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Soft matter studies materials whose large-scale structures respond strongly to modest mechanical or thermal disturbances, including polymers, liquid crystals and colloids. Polymer physics connects chain conformations to material response; the coil-stretch transition is one example.
Condensed matter physics studies the collective behavior of matter with many interacting constituents, especially solids and liquids. Crystal structure, electron interactions and thermal motion produce properties that are not apparent from one isolated atom.
A phonon describes a collective lattice vibration, while superconductivity involves a coherent many-electron state. The same microscopic ingredients can produce different phases as temperature, pressure or composition changes. Experiments connect structural, transport, magnetic and spectroscopic measurements with models of those phases.
A molecular motor couples an energy supply to directed mechanical motion. ATP synthase provides a rotary example.
Autoradiography localizes a radioactive label through its effect on a recording medium. In electron microscopy, developed photographic grains are compared with specimen structures; their positions have finite localization precision.
Pulse-chase analysis marks a cohort during a short pulse, then follows it while unlabeled precursor reduces subsequent labeling during the chase. Label specificity and effective suppression of new incorporation constrain interpretation.
Structure of ATP synthase under strain during catalysis by Hui Guo and John L. Rubinstein by
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Cited passages: abstract; Introduction; Figure 1. Yeast hydrolysis conditions; synthesis-related interpretation is distinguished.
Temperature Dependence of Single Molecule Rotation of the Escherichia coli ATP Synthase F1 Sector Reveals the Importance of γ-β Subunit Interactions in the Catalytic Dwell by Mizuki Sekiya and others by
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Journal of Biological Chemistry 284, 22401–22410 (2009).
Rotary catalysis of FoF1-ATP synthase by Rikiya Watanabe by
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Structure of a bacterial ATP synthase by Hui Guo and others by
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Direct observation of the rotation of F1-ATPase by Hiroyuki Noji and others by
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By Hiroyuki Noji, Ryohei Yasuda, Masasuke Yoshida, and Kazuhiko Kinosita Jr.. Nature 386, 299–302; published 20 March 1997. DOI 10.1038/386299a0.
Cited passages: publisher abstract and author information. The abstract describes fluorescent-filament observation of isolated F1 rotation; it does not establish the complete membrane-coupled synthesis assay.
Conservation of plasmid maintenance functions between linear and circular plasmids in Borrelia burgdorferi by Philip E. Stewart and others by
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By Philip E. Stewart, George Chaconas and Patricia Rosa. Journal of Bacteriology 185(10), 3202–3209 (May 2003).
Publication record and abstract: pubmed.ncbi.nlm.nih.gov/12730180/
Only the abstract’s opening statement about natural linear and circular plasmids is cited.
Cited passages: Plasmid Elements, Fig. 2 and feature table; Working with Plasmids; Molecular Cloning.
DNA cloning: A personal view after 40 years by Stanley Norman Cohen by
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By Stanley Norman Cohen, credited as Stanley N. Cohen. Proceedings of the National Academy of Sciences 110(39), 15521–15529; online 16 September 2013, issue 24 September 2013.
Retrospective: pmc.ncbi.nlm.nih.gov/articles/PMC3785787/
The Citric Acid Cycle (Boston University lecture slides) by
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Unsigned slides hosted by Boston University. No named author, instructor or publication date is established; the filename does not establish those roles or dates.
Lecture slides: www.bu.edu/aldolase/biochemistry2/12_TCA%20Cycle_4_2024.pdf
Nobel Lecture by Hans Adolf Krebs, delivered 11 December 1953.
Inspected transcription: studyres.com/doc/1333386/hans-a.-krebs---nobel-lecture
Cited passages: printed pp. 399–404, especially Table 1.
Tissue fractionation studies. 1. The existence of a mitochondria-linked, enzymically inactive form of acid phosphatase in rat-liver tissue by Jacques Berthet and Christian de Duve by
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By Jacques Berthet and Christian de Duve, credited as J. Berthet and C. de Duve. Published in Biochemical Journal 50(2), 174–181, December 1951; received 28 March 1951. The received date is distinct from publication. Portland Press hosts the publisher PDF.
Inspected passage: indexed first-page text, printed p. 174, introduction and Methods, Fractionation of tissue constituents. The full original PDF and subsequent pages were not inspected; this locator does not support claims about unseen tables, numerical activity magnitudes, exact spin settings or specific disruption reagents.
Exploring Cells with a Centrifuge by Christian de Duve by
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Nobel lecture by Christian de Duve, delivered 12 December 1974. This is the lecture date, not an established online publication date. NobelPrize.org hosts the official document; the inspected text was a transcription on Doczz because the official PDF could not be fetched.
Official lecture PDF: www.nobelprize.org/uploads/2018/06/duve-lecture.pdf
Inspected transcription: doczz.net/doc/8221300/christian-de-duve---nobel-lecture
Cited passages: printed pp. 152–159, Figures 1–7, fractionation and enzyme latency; pp. 161–164, microscopy. This is a primary investigator’s retrospective account; it does not replace direct inspection of the original assay paper.
Methods in Enzymology, volume 457: Mitochondrial Function, Part B by
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Edited collection, subtitled Mitochondrial Protein Kinases, Protein Phosphatases and Mitochondrial Diseases, published by Elsevier in 2009. Individual contribution authors are distinct from volume editors; no whole-volume personal authorship is assigned.
Investigating the light dependent reaction in photosynthesis at Practical Biology by
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Official Practical Biology teaching protocol. No individual author byline is established; the site’s institutional issuance and hosting are distinct from personal authorship. September 2008 identifies its safety check, not a publication date. The worker inspected indexed official text; direct page access was unavailable.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.Figure 3. Visual Studio Code extension installation.Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. - Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact





