Here is a list of work that helped me in writing "Molecular Storms" but does not appear in the end-of-chapter bibliographies.
Many of the academic papers are behind paywalls. Often, simply searching for the title will bring up a public version. For useful tips on how to find papers, see the (now deceased) Ronin Institute's guidance here.
Chapter 4: The Joy of Thermodynamics
Steam engines: an economic historian's perspective is here.
Carnot cycle: the Wikipedia page gives a good overview.
"English translation" of the three laws: In Astounding Science Fiction from 1956, p43, available here.
James Joule and the law of conservation of energy: a review paper is here.
The third law: Wikipedia gives a good overview here, and some recent work on the connection with quantum physics is here.
"Fourth laws": two attempts to justify a fourth law are here and here.
The role of time in physics: see ch30 of Sir Roger Penrose's "The road to reality"
Is the low-entropy initial state of the universe improbable? A paper from 2004 suggests otherwise. The essence of the argument is that if the final state of the universe has infinite entropy then any initial state with finite entropy will be low entropy compared to this final state. For a critical view, see here.
Chapter 5: The Engines of Creation
Descartes and vortices: section 7 of the Stanford Encyclopedia article is a good place to start.
Kelvin and vortices: the Wikipedia article is here.
Vortices in an electron fluid: the published version is here, the pre-print here.
The demon, and a device capable of reversible measuremet: see the 1987 Scientific American article here.
Chapter 6: From Big Bang to Big Freeze
Black holes: the classic, but rather technical papers are - Bekenstein - Black holes and the second law; Hawking - The four laws of black hole mechanics; Hawking - Particle creation by black holes.
Stellar fusion: see Illiadis - Nuclear physics of stars, available here.
Stellar evolution: the Wikipedia article here is good place to start.
Vortices in the earth's core: a 1999 article from Nature.
Extraterrestrial vortices: The Wikipedia article is here.
Convection in the mantle: The Wikipedia article is here.
Chapter 9: Cellular Matters
For data on cells in general: Harvard BioNumbers
For data on E. coli: Ecocyc
Molecular crowding: there is an interesting discussion here and a model of the impact of crowding on search here.
Proteins: an inteeresting disucssion of the physics of proteins is here.
Lipids: The Wikipedia page is here and a more chemistry-oriented discussion here.
The shape of DNA: an article here.
The bacterium with the smallest genome: Wikipedia.
Chapter 10: Assembly Lines
Glycolysis and biosynthesis: see Table 4.1 in Kim and Gadd - Bacterial physiology and metabolism. Available here.
The citric acid cycle and biosynthesis: see Chapter 2 of Alberts et al - Molecular biology of the cell. Available here.
The synthesis of guanosine : see figure 6.21 in Kim and Gadd - Bacterial physiology and metabolism. Available here.
Chapter 11: Enzymes and Demons
The importance of water for enzyme shape and function: a 2016 article here.
Energy transport in proteins: a 2021 article here.
Binding energy and structural changes: a 2017 article here.
Cell regulation: an overview here.
Kinesin motors: some fascinating work here. The videos, under "Supplementary material" are well worth studying.
Chapter 13: Cellular Dreams
How many cells are there on earth? : one answer is here.
Different types of RNA: Wikipedia has a list here.
Ratchet mechanism in DNA polymerase: an article here.
Rates of protein synthesis: a 2014 article here.
Heat shock response: a discussion is in Chapter 12 of Kim and Gadd - Bacterial physiology and metabolism. Available here.
The replisome : a 2015 article here.
FtsZ and treadmilling: a 2017 article here.
Reactivating primitive cell division: a 2013 article here.
Chapter 14: The Whole Cell
An excellent overview of some connections between physics and life: a 2011 article here.
A textbook discussion of fluctuation theorems: section 6.5.2 of Attard - Beyond the second law. Available here.
Bacterial ageing: a 2017 article here.
Assembly of ribosomes: a 2011 article here.
The complexity of life: see the discussion in Chapter 4 of Dyson - Origins of life. Available here.
Chapter 15: The Origin of Life
Conditions on the early earth: a 2007 article here and one from 2012 here.
Environments for the origin of life: clay, silica, tectonic faults, sediments, ice, pumice, aerosols.
Volcanic islands: for a list, see Wikipedia.
Details of hydrothermal ponds: a 2019 article here.
Hydrocarbons in vents: a 2008 article here.
Cofactors and enzymes: a 2001 article here; one from 2012 here.
Non-enzymatic reactions in metabolism: a 2015 article here.
Cycles and polymerization: the original 1978 article here; empirical work from 2018 here; the thermodynamics here; some theoretical work from 2016 here; then evidence for proteins, lipids and RNA.
Electron bifurcation: a review from 2016 is here.
Energy and vents: a 2012 article here.
Sources of proton gradients: from heat flow here, in condensates here.
Green rust: a 2018 article here.
Vents vs ponds: an entertaining polemic here.
Carts and cars: the earliest evidence of wheeled vehicles discussed here.