{"id":"https://openalex.org/W7204106929","doi":"https://doi.org/10.48550/arxiv.2608.23245","title":"FDTBX - Computational Tools for Simulation of X-ray Fiber Diffraction Patterns from Atomic Coordinates","display_name":"FDTBX - Computational Tools for Simulation of X-ray Fiber Diffraction Patterns from Atomic Coordinates","publication_year":2026,"publication_date":"2026-08-24","ids":{"openalex":"https://openalex.org/W7204106929","doi":"https://doi.org/10.48550/arxiv.2608.23245"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2608.23245","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2608.23245","pdf_url":"https://arxiv.org/pdf/2608.23245","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2608.23245","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044232169","display_name":"Pawel Sikorski","orcid":"https://orcid.org/0000-0001-9413-1623","observed_orcids":["https://orcid.org/0000-0001-9413-1623"]},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Sikorski, Pawel","raw_affiliation_strings":["Department of Physics , Norwegian University of Science and Technology (NTNU) , Trondheim , Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics , Norwegian University of Science and Technology (NTNU) , Trondheim , Norway","institution_ids":["https://openalex.org/I204778367"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044232169"],"corresponding_institution_ids":["https://openalex.org/I204778367"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9096999764442444,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T11162","display_name":"Enzyme Structure and Function","score":0.9096999764442444,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T12613","display_name":"X-ray Diffraction in Crystallography","score":0.08410000056028366,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/x-ray-fiber-diffraction","display_name":"X-ray fiber diffraction","score":0.9259999990463257},{"id":"https://openalex.org/keywords/diffraction-pattern-simulation","display_name":"diffraction pattern simulation","score":0.9610000252723694},{"id":"https://openalex.org/keywords/atomic-coordinates","display_name":"atomic coordinates","score":0.7310000061988831},{"id":"https://openalex.org/keywords/orientational-disorder","display_name":"orientational disorder","score":0.824999988079071},{"id":"https://openalex.org/keywords/thermal-disorder","display_name":"thermal disorder","score":0.8090000152587891},{"id":"https://openalex.org/keywords/debye-waller-factor","display_name":"Debye-Waller factor","score":0.8840000033378601},{"id":"https://openalex.org/keywords/fibrous-proteins","display_name":"fibrous proteins","score":0.7990000247955322},{"id":"https://openalex.org/keywords/amyloid","display_name":"amyloid","score":0.8809999823570251},{"id":"https://openalex.org/keywords/supramolecular-self-assembly","display_name":"supramolecular self-assembly","score":0.6520000100135803},{"id":"https://openalex.org/keywords/polymers","display_name":"polymers","score":0.4350000023841858}],"concepts":[{"id":"https://openalex.org/C17216458","wikidata":"https://www.wikidata.org/wiki/Q3894995","display_name":"Paracrystalline","level":2,"score":0.847100019454956},{"id":"https://openalex.org/C207114421","wikidata":"https://www.wikidata.org/wiki/Q133900","display_name":"Diffraction","level":2,"score":0.6870999932289124},{"id":"https://openalex.org/C89957378","wikidata":"https://www.wikidata.org/wiki/Q164129","display_name":"Reciprocal lattice","level":3,"score":0.5759000182151794},{"id":"https://openalex.org/C137637335","wikidata":"https://www.wikidata.org/wiki/Q899604","display_name":"Crystallite","level":2,"score":0.5527999997138977},{"id":"https://openalex.org/C184652730","wikidata":"https://www.wikidata.org/wiki/Q2357982","display_name":"Attenuation","level":2,"score":0.5371999740600586},{"id":"https://openalex.org/C94915269","wikidata":"https://www.wikidata.org/wiki/Q1834857","display_name":"Detector","level":2,"score":0.5245000123977661},{"id":"https://openalex.org/C65636608","wikidata":"https://www.wikidata.org/wiki/Q1397400","display_name":"Fiber