Biological physics Energy2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载

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Part Ⅰ Mysteries，Metaphors，Models3

Chapter 1 What the Ancients Knew3

1.1 Heat3

1.1.1 Heat is a form of energy4

1.1.2 Just a little history6

1.1.3 Preview：The concept of free energy8

1.2 How life generates order9

1.2.1 The puzzle of biological order9

1.2.2 Osmotic flow as a paradigm for free energy transduction12

1.2.3 Preview：Disorder as information14

1.3 Excursion：Commercials，philosophy，pragmatics15

1.4 How to do better on exams （and discover new physical laws）18

1.4.1 Most physical quantities carry dimensions18

1.4.2 Dimensional analysis can help you catch errors and recall definitions20

1.4.3 Dimensional analysis can also help you formulate hypotheses22

1.4.4 Some notational conventions involving flux and density22

1.5 Other key ideas from physics and chemistry23

1.5.1 Molecules are small23

1.5.2 Molecules are particular spatial arrangements of atoms25

1.5.3 Molecules have well-defined internal energies26

1.5.4 Low-density gases obey a universal law27

The big picture28

Track 230

Problems31

Chapter 2 What’s Inside Cells35

2.1 Cell physiology37

2.1.1 Internal gross anatomy40

2.1.2 External gross anatomy43

2.2 The molecular parts list45

2.2.1 Small molecules46

2.2.2 Medium-sized molecules48

2.2.3 Big molecules50

2.2.4 Macromolecular assemblies54

2.3 Bridging the gap：Molecular devices54

2.3.1 The plasma membrane55

2.3.2 Molecular motors58

2.3.3 Enzymes and regulatory proteins58

2.3.4 The overall flow of information in cells59

The big picture62

Track 263

Problems64

Part Ⅱ Diffusion，Dissipation，Drive69

Chapter 3 The Molecular Dance69

3.1 The probabilistic facts of life69

3.1.1 Discrete distributions70

3.1.2 Continuous distributions71

3.1.3 Mean and variance73

3.1.4 Addition and multiplication rules75

3.2 Decoding the ideal gas law78

3.2.1 Temperature reflects the average kinetic energy of thermal motion78

3.2.2 The complete distribution of molecular velocities is experimentally measurable82

3.2.3 The Boltzmann distribution83

3.2.4 Activation barriers control reaction rates86

3.2.5 Relaxation to equilibrium87

3.3 Excursion：A lesson from heredity89

3.3.1 Aristotle weighs in89

3.3.2 Identifying the physical carrier of genetic information90

3.3.3 Schrodinger’s summary：Genetic information is structural96

The big picture101

Track 2104

Problems105

Chapter 4 Random Walks，Friction，and Diffusion108

4.1 Brownian motion109

4.1.1 Just a little more history109

4.1.2 Random walks lead to diffusive behavior110

4.1.3 The diffusion law is model independent117

4.1.4 Friction is quantitatively related to diffusion118

4.2 Excursion：Einstein’s role121

4.3 Other random walks122

4.3.1 The conformation of polymers122

4.3.2 Vista：Random walks on Wall Street126

4.4 More about diffusion127

4.4.1 Diffusion rules the subcellular world127

4.4.2 Diffusion obeys a simple equation128

4.4.3 Precise statistical prediction of random processes131

4.5 Functions，derivatives，and snakes under the rug132

4.5.1 Functions describe the details of quantitative relationships132

4.5.2 A function of two variables can be visualized as a landscape134

4.6 Biological applications of diffusion135

4.6.1 The permeability of artificial membranes is diffusive135

4.6.2 Diffusion sets a fundamental limit on bacterial metabolism138

4.6.3 The Nernst relation sets the scale of membrane potentials139

4.6.4 The electrical resistance of a solution reflects frictional dissipation142

4.6.5 Diffusion from a point gives a spreading，Gaussian profile142

The big picture144

Track 2147

Problems153

