Reading
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 Ronin Institute's guidance here.
Chapter 4:
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"
Chapter 5:
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:
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:
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:
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:
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:
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:
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:
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.