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Sailing the Ocean of Complexity: Lessons from the Physics-Biology Frontier [Kietas viršelis]

(Senior Research Executive and Principal Investigator, La Sapienza, Italian Institute of Technology, Rome)
  • Formatas: Hardback, 390 pages, aukštis x plotis x storis: 240x162x26 mm, weight: 832 g, 186 line drawings and colour halftones
  • Išleidimo metai: 01-Jun-2022
  • Leidėjas: Oxford University Press
  • ISBN-10: 0192897896
  • ISBN-13: 9780192897893
Kitos knygos pagal šią temą:
Sailing the Ocean of Complexity: Lessons from the Physics-Biology FrontierDidesnis paveikslėlis
  • Formatas: Hardback, 390 pages, aukštis x plotis x storis: 240x162x26 mm, weight: 832 g, 186 line drawings and colour halftones
  • Išleidimo metai: 01-Jun-2022
  • Leidėjas: Oxford University Press
  • ISBN-10: 0192897896
  • ISBN-13: 9780192897893
Kitos knygos pagal šią temą:
Pastovi nuoroda: https://www.kriso.lt/db/9780192897893.html
Raktažodžiai:
"Both superb and essential... Succi, with clarity and wit, takes us from quarks and Boltzmann to soft matter - precisely the frontier of physics and life." Stuart Kauffman, MacArthur Fellow, Fellow of the Royal Society of Canada, Gold Medal Accademia Lincea

We live in a world of utmost complexity, outside and within us. There are thousand of billions of billions of stars out there in the Universe, a hundred times more molecules in a glass of water, and another hundred times more in our body, all working in sync to keep us alive and well. At face value,
such numbers spell certain doom for our ability to make any sense at all of the world around and within us. And yet, they don't. Why, and how - this book endeavours to provide an answer to these questions with specific reference to a selected window of the physics-biology interface. The story
unfolds over four main Parts.

Part I provides an introduction to the main organizational principles which govern the functioning of complex systems in general, such as nonlinearity, nonlocality and ultra-dimensions.

Part II deals with thermodynamics, the science of change, starting with its historical foundations laid down in the 19th century, and then moving on to its modern and still open developments in connection with biology and cosmology.

Part III deals with the main character of this book, free energy, and the wondrous scenarios opened up by its merger with the modern tools of statistical physics. It also describes the basic facts about soft matter, the state of matter most relevant to biological organisms.

Finally, Part IV discusses the connection between time and complexity, and its profound implications on the human condition, i.e. the one-sided nature of time and the awareness of human mortality. It concludes with a few personal considerations about the special place of emotions and humility in
science.

Recenzijos

This book gives a nontechnical survey of complex systems, strongly emphasizing the connection of fundamental physics to biology. Starting with a very nice foundational discussion, the Succi goes on to look at the connection developed by Boltzmann between microscopic physics and macroscopic biology...the thoughtful reader will be rewarded. * Choice * This is an interesting exploration of how the complex macroscopic world is derivable from microscopic physics, and how the non-linearity of complex systems leads to issues of predictability and at the same time accounts for physical structures. The author gives personal comments on his own appreciation of the physics throughout the book, as well as a thought-provoking conclusion suggesting that our experience of time is a consequence of the emergence of complexity. * E. Kincanon, Gonzaga University, CHOICE connect * Complexity is between the two infinities "very big" and "very small" - always a fascinating subject. The author explains things in a very easy-going way, and adds some entertaining stories and thoughts which make it entertaining to read. * Christian Beck, Queen Mary University of London * Complexity science is of critical importance in the modern world, but not on the radar screen of the average reader. This book, designed for the general public, is intended to fix that problem in a very enjoyable and entertaining style. * Bruce Boghosian, Tufts University * A fresh and competent view on a very interesting scientific topic. * Guido Caldarelli, School IMT Alti Studi Lucca * Sauro Succi's new book is both superb and essential. Succi, with clarity and wit, takes us from quarks and Boltzmann to soft matter - precisely the frontier of physics and life. Someone said, There is no truth beyond magic. Succi shows us the magic at the edge of life. * Stuart Kauffman, MacArthur Fellow, Fellow of the Royal Society of Canada, Gold Medal Accademia Lincea *

