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Nelson  \nDraft December 8, 2002  \n2  \nNot chaos-like together crush’d and bruis’d,  \nBut, as the world, harmoniously confus’d:  \nWhere order in variety we see,  \nAnd where, though all things differ, all agree.  \n– Alexander Pope, 1713  \nFrontispiece: DNA from a bacterium that has been lysed (burst), for example by osmotic shock (12200× magnification) . The bacterial genome that once occupied a small region in the center of the figure now extends in a series of loops from the core structure (arrow) . From (Wolfe, 1985) .  \ni  \nAbout this manuscript:  \nHere is the first half of the text. (The second half will come in about a month.)  \nThere is some good news and some bad news. The good news is that your text for this course is free, apart from duplication costs. The bad news is that you have to help me write it. No, wait! That’s good news: Here’s your chance to tell an author where all the confusing bits are, what things I’ve wrongly assumed you already know, what questions are phrased ambiguously, and soon. Please pass all these comments, and more, on to me via your professor.  \nPhilip Nelson, 12/02  \nContents  \nTo the student viii  \nTo the instructor xii  \nPart I: Mysteries, Metaphors, Models 1  \n1 What the ancients knew 2  \n1.1 Heat ................................................. 2  \n1.1.1 Heat is a form of energy .................................. 3  \n1.1.2 Just a little history ..................................... 4  \n1.1.3 Preview: The concept of free energy ........................... 6  \n1.2 How life generates order ...................................... 7  \n1.2.1 The puzzle of biological order ............................... 7  \n1.2.2 A paradigm for free energy transduction ......................... 10  \n1.3  Excursion:  Commercials, philosophy, pragmatics ........................ 13  \n1.4 How to do better on exams (and discover new physical laws) ................. 15  \n1.4.1 Dimensions and units ................................... 15  \n1.4.2 Using dimensional analysis to catch errors and recall definitions ............ 17  \n1.4.3 Using dimensional analysis to formulate hypotheses .................. 18  \n1.4.4 Some notational conventions involving flux and density ................ 19  \n1.5 Other key ideas from physics and chemistry ........................... 20  \n1.5.1 Molecules are small ..................................... 20  \n1.5.2 Molecules are particular spatial arrangements of atoms ................. 21  \n1.5.3 Molecules have definite internal energies ......................... 22  \n1.5.4 Low-density gases obey a universal law .......................... 23  \nThe big picture ........................................... 24  \n Track 2  ............................................... 26  \nProble.m.s .................................................. 27  \n2 What’s inside cells 30  \n2.1 Cell physiology ........................................... 32  \n2.1.1 Internal gross anatomy ................................... 34  \n2.1.2 External gross anatomy .................................. 38  \n2.2 The molecular parts list ...................................... 41  \n2.2.1 Small molecules ....................................... 41  \n2.2.2 Medium-size molecules ................................... 42  \n2.2.3 Big molecules ........................................ 45  \n2.2.4 Macromolecular assemblies ................................ 46  \n2.3 Bridging the gap: Molecular devices ............................... 48  \n2.3.1 The plasma membrane ................................... 49  \n2.3.2 Molecular motors ...................................... 50  \n2.3.3 Enzymes and regulatory proteins ............................. 56  \n2.3.4 The overall flow of information in cells .......................... 56  \nThe big picture .............................","cbCaieUHUWflv29N","https://ap.wps.com/l/cbCaieUHUWflv29N","pdf",9821845,532,"English","# Contents\n## About this manuscript\n## Part I: Mysteries, Metaphors, Models\n### 1 What the ancients knew\n#### 1.1 Heat\n#### 1.2 How life generates order\n#### 1.3 Excursion: Commercials, philosophy, pragmatics\n#### 1.4 How to do better on exams (and discover new physical laws)\n#### 1.5 Other key ideas from physics and chemistry\n### 2 What’s inside cells\n## Part II: Diffusion, Dissipation, Drive\n### 3 The molecular dance\n### 4 Random walks, friction, and diffusion","[{\"question\":\"What is the manuscript’s main theme across the two parts?\",\"answer\":\"It connects biological organization and cellular function to physical principles, first through models and free energy ideas, then through probabilistic foundations for diffusion and dissipation.\"},{\"question\":\"How does the text approach studying the material and performing on exams?\",\"answer\":\"It includes a dedicated section on how to do better on exams, emphasizing dimensional analysis to check errors, recall definitions, and formulate hypotheses.\"},{\"question\":\"Which topics are covered under Part II: Diffusion, Dissipation, Drive?\",\"answer\":\"It develops the molecular dance using distributions and the ideal gas law, then treats transport via random walks, friction, and diffusion, including Brownian motion and related laws.\"}]","Biological Physics: Energy, Information, Life | PDF",1789974446,1341]