diffraction","level":4,"score":0.4950000047683716},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.4790000021457672},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.4713999927043915},{"id":"https://openalex.org/C50515024","wikidata":"https://www.wikidata.org/wiki/Q826582","display_name":"X-ray crystallography","level":3,"score":0.3490000069141388},{"id":"https://openalex.org/C519885992","wikidata":"https://www.wikidata.org/wiki/Q161","display_name":"Fiber","level":2,"score":0.34630000591278076},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.31929999589920044},{"id":"https://openalex.org/C194232370","wikidata":"https://www.wikidata.org/wiki/Q162","display_name":"Optical fiber","level":2,"score":0.31200000643730164},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3102000057697296},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3059000074863434},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.29350000619888306},{"id":"https://openalex.org/C49040817","wikidata":"https://www.wikidata.org/wiki/Q193091","display_name":"Optoelectronics","level":1,"score":0.27140000462532043},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2703999876976013},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.26980000734329224},{"id":"https://openalex.org/C30475298","wikidata":"https://www.wikidata.org/wiki/Q909554","display_name":"Computational physics","level":1,"score":0.2669999897480011},{"id":"https://openalex.org/C39693636","wikidata":"https://www.wikidata.org/wiki/Q847354","display_name":"Bragg's law","level":3,"score":0.2630999982357025},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2605000138282776},{"id":"https://openalex.org/C204530211","wikidata":"https://www.wikidata.org/wiki/Q752823","display_name":"Thermal","level":2,"score":0.2581000030040741},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.25679999589920044},{"id":"https://openalex.org/C34445779","wikidata":"https://www.wikidata.org/wiki/Q1571347","display_name":"Collimated light","level":3,"score":0.2547000050544739},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.2538999915122986}],"mesh":[],"locations_count":5,"locations":[{"id":"pmh:oai:arXiv.org:2608.23245","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2608.23245","pdf_url":"https://arxiv.org/pdf/2608.23245","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2608.23245","doi":"https://doi.org/10.48550/arxiv.2608.23245","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2608.23245","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.5281/zenodo.21294602","doi":"https://doi.org/10.5281/zenodo.21294602","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21294602","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"ComputationalNotebook"},{"id":"doi:10.5281/zenodo.21294603","doi":"https://doi.org/10.5281/zenodo.21294603","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21294603","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"ComputationalNotebook"},{"id":"doi:10.5281/zenodo.23189395","doi":"https://doi.org/10.5281/zenodo.23189395","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23189395","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"ComputationalNotebook"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2608.23245","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2608.23245","pdf_url":"https://arxiv.org/pdf/2608.23245","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204106929.pdf","grobid_xml":"https://content.openalex.org/works/W7204106929.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1568104740","https://openalex.org/W1582727954","https://openalex.org/W1977224439","https://openalex.org/W1989494816","https://openalex.org/W1996442036","https://openalex.org/W2101298197","https://openalex.org/W2126466006","https://openalex.org/W2140992384","https://openalex.org/W2524096847","https://openalex.org/W4206872134"],"related_works":["https://openalex.org/W2558491957","https://openalex.org/W4298072016","https://openalex.org/W6922796024","https://openalex.org/W2914948616","https://openalex.org/W3024376034","https://openalex.org/W2032544511","https://openalex.org/W3134919546","https://openalex.org/W2136856454","https://openalex.org/W2782730752","https://openalex.org/W41641349"],"abstract_inverted_index":{"FDTBX":[0],"-":[1,15,167,171,178,187,199,217],"Computational":[2],"Tools":[3],"for":[4,27,99,123],"Simulation":[5],"of":[6,17,277],"X-ray":[7,29],"Fiber":[8,37],"Diffraction":[9],"Patterns":[10],"from":[11,33,83,159],"Atomic":[12],"Coordinates.":[13],"V2.1.0":[14],"24th":[16],"August":[18],"2026.":[19],"ABOUT":[20],"fdtbx":[21,91,112],"is":[22,131,157],"an":[23,109,200,220,268],"open-source":[24],"Python":[25],"module":[26],"simulating":[28,81],"fiber":[30,115],"diffraction":[31,38,116,135],"patterns":[32,82,117],"atomic":[34,110],"coordinate":[35],"models.":[36],"underpins":[39],"landmarkwork":[40],"in":[41,118,224,242,296],"structural":[42],"biology,":[43],"polymer":[44,213],"science,":[45,214],"and":[46,56,58,64,74,86,102,143,194,215,240,273],"materials":[47,60],"science":[48],"\u2014":[49],"the":[50,124,151,155,275,297],"DNA":[51],"double":[52],"helix,":[53],"protein":[54],"alpha-helices":[55],"beta-sheets,":[57],"fibrous":[59],"such":[61],"ascellulose,":[62],"collagen,":[63],"synthetic":[65],"polymers.":[66],"Because":[67],"these":[68],"paracrystalline":[69],"samples":[70],"give":[71],"broad,":[72],"weak,":[73],"overlapping":[75],"reflections,":[76],"analysis":[77],"relies":[78],"onmodel-based":[79],"refinement:":[80],"candidate":[84],"models":[85],"comparing":[87],"them":[88],"with":[89,96,245],"experiment.":[90],"provides":[92],"that":[93,127],"simulation":[94],"engine,":[95],"anarchitecture":[97],"built":[98,132],"readability,":[100],"extensibility,":[101],"multicore":[103],"computation.":[104],"What":[105],"it":[106],"does":[107],"Given":[108],"model,":[111],"generates":[113],"realistic":[114],"detector":[119,162],"space":[120],"while":[121],"accounting":[122],"disorder":[125,177,186,198],"effects":[126,165],"dominate":[128],"realspecimens.":[129],"It":[130],"on":[133],"Fourier-transform":[134],"theory.":[136],"Structure":[137],"factors":[138],"are":[139],"computed":[140],"via":[141],"cctbx,":[142],"every":[144],"broadening":[145,174,193],"or":[146,261],"attenuation":[147,203],"effect":[148],"enters":[149],"through":[150],"convolution":[152],"theorem":[153],"before":[154],"pattern":[156],"mapped":[158],"reciprocal":[160],"to":[161,228,265,267],"coordinates.":[163],"Modeled":[164],"include:":[166],"Finite":[168],"crystallite":[169,179],"size":[170],"order-independent":[172],"peak":[173],"(~1/L).-":[175],"Orientational":[176],"misalignment":[180],"smears":[181],"reflections":[182],"into":[183],"arcs.-":[184],"Paracrystalline":[185],"Hosemann":[188],"g-factor":[189],"formalism,":[190],"giving":[191],"order-dependent":[192],"intensity":[195],"loss.-":[196],"Thermal":[197],"independent":[201],"Debye-Waller":[202],"factor.":[204],"Applications":[205],"Structural":[206],"biology":[207],"(fibrous":[208],"proteins,":[209],"amyloids,":[210],"supramolecular":[211],"assemblies),":[212],"nanotechnology":[216],"offered":[218],"as":[219],"open,":[221],"reproducible":[222],"tool":[223],"afield":[225],"where":[226],"access":[227],"specialized":[229],"software":[230],"has":[231],"often":[232],"been":[233],"limiting.":[234],"Quick":[235],"start":[236],"(Jupyter)":[237],"create":[238,248],"venv":[239],"install":[241,253,257,266,287],"editable":[243],"mode":[244],"dev":[246],"extrasconda":[247],"-n":[249],"fdtbx-devcanda":[250],"activate":[251],"fdtbx-devconda":[252],"mamba":[254,286],"-c":[255],"conda-forgemamba":[256],"-f":[258,288],"environment.ymljupyter":[259,289],"lab":[260,290],"if":[262],"you":[263],"want":[264],"existing":[269],"env:":[270],"Edit":[271],"environment.yml":[272],"add":[274],"name":[276,281],"your":[278],"env":[279],"under":[280],"name:":[282],"fdtbx-dev":[283],"Then":[284],"run:":[285],"In":[291],"a":[292],"notebook":[293],"cell":[294],"(example":[295],"notebooks":[298],"folder)":[299],"import":[300],"fdtbxfdtbx.__version__":[301],"#":[302],"LicenseMIT":[303],"\u00a9":[304],"2026":[305],"Pawel":[306],"Sikorski":[307]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-08-25T00:00:00"}