List of Abbreviations
xxii
Part I Complexity
1 Introducing Complexity
3(12)
1.1 Big science and the inner frontier
3(2)
1.2 What is a complex system?
5(2)
1.3 The science of sciences?
7(2)
1.4 Universality and individuality
9(1)
1.5 Relevant and irrelevant details
10(2)
1.6 The gifts we neither understand nor deserve
12(2)
1.7 Summary
14(1)
2 The Guiding Barriers
15(19)
2.1 The three barriers
15(1)
2.2 The common threads of Complexity
15(1)
2.3 Nonlinearity
16(5)
2.3.1 The superposition principle
19(1)
2.3.2 Multiscale coupling
20(1)
2.4 Nonlocality
21(6)
2.4.1 Memory, history, and hierarchy
23(1)
2.4.2 The Deborah number
24(2)
2.4.3 Chicken-egg causality
26(1)
2.5 Hyperland and ultradimensions
27(5)
2.5.1 Lost in wasteland?
28(3)
2.5.2 The hyperNile
31(1)
2.6 Summary
32(2)
3 Competition and Cooperation
34(14)
3.1 The two big C's
34(1)
3.2 Order & Disorder
34(2)
3.3 Symmetry and broken symmetry
36(1)
3.4 Equilibrium & non-equilibrium
37(4)
3.4.1 The ever-shifting battle
37(1)
3.4.2 Stable and unstable equilibria
38(1)
3.4.3 Conditional equilibrium
39(1)
3.4.4 One, none, or many equilibria?
40(1)
3.5 Smoothness/roughness
41(5)
3.5.1 Zeno's paradox: Achilles and the tortoise
42(1)
3.5.2 A new beauty in town: Fractals
43(2)
3.5.3 Computer simulation
45(1)
3.6 Summary
46(1)
3.7 Appendix 3.1: Summing series
47(1)
4 Nonlinearity, the Mother of Complexity
48(12)
4.1 Anna Karenina
48(1)
4.2 Linear math
48(2)
4.2.1 Entry discount
50(1)
4.3 Nonlinear math
50(2)
4.3.1 More or less?
52(1)
4.4 Pitagora's theorem and beyond
52(2)
4.5 Nonlinear materials
54(1)
4.6 Butterflies and elephants
55(3)
4.7 Summary
58(1)
4.8 Appendix 4.1: Nonlinear functions
58(1)
4.9 Appendix 4.2: How much is it two plus two?
59(1)
5 The Dark Side of Nonlinearity
60(16)
5.1 Introducing chaos
60(3)
5.1.1 Surprises over lunchtime
61(2)
5.2 A closer look at chaos
63(1)
5.2.1 Population dynamics
63(1)
5.3 Entry competition: The logistic map
64(2)
5.4 Chaos: Lost and found
66(4)
5.4.1 Are maps realistic?
69(1)
5.5 From chaos to turbulence
70(3)
5.5.1 The energy cascade
71(1)
5.5.2 The Reynolds number
72(1)
5.6 The pleasure of being unpredictable
73(1)
5.7 Appendix 5.1: More on the logistic map
74(2)
6 The Bright Side of Nonlinearity
76(12)
6.1 Constructive chaos
76(1)
6.2 Nonlinear cooperation
77(1)
6.3 Moving information across scales
77(1)
6.4 From large to small: Breakup
77(2)
6.5 From small to large: Coalescence
79(3)
6.6 Morphogenesis: The Turing model
82(3)
6.7 Summary
85(1)
6.8 Appendix 6.1 Breakup and coalescence
86(1)
6.9 Appendix 6.2 Wave steepening
86(2)
7 Networks, the Fabric of Complexity
88(25)
7.1 A must in Complexity
88(1)
7.2 Rules and equations
88(1)
7.3 Dismantling Zeno's trick: The lattice world
89(1)
7.4 Hamletic fluids: Lattice gas cellular automata
90(3)
7.5 Probabilistic fluids: Lattice Boltzmann
93(2)
7.6 A new kind of science?
95(1)
7.7 Is the Universe a gigantic self-computing automaton?
96(2)
7.7.1 The take-home lesson of lattice fluids
98(1)
7.8 From lattices to general networks
98(1)
7.9 Network basics
99(1)
7.9.1 Statistical properties
100(1)
7.10 Metric versus topological networks
100(1)
7.11 Random networks