Chapter 5 Life in the Slow Lane：The Low Reynolds-Number World158

5.1 Friction in fluids158

5.1.1 Sufficiently small particles can remain in suspension indefinitely158

5.1.2 The rate of sedimentation depends on solvent viscosity160

5.1.3 It’s hard to mix a viscous liquid161

5.2 Low Reynolds number163

5.2.1 A critical force demarcates the physical regime dominated by friction164

5.2.2 The Reynolds number quantifies the relative importance of friction and inertia166

5.2.3 The time-reversal properties of a dynamical law signal its dissipative character169

5.3 Biological applications172

5.3.1 Swimming and pumping172

5.3.2 To stir or not to stir？177

5.3.3 Foraging，attack，and escape178

5.3.4 Vascular networks179

5.3.5 Viscous drag at the DNA replication fork182

5.4 Excursion：The character of physical Laws184

The big picture185

Track 2187

Problems190

Chapter 6 Entropy，Temperature，and Free Energy195

6.1 How to measure disorder196

6.2.Entropy199

6.2.1 The Statistical Postulate199

6.2.2 Entropy is a constant times the maximal value of disorder200

6.3 Temperature202

6.3.1 Heat flows to maximize disorder202

6.3.2 Temperature is a statistical property of a system in equilibrium203

6.4 The Second Law206

6.4.1 Entropy increases spontaneously when a constraint is removed206

6.4.2 Three remarks209

6.5 Open systems210

6.5.1 The free energy of a subsystem reflects the competition between entropy and energy210

6.5.2 Entropic forces can be expressed as derivatives of the free energy213

6.5.3 Free energy transduction is most efficient when it proceeds in small，controlled steps214

6.5.4 The biosphere as a thermal engine216

6.6 Microscopic systems217

6.6.1 The Boltzmann distribution follows from the Statistical Postulate218

6.6.2 Kinetic interpretation of the Boltzmann distribution220

6.6.3 The minimum free energy principle also applies to microscopic subsystems223

6.6.4 The free energy determines the populations of complex two-state systems225

6.7 Excursion：“RNA folding as a two-state system” by J.Liphardt，I.Tinoco，Jr.，and C.Bustamante226

The big picture229

Track 2232

Problems239

Chapter 7 Entropic Forces at Work245

7.1 Microscopic view of entropic forces246

7.1.1 Fixed-volume approach246

7.1.2 Fixed-pressure approach247

7.2 Osmotic pressure248

7.2.1 Equilibrium osmotic pressure follows the ideal gas law248

7.2.2 Osmotic pressure creates a depletion force between large molecules251

7.3 Beyond equilibrium：Osmotic flow254

7.3.1 Osmotic forces arise from the rectification of Brownian motion255

7.3.2 Osmotic flow is quantitatively related to forced permeation259

7.4 A repulsive interlude260

7.4.1 Electrostatic interactions are crucial for proper cell functioning261

7.4.2 The Gauss Law263

7.4.3 Charged surfaces are surrounded by neutralizing ion clouds264

7.4.4 The repulsion of like-charged surfaces arises from compression of their ion clouds269

7.4.5 Oppositely charged surfaces attract by counterion release272

7.5 Special properties of water273

7.5.1 Liquid water contains a loose network of hydrogen bonds273

7.5.2 The hydrogen-bond network affects the solubility of small molecules in water276

7.5.3 Water generates an entropic attraction between nonpolar objects280

The big picture281

Track 2283

Problems290

Chapter 8 Chemical Forces and Self-Assembly294

8.1 Chemical potential294

8.1.1 μ measures the availability of a particle species295

8.1.2 The Boltzmann distribution has a simple generalization accounting for particle exchange298

8.2 Chemical reactions299

8.2.1 Chemical equilibrium occurs when chemical forces balance299

8.2.2 Δ G gives a universal criterion for the direction of a chemical reaction301

