Physics of biomolecules and cells
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CONTENTS
Lecturers |
xi |
Participants |
xiii |
Pr´eface |
xvii |
Preface |
xxi |
Contents |
xxv |
Course 1. Physics of Protein-DNA Interaction |
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by R.F. Bruinsma |
1 |
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1 Introduction |
3 |
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1.1 The central dogma and bacterial gene expression . . . . . . . . . . |
3 |
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1.1.1 |
Two families . . . . . . . . . . . . . . . . . . . . . . . . . . |
3 |
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1.1.2 |
Prokaryote gene expression . . . . . . . . . . . . . . . . . . |
5 |
1.2 |
Molecular structure . . . . . . . . . . . . . . . . . . . . . . . . . . |
8 |
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1.2.1 |
Chemical structure of DNA . . . . . . . . . . . . . . . . . . |
8 |
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1.2.2 |
Physical structure of DNA . . . . . . . . . . . . . . . . . . . |
10 |
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1.2.3 |
Chemical structure of proteins . . . . . . . . . . . . . . . . |
12 |
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1.2.4 |
Physical structure of proteins . . . . . . . . . . . . . . . . . |
14 |
2 Thermodynamics and kinetics of repressor-DNA interaction |
16 |
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2.1 Thermodynamics and the lac repressor . . . . . . . . . . . . . . . . |
16 |
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2.1.1 The law of mass action . . . . . . . . . . . . . . . . . . . . |
16 |
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2.1.2 Statistical mechanics and operator occupancy . . . . . . . . |
19 |
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2.1.3 Entropy, enthalpy, and direct read-out . . . . . . . . . . . . |
20 |
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2.1.4 |
The lac repressor complex: A molecular machine . . . . . . |
23 |
2.2 |
Kinetics of repressor-DNA interaction . . . . . . . . . . . . . . . . |
26 |
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2.2.1 |
Reaction kinetics . . . . . . . . . . . . . . . . . . . . . . . . |
26 |
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2.2.2 |
Debye–Smoluchowski theory . . . . . . . . . . . . . . . . . . |
28 |
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2.2.3 |
BWH theory . . . . . . . . . . . . . . . . . . . . . . . . . . |
30 |
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2.2.4 Indirect read-out and induced fit . . . . . . . . . . . . . . . |
32 |
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xxvi
3 DNA deformability and protein-DNA interaction |
34 |
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3.1 |
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
34 |
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3.1.1 Eukaryotic gene expression and Chromatin condensation . . |
34 |
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3.1.2 A mathematical experiment and White’s theorem . . . . . . |
37 |
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3.2 |
The worm-like chain . . . . . . . . . . . . . . . . . . . . . . . . . . |
40 |
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3.2.1 Circular DNA and the persistence length . . . . . . . . . . |
42 |
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3.2.2 Nucleosomes and the Marky–Manning transition . . . . . . |
42 |
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3.2.3 |
Protein-DNA interaction under tension . . . . . . . . . . . |
45 |
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3.2.4 |
Force-Extension Curves . . . . . . . . . . . . . . . . . . . . |
47 |
3.3 |
The RST model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
50 |
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3.3.1 |
Structural sequence sensitivity . . . . . . . . . . . . . . . . |
50 |
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3.3.2 |
Thermal fluctuations . . . . . . . . . . . . . . . . . . . . . . |
52 |
4 Electrostatics in water and protein-DNA interaction |
53 |
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4.1 |
Macro-ions and aqueous electrostatics . . . . . . . . . . . . . . . . |
54 |
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4.2 |
The primitive model . . . . . . . . . . . . . . . . . . . . . . . . . . |
56 |
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4.2.1 |
The primitive model: Ion-free . . . . . . . . . . . . . . . . . |
57 |
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4.2.2 |
The primitive model: DH regime . . . . . . . . . . . . . . . |
57 |
4.3 |
Manning condensation . . . . . . . . . . . . . . . . . . . . . . . . . |
58 |
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4.3.1 |
Charge renormalization . . . . . . . . . . . . . . . . . . . . |
58 |
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4.3.2 |
Primitive model: Oosawa theory . . . . . . . . . . . . . . . |
59 |
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4.3.3 |
Primitive model: Free energy . . . . . . . . . . . . . . . . . |
61 |
4.4Counter-ion release and non-specific protein-DNA interaction . . . 63
4.4.1 Counter-ion release . . . . . . . . . . . . . . . . . . . . . . . 63
4.4.2Nucleosome formation and the isoelectric instability . . . . 64
Course 2. Mechanics of Motor Proteins |
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by J. Howard |
69 |
1 |
Introduction |
71 |
2 |
Cell motility and motor proteins |
72 |
3 |
Motility assays |
73 |
4 |
Single-molecules assays |
75 |
5 |
Atomic structures |
77 |
6 |
Proteins as machines |
78 |
7 |
Chemical forces |
80 |
8 |