101(2)
7.12 Scale-free networks
103(3)
7.12.1 Tolerance to outliers
104(1)
7.12.2 The Matthew effect
105(1)
7.13 Small worlds
106(2)
7.13.1 Entry fragility
108(1)
7.14 Complex adaptive networks
108(2)
7.15 Summary
110(3)
Part II The Science of Change
8 Old but Gold: Thermodynamics
113(23)
8.1 The science of (slow) change
113(1)
8.2 The cosmic prima donnas
114(1)
8.3 Energy: Transformation and conservation
114(5)
8.3.1 The many faces of potential energy
117(2)
8.4 What is heat?
119(3)
8.4.1 Work and zero temperature
120(2)
8.5 Much ado about something: The Carnot cycle
122(3)
8.6 The mirage of perfect efficiency
125(2)
8.7 Heat and dissipation
127(1)
8.8 Entropy
128(3)
8.9 The Second Principle of Thermodynamics
131(1)
8.10 The arrow of time
132(2)
8.11 The rules of the game
134(1)
8.12 Summary
135(1)
9 The Man Who Trusted Atoms
136(23)
9.1 The microscopic roots of thermodynamics
136(1)
9.2 Ludwig Boltzmann
137(2)
9.2.1 Kinetic theory of gases
137(2)
9.3 Entry probability
139(1)
9.4 Local and global equilibria
139(5)
9.4.1 Maxwell-Boltzmann local equilibrium distribution
141(2)
9.4.2 The fatal attraction of conservation laws
143(1)
9.5 From molecules to entropy
144(1)
9.6 Entropic forces
145(2)
9.6.1 Entropy and happiness
147(1)
9.7 Temperature: The entropic trigger
147(1)
9.8 Underpressure
148(2)
9.9 The microscopic face of dissipation
150(2)
9.10 Entropy
152(3)
9.10.1 Entropy and time
152(1)
9.10.2 Entropy, information, and scrambled eggs
153(2)
9.10.3 Caveat: Entropy and Disorder
155(1)
9.11 Summary
155(1)
9.12 Appendix 9.1: Boltzmann's kinetic theory
156(3)
10 Biological Escapes
159(16)
10.1 The new alliance
159(1)
10.2 Biological escapes
159(1)
10.3 Open systems
160(2)
10.4 Out of equilibrium
162(2)
10.5 Dissipative structures
164(1)
10.6 Conduction and convection
165(1)
10.7 A new thermal deal
166(1)
10.8 Where is nonlinearity?
167(2)
10.9 Take-home's
169(1)
10.10 Tomaso Albinoni
169(2)
10.11 Emergent life?
171(1)
10.12 Summary: Life on borrowed time
172(1)
10.13 Appendix 10.1: Rayleigh-Benard equations
173(2)
11 Cosmological Escapes
175(20)
11.1 The cosmic trio
175(1)
11.2 The living Universe
175(1)
11.3 Basic facts about gravity
175(1)
11.4 Newton's theory of universal gravitation
176(3)
11.4.1 The fatal grip of gravity
176(2)
11.4.2 Gravity is weak
178(1)
11.4.3 Gravity is long-ranged
178(1)
11.5 Gravitational thermodynamics
179(1)
11.6 Gravitational balloons
180(2)
11.6.1 Entropy and gravity
181(1)
11.7 Cosmological thermodynamics
182(1)
11.8 Einstein's theory of general gravitation
182(2)
11.8.1 Entry general relativity
183(1)
11.9 Cosmological chronicles
184(3)
11.9.1 Georges Lemaitre
185(2)
11.10 Pause of reflection
187(1)
11.10.1 Dancing in the dark
187(1)
11.10.2 Singularities
187(1)
11.11 Black hole thermodynamics
188(1)
11.12 Black holes get grey (not much though ...)
189(4)
11.12.1 Bekenstein--Hawking black hole entropy
191(2)
11.13 The thermal history of the Universe
193(1)
11.14 Summary
193(2)
12 Free Energy
195(16)
12.1 Energy goes free
195(1)
12.2 Nature's spending review
195(3)
12.2.1 Walls and Doors
196(2)
12.3 Beautiful mountains
198(1)
12.4 Chemical mountains