8.2.3 Kinetic interpretation of complex equilibria306

8.2.4 The primordial soup was not in chemical equilibrium307

8.3 Dissociation308

8.3.1 Ionic and partially ionic bonds dissociate readily in water308

8.3.2 The strengths of acids and bases reflect their dissociation equilibrium constants309

8.3.3 The charge on a protein varies with its environment311

8.3.4 Electrophoresis can give a sensitive measure of protein composition312

8.4 Self-assembly of amphiphiles315

8.4.1 Emulsions form when amphiphilic molecules reduce the oil-water interface tension315

8.4.2 Micelles self-assemble suddenly at a critical concentration317

8.5 Excursion：On fitting models to data321

8.6 Self-assembly in cells322

8.6.1 Bilayers self-assemble from two-tailed amphiphiles322

8.6.2 Vista：Macromolecular folding and aggregation327

8.6.3 Another trip to the kitchen330

The big picture332

Track 2335

Problems337

Part Ⅲ Molecules，Machines，Mechanisms341

Chapter 9 Cooperative Transitions in Macromolecules341

9.1 Elasticity models of polymers342

9.1.1 Why physics works （when it does work）342

9.1.2 Four phenomenological parameters characterize the elasticity of a long，thin rod344

9.1.3 Polymers resist stretching with an entropic force347

9.2 Stretching single macromolecules350

9.2.1 The force-extension curve can be measured for single DNA molecules350

9.2.2 A two-state system qualitatively explains DNA stretching at low force352

9.3 Eigenvalues for the impatient354

9.3.1 Matrices and eigenvalues354

9.3.2 Matrix multiplication357

9.4 Cooperativity358

9.4.1 The transfer matrix technique allows a more accurate treatment of bend cooperativity358

9.4.2 DNA also exhibits linear stretching elasticity at moderate applied force361

9.4.3 Cooperativity in higher-dimensional systems gives rise to infinitely sharp phase transitions363

9.5 Thermal，chemical，and mechanical switching363

9.5.1 The helix-coil transition can be observed by using polarized light364

9.5.2 Three phenomenological parameters describe a given helix-coil transition366

9.5.3 Calculation of the helix-coil transition369

9.5.4 DNA also displays a cooperative “melting” transition373

9.5.5 Applied mechanical force can induce cooperative structural transitions in macromolecules375

9.6 Allostery376

9.6.1 Hemoglobin binds four oxygen molecules cooperatively376

9.6.2 Allostery often involves relative motion of molecular subunits379

9.6.3 Vista：Protein substates380

The big picture382

Track 2384

Problems396

Chapter 10 Enzymes and Molecular Machines401

10.1 Survey of molecular devices found in cells402

10.1.1 Terminology402

10.1.2 Enzymes display saturation kinetics403

10.1.3 All eukaryotic cells contain cyclic motors404

10.1.4 One-shot machines assist in cell locomotion and spatial organization407

10.2 Purely mechanical machines409

10.2.1 Macroscopic machines can be described by an energy landscape409

10.2.2 Microscopic machines can step past energy barriers413

10.2.3 The Smoluchowski equation gives the rate of a microscopic machine415

10.3 Molecular implementation of mechanical principles422

10.3.1 Three ideas423

10.3.2 The reaction coordinate gives a useful reduced description of a chemical event423

10.3.3 An enzyme catalyzes a reaction by binding to the transition state425

10.3.4 Mechanochemical motors move by random-walking on a two-dimensional landscape431

10.4 Kinetics of real enzymes and machines432

10.4.1 The Michaelis-Menten rule describes the kinetics of simple enzymes433

10.4.2 Modulation of enzyme activity436

10.4.3 Two-headed kinesin as a tightly coupled，perfect ratchet437

10.4.4 Molecular motors can move even without tight coupling or a power stroke446

10.5 Vista：Other molecular motors451

The big picture451

Track 2455

Problems464

Chapter 11 Machines in Membranes469

11.1 Electroosmotic effects469

11.1.1 Before the ancients469

11.1.2 Ion concentration differences create Nernst potentials470

11.1.3 Donnan equilibrium can create a resting membrane potential474

11.2 Ion pumping476

11.2.1 Observed eukaryotic membrane potentials imply that these cells are far from Donnan equilibrium476

11.2.2 The Ohmic conductance hypothesis478

11.2.3 Active pumping maintains steady-state membrane potentials while avoiding large osmotic pressures481

11.3 Mitochondria as factories486

11.3.1 Busbars and driveshafts distribute energy in factories487

11.3.2 The biochemical backdrop to respiration487

11.3.3 The chemiosmotic mechanism identifies the mitochondrial inner membrane as a busbar491

11.3.4 Evidence for the chemiosmotic mechanism492

11.3.5 Vista：Cells use chemiosmotic coupling in many other contexts496

11.4 Excursion：“Powering up the flagellar motor” by H.C.Berg and D.Fung497

The big picture499

Track 2501

Problems503

Chapter 12 Nerve Impulses505

12.1 The problem of nerve impulses506

12.1.1 Phenomenology of the action potential506

12.1.2 The cell membrane can be viewed as an electrical network509

12.1.3 Membranes with Ohmic conductance lead to a linear cable equation with no traveling wave solutions514

12.2 Simplified mechanism of the action potential518

12.2.1 The puzzle518

12.2.2 A mechanical analogy519

12.2.3 Just a little more history521

12.2.4 The time course of an action potential suggests the hypothesis of voltage gating524

12.2.5 Voltage gating leads to a nonlinear cable equation with traveling wave solutions527

12.3 The full Hodgkin-Huxley mechanism and its molecular underpinnings532

12.3.1 Each ion conductance follows a characteristic time course when the membrane potential changes532

12.3.2 The patch clamp technique allows the study of single ion channel behavior536

12.4 Nerve，muscle，synapse545

12.4.1 Nerve cells are separated by narrow synapses545

12.4.2 The neuromuscular junction546

12.4.3 Vista：Neural computation548

The big picture549

Track 2552

Problems553

Epilogue557

Appendix A Global List of Symbols and Units559

Notation559

Named quantities560

Dimensions565

Units565

Appendix B Numerical Values569

Fundamental constants569

Magnitudes569

Specialized values571

Appendix C Additional Problems575

Problems for Chapter 1575

Problems for Chapter 2577

Problems for Chapter 3578

Problems for Chapter 4579

Problems for Chapter 5584

Problems for Chapter 6586

Problems for Chapter 7588

Problems for Chapter 8592

Problems for Chapter 9594

Problems for Chapter 10596

Problems for Chapter 11602

Problems for Chapter 12604

Credits607

Bibliography609

Index623