E ect of force on chemical equilibria |
81 |
9 |
E ect of force on the rates of chemical reactions |
82 |
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xxvii |
10 |
Absolute rate theories |
85 |
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11 |
Role of thermal fluctuations in motor reactions |
87 |
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12 |
A mechanochemical model for kinesin |
89 |
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13 |
Conclusions and outlook |
92 |
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Course 3. Modelling Motor Protein Systems |
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by T. Duke |
95 |
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1 |
Making a move: Principles of energy transduction |
98 |
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1.1 |
Motor proteins and Carnot engines . . . . . . . . . . . . . . . . . |
. 98 |
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1.2 |
Simple Brownian ratchet . . . . . . . . . . . . . . . . . . . . . . . . |
99 |
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1.3 |
Polymerization ratchet . . . . . . . . . . . . . . . . . . . . . . . . . |
100 |
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1.4 |
Isothermal ratchets . . . . . . . . . . . . . . . . . . . . . . . . . . . |
103 |
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1.5 |
Motor proteins as isothermal ratchets . . . . . . . . . . . . . . . . |
104 |
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1.6 |
Design principles for e ective motors . . . . . . . . . . . . . . . . . |
105 |
2 |
Pulling together: Mechano-chemical model of actomyosin |
108 |
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2.1 |
Swinging lever-arm model . . . . . . . . . . . . . . . . . . . . . . . |
108 |
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2.2 |
Mechano-chemical coupling . . . . . . . . . . . . . . . . . . . . . . |
110 |
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2.3 |
Equivalent isothermal ratchet . . . . . . . . . . . . . . . . . . . . . |
111 |
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2.4 |
Many motors working together . . . . . . . . . . . . . . . . . . . . |
112 |
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2.5 |
Designed to work . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
115 |
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2.6 |
Force-velocity relation . . . . . . . . . . . . . . . . . . . . . . . . . |
116 |
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2.7 |
Dynamical instability and biochemical synchronization . . . . . . . |
118 |
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2.8 |
Transient response of muscle . . . . . . . . . . . . . . . . . . . . . |
119 |
3 |
Motors at work: Collective properties of motor proteins |
119 |
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3.1 |
Dynamical instabilities . . . . . . . . . . . . . . . . . . . . . . . . . |
119 |
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3.2 |
Bidirectional movement . . . . . . . . . . . . . . . . . . . . . . . . |
120 |
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3.3 |
Critical behaviour . . . . . . . . . . . . . . . . . . . . . . . . . . . |
121 |
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3.4 |
Oscillations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
124 |
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3.5 |
Dynamic buckling instability . . . . . . . . . . . . . . . . . . . . . |
125 |
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3.6 |
Undulation of flagella . . . . . . . . . . . . . . . . . . . . . . . . . |
127 |
4 |
Sense and sensitivity: Mechano-sensation in hearing |
129 |
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4.1 |
System performance . . . . . . . . . . . . . . . . . . . . . . . . . . |
129 |
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4.2 |
Mechano-sensors: Hair bundles . . . . . . . . . . . . . . . . . . . . |
130 |
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4.3 |
Active amplification . . . . . . . . . . . . . . . . . . . . . . . . . . |
131 |
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4.4 |
Self-tuned criticality . . . . . . . . . . . . . . . . . . . . . . . . . . |
133 |
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4.5 |
Motor-driven oscillations . . . . . . . . . . . . . . . . . . . . . . . . |
134 |
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4.6 |
Channel compliance and relaxation oscillations . . . . . . . . . . . |
136 |
xxviii |
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4.7 |
Channel-driven oscillations . . . . . . . . . . . . . . . . . . . . . . |
138 |
4.8 |
Hearing at the noise limit . . . . . . . . . . . . . . . . . . . . . . . |
139 |
Course 4. Dynamic Force Spectroscopy |
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by E. Evans and P. Williams |
145 |
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Part 1: E. Evans and P. Williams |
147 |
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1 Dynamic force spectroscopy. I. Single bonds |
147 |
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1.1 |
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
147 |
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1.1.1 Intrinsic dependence of bond strength on time frame |
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for breakage . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
1.1.2Biomolecular complexity and role for dynamic force
spectroscopy . . . . . . . . . . . . . . . . . . . . . |
. . . . . 148 |
1.1.3 Biochemical and mechanical perspectives of bond strength . 150 |
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1.1.4 Relevant scales for length, force, energy, and time . |
. . . . . 