199(2)
12.5 Chemical time
201(2)
12.6 Stopovers in the landscape
203(1)
12.7 The duel and the duet
204(3)
12.8 In the biological world
207(1)
12.9 Summary
207(1)
12.10 Appendix 12.1: Arrhenius law
208(3)
Part III The Physics-Biology Interface
13 Survival in Molecular Hyperland, the Ozland Valleys
211(25)
13.1 A tour to molecular hyperland
211(1)
13.2 Topography
211(3)
13.2.1 Surviving in hyperland
212(1)
13.2.2 Weeding out wasteland
213(1)
13.3 The art of coarse graining
214(1)
13.4 Order parameters
215(1)
13.5 Modelling DNA translocation
216(2)
13.5.1 DNA hyperland
216(2)
13.6 Coarse-graining DNA
218(2)
13.7 Coarse-grained molecular dynamics
220(2)
13.7.1 Molecular trains and their delays
220(2)
13.8 Extreme coarse-graining: Lineland
222(1)
13.9 The Langevin approach
223(4)
13.10 Biological ballerinas: Protein folding
227(2)
13.11 Coarse-graining proteins
229(1)
13.12 Of proteins and monkeys: The Levinthal's paradox
230(2)
13.13 Why does it work (when it does ...)?
232(1)
13.13.1 The closure problem
232(1)
13.14 Summary
233(1)
13.15 Appendix 13.1: Order parameter for translocation
234(2)
14 Free-Energy Funnels
236(26)
14.1 Navigating the free-energy landscape, on time
236(1)
14.2 Is time the hero?
236(1)
14.3 Rare events are rare, not impossible
237(3)
14.3.1 Long enough
237(2)
14.3.2 Biological blue moon time
239(1)
14.4 Deep corrugations: The funnel
240(2)
14.4.1 Fun (nel) time
241(1)
14.5 Picasso and the proteins
242(2)
14.6 The principle of minimal frustration
244(3)
14.6.1 Stravinski's constrained freedom
246(1)
14.7 Broken constraints
247(3)
14.8 The good and the bad funnels
250(1)
14.8.1 Beacons in The Ocean of Complexity
250(1)
14.9 Navigation routes in the landscape
251(2)
14.9.1 Down the steepest slope
251(1)
14.9.2 With a little help from our molecular chaos friend
251(2)
14.10 Protein folding revisited
253(2)
14.10.1 Multiple-Order parameters
254(1)
14.11 The gifts of non-equilibrium
255(2)
14.11.1 From mountains to quicksand
255(1)
14.11.2 Burnt bridges and cryptic pockets
256(1)
14.11.3 Trains that don't pass twice
256(1)
14.12 The quark, the jaguar, and the free-energy principle
257(1)
14.13 Summary
258(1)
14.14 Appendix 14.1 Funnel acceleration
258(1)
14.15 Appendix 14.2 Mistaking rare events for impossible ones
259(3)
15 Soft Matter, the Stuff that Dreams are Made of
262(25)
15.1 Back to the ground
262(1)
15.2 The stuff that dreams are made of
262(1)
15.3 States of matter
263(4)
15.3.1 The magnificent three: gas, liquid, and solid
264(1)
15.3.2 Hybrid states of matter
265(2)
15.4 The physics-chemistry-biology interface
267(1)
15.5 Molecular interactions
268(1)
15.5.1 What a bore?
269(1)
15.6 Electrostatic forces
269(4)
15.6.1 Electrostatic instability
270(2)
15.6.2 Long-range attraction and short-range repulsion
272(1)
15.7 Polarization
273(2)
15.7.1 Polar molecules
275(1)
15.8 Dispersion forces
275(6)
15.8.1 Van der Waals and Lennard--Jones
275(4)
15.8.2 Capillary forces
279(1)
15.8.3 The wall builder
280(1)
15.9 More dispersion forces
281(2)
15.10 Pause of reflection: The ouroboros
283(1)
15.10.1 Die-hard prejudices
284(1)
15.11 Beyond dissipative structures?
284(1)
15.12 Summary
285(1)
15.13 Appendix 15.1: Surface tension and Laplace's law
286(1)
16 Water, the Wonderfluid
287(22)
16.1 Introduction
287(1)
16.2 The magic fluid we call water
287(2)
16.2.1 Water anomalies
288(1)
16.2.2 Water molecular networks
289(1)
16.3 The third thing
289(1)
16.4 Matters of packing
290(3)
16.4.1 Entropy is not (just) Disorder
292(1)
16.5 My name is Bond, H-Bond
293(1)
16.6 Hydropathy, the molecular builder
294(2)
16.7 Back to protein folding
296(1)
16.7.1 Molecular storms
297(1)
16.8 Intra-molecular interactions
297(2)
16.9 Funnel explained?
299(2)
16.9.1 Caveat
300(1)
16.10 The Theory of Something
301(1)
16.10.1 And The Theory of Everything Else
302(1)
16.11 Dispelling prejudices: Can you imitate birds?
302(2)
16.12 Summary
304(5)
Part IV Complexity and the Human Condition
17 Time, Complexity and the Human Condition
309(18)
17.1 What is time?
309(2)
17.1.1 The transformations of time
309(2)
17.2 Emergent time
311(4)
17.2.1 Crossing the Boltzmann bridge
312(3)
17.3 Psycho time
315(1)
17.3.1 Brain and tears: The human condition
315(1)
17.4 Biological time
316(4)
17.4.1 Le temps de philosophes
317(1)
17.4.2 Time travel and the fear of uncertainty
318(2)
17.5 Putting the times together: Time is us
320(3)
17.5.1 Tears in the rain
321(2)
17.6 Who wants to live forever?
323(3)
17.6.1 Are atoms immortal?
324(1)
17.6.2 The quest for immortality, in Silicon Valley
325(1)
17.7 Summary
326(1)
18 Harness the Hybris: Hallelujah!
327(12)
18.1 Escape from Helsinki: Eyjafjallajokull!
327(1)
18.2 Harness the hybris
328(2)
18.2.1 Should I be doing science?
329(1)
18.3 These are the two wings
330(1)
18.3.1 Typecast stereotypes
330(1)
18.4 A jump into the blue
331(1)
18.5 Of sparrows and lilies
332(2)
18.6 It's April again, COVID-19 time
334(2)
18.7 Do not worry
336(3)
Epilogue
337(1)
Acknowledgements
338(1)
19 Appendices
339(17)
19.1 Numbers
339(6)
19.1.1 Scientific notation
339(1)
19.1.2 Exponential and logarithms
340(2)
19.1.3 Factorial
342(1)
19.1.4 Large numbers: Gates, Bezos, and Avogadro
342(1)
19.1.5 Huge numbers: Googol
343(1)
19.1.6 Towards monster numbers: DNA
343(1)
19.1.7 Monster numbers and beyond: Googolpex and Penrose
344(1)
19.1.8 Logarithmic survival
345(1)
19.2 Thermodynamics
345(3)
19.2.1 Thermodynamic variables
345(1)
19.2.2 The First Principle of Thermodynamics
346(1)
19.2.3 The Second Principle of Thermodynamics
347(1)
19.2.4 The Third Principle of Thermodynamics
347(1)
19.2.5 The Fourth Principle of Thermodynamics (in jesting mode ...)
348(1)
19.3 Quantum physics
348(8)
19.3.1 Classical mechanics
349(1)
19.3.2 Classical waves
350(1)
19.3.3 Quantum mechanics
350(6)
References 356(6)
Index 362
Sauro Succi graduated in Nuclear Engineering from the University of Bologna and holds a PhD in Physics from the Swiss Polytechnique Institute in Lausanne. He has been working at several Italian and European institutions, including the Max Planck Institute for Plasma Physics, EPFL, IBM Europe, The Italian National Research Council and lately the Italian Institute of Technology. He also held numerous teaching and research appointments in Europe and USA, particularly at Harvard University.