603168964385986},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18504664301872253},{"id":"https://openalex.org/keywords/cellulase","display_name":"Cellulase","score":0.18066471815109253}],"concepts":[{"id":"https://openalex.org/C125235067","wikidata":"https://www.wikidata.org/wiki/Q128700","display_name":"Cell wall","level":2,"score":0.9357688426971436},{"id":"https://openalex.org/C2779251873","wikidata":"https://www.wikidata.org/wiki/Q80294","display_name":"Cellulose","level":2,"score":0.7157940864562988},{"id":"https://openalex.org/C201194858","wikidata":"https://www.wikidata.org/wiki/Q898238","display_name":"Steric effects","level":2,"score":0.6590970754623413},{"id":"https://openalex.org/C2780756937","wikidata":"https://www.wikidata.org/wiki/Q188154","display_name":"Pectin","level":2,"score":0.6449429988861084},{"id":"https://openalex.org/C147302496","wikidata":"https://www.wikidata.org/wiki/Q8004621","display_name":"Secondary cell wall","level":3,"score":0.6213223934173584},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.596938967704773},{"id":"https://openalex.org/C100817775","wikidata":"https://www.wikidata.org/wiki/Q134219","display_name":"Polysaccharide","level":2,"score":0.5914660692214966},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.5607267618179321},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5015981197357178},{"id":"https://openalex.org/C2776125036","wikidata":"https://www.wikidata.org/wiki/Q2749932","display_name":"Trichoderma reesei","level":4,"score":0.41707417368888855},{"id":"https://openalex.org/C2779741953","wikidata":"https://www.wikidata.org/wiki/Q1132297","display_name":"Xyloglucan","level":3,"score":0.4155576527118683},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4106099605560303},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3555629253387451},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.19603168964385986},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18504664301872253},{"id":"https://openalex.org/C141603559","wikidata":"https://www.wikidata.org/wiki/Q410324","display_name":"Cellulase","level":3,"score":0.18066471815109253}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/computation2020023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2020023","pdf_url":"https://www.mdpi.com/2079-3197/2/2/23/pdf?version=1399281075","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:97f8008b919a4984951eb8085c391d1e","is_oa":true,"landing_page_url":"https://doaj.org/article/97f8008b919a4984951eb8085c391d1e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation, Vol 2, Iss 2, Pp 23-46 (2014)","raw_type":"article"},{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/27356","is_oa":true,"landing_page_url":"http://hdl.handle.net/2292/27356","pdf_url":null,"source":{"id":"https://openalex.org/S7407055463","display_name":"ResearchSpace (University of Auckland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I154130895","host_organization_name":"University of Auckland","host_organization_lineage":["https://openalex.org/I154130895"],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.3390/computation2020023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2020023","pdf_url":"https://www.mdpi.com/2079-3197/2/2/23/pdf?version=1399281075","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6100000143051147,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1968029714.pdf","grobid_xml":"https://content.openalex.org/works/W1968029714.grobid-xml"},"referenced_works_count":81,"referenced_works":["https://openalex.org/W169744590","https://openalex.org/W639760055","https://openalex.org/W1165896209","https://openalex.org/W1497475797","https://openalex.org/W1556494981","https://openalex.org/W1595096996","https://openalex.org/W1601971808","https://openalex.org/W1815958519","https://openalex.org/W1963723331","https://openalex.org/W1967047248","https://openalex.org/W1969231606","https://openalex.org/W1969797855","https://openalex.org/W1970085393","https://openalex.org/W1970408026","https://openalex.org/W1971953727","https://openalex.org/W1972448623","https://openalex.org/W1977431391","https://openalex.org/W1977561071","https://openalex.org/W1981386238","https://openalex.org/W1983206400","https://openalex.org/W1986425871","https://openalex.org/W1998606501","https://openalex.org/W2001396309","https://openalex.org/W2003604861","https://openalex.org/W2009078860","https://openalex.org/W2015707373","https://openalex.org/W2027798195","https://openalex.org/W2030764529","https://openalex.org/W2031558918","https://openalex.org/W2031651310","https://openalex.org/W2032141838","https://openalex.org/W2033694577","https://openalex.org/W2034809239","https://openalex.org/W2044723828","https://openalex.org/W2068993220","https://openalex.org/W2070093643","https://openalex.org/W2074716130","https://openalex.org/W2081893847","https://openalex.org/W2085492900","https://openalex.org/W2088537667","https://openalex.org/W2093858400","https://openalex.org/W2094193740","https://openalex.org/W2096818246","https://openalex.org/W2099202385","https://openalex.org/W2102071849","https://openalex.org/W2103284727","https://openalex.org/W2108102848","https://openalex.org/W2111321083","https://openalex.org/W2112521269","https://openalex.org/W2114615912","https://openalex.org/W2120838110","https://openalex.org/W2120931275","https://openalex.org/W2121727772","https://openalex.org/W2122437806","https://openalex.org/W2126210768","https://openalex.org/W2127794343","https://openalex.org/W2137641040","https://openalex.org/W2142175142","https://openalex.org/W2144014493","https://openalex.org/W2145885194","https://openalex.org/W2148693790","https://openalex.org/W2149279556","https://openalex.org/W2155127265","https://openalex.org/W2157043788","https://openalex.org/W2159080918","https://openalex.org/W2164623799","https://openalex.org/W2165194260","https://openalex.org/W2165531833","https://openalex.org/W2167057100","https://openalex.org/W2168201179","https://openalex.org/W2190882761","https://openalex.org/W2326110901","https://openalex.org/W2332085633","https://openalex.org/W2594199174","https://openalex.org/W2913400639","https://openalex.org/W3011439212","https://openalex.org/W3119108935","https://openalex.org/W3123632726","https://openalex.org/W4297785242","https://openalex.org/W6684716093","https://openalex.org/W6842908933"],"related_works":["https://openalex.org/W4293721672","https://openalex.org/W2106091095","https://openalex.org/W1974966154","https://openalex.org/W3003543135","https://openalex.org/W4205446356","https://openalex.org/W3215272731","https://openalex.org/W2008672231","https://openalex.org/W3020801486","https://openalex.org/W2249234990","https://openalex.org/W3026010236"],"abstract_inverted_index":{"We":[0],"have":[1,96],"developed":[2],"a":[3,21,33,71,91,101,118,149],"novel":[4],"3-D,":[5,150],"agent-based":[6],"model":[7,66,125,181],"of":[8,15,35,61,73,84,93,100,107,142,153,157,163,186],"cell-wall":[9,17,54,206],"digestion":[10],"to":[11,23,67,70,81,147,170,208],"improve":[12],"our":[13],"understanding":[14],"ruminal":[16],"digestion.":[18],"It":[19,189],"offers":[20],"capability":[22],"study":[24],"cell":[25,76,85,103,121,159,165,176],"walls":[26,77,86,173],"and":[27,38,41,46,56,59,80,110,123,131,133,145,178,220],"their":[28,44,191],"enzymatic":[29,114,225],"modification,":[30],"by":[31,42,87],"providing":[32],"representation":[34,152],"cellulose":[36],"microfibrils":[37],"non-cellulosic":[39],"polysaccharides":[40],"simulating":[43],"spatial":[45],"catalytic":[47],"interactions":[48],"with":[49],"enzymes.":[50,89,188],"One":[51],"can":[52,167,182],"vary":[53],"composition":[55,162],"the":[57,65,82,98,105,124,140,154,158,164,195],"types":[58,177],"numbers":[60],"enzyme":[62],"molecules,":[63],"allowing":[64,202],"be":[68,168,209],"applied":[69],"range":[72],"systems":[74],"where":[75],"are":[78,137,213,218,227],"degraded":[79],"modification":[83],"endogenous":[88],"As":[90],"proof":[92],"principle,":[94],"we":[95],"modelled":[97],"wall":[99,122,166],"mesophyll":[102],"from":[104,205,224],"leaf":[106],"perennial":[108],"ryegrass":[109],"then":[111],"simulated":[112],"its":[113],"degradation.":[115],"This":[116],"is":[117],"primary,":[119],"non-lignified":[120],"includes":[126],"cellulose,":[127],"hemicelluloses":[128],"(glucuronoarabinoxylans,":[129],"1,3;1,4-\u03b2-glucans,":[130],"xyloglucans)":[132],"pectin.":[134],"These":[135],"polymers":[136,207],"represented":[138],"at":[139],"level":[141],"constituent":[143],"monosaccharides,":[144],"assembled":[146],"form":[148],"meso-scale":[151],"molecular":[155],"structure":[156],"wall.":[160],"The":[161,180],"parameterised":[169],"represent":[171],"different":[172,175,187],"in":[174],"taxa.":[179],"contain":[183],"arbitrary":[184],"combinations":[185],"simulates":[190],"random":[192],"diffusion":[193],"through":[194],"polymer":[196],"networks":[197],"taking":[198],"collisions":[199],"into":[200],"account,":[201],"steric":[203],"hindrance":[204],"modelled.":[210],"Steric":[211],"considerations":[212],"included":[214],"when":[215],"target":[216],"bonds":[217],"encountered,":[219],"breakdown":[221],"products":[222],"resulting":[223],"activity":[226],"predicted.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
