Thesis by publication. 
Ch. 1a & 2 permitted as Elsevier publications. Elsevier has a policy of allowing articles to remain in theses.  https://www.elsevier.com/about/policies/copyright/permissions (click on Can I include/use my article in my thesis/dissertation).
Ch. 1b, 3, 5b, 6 are permitted by CC licences. Requires citation, link to published version, & link to the license. 
Ch. 4 & 5a not yet published at this time. As per current instructions articles left in thesis.
Appendix contains published versions of articles. All permitted.   They are either Elsevier articles or articles with CC licences. Elsevier has a policy of allowing articles to remain in theses.  https://www.elsevier.com/about/policies/copyright/permissions (click on Can I include/use my article in my thesis/dissertation)
*One page inserted after 'Details of included papers: thesis by publication' page to display citations, links to published version & CC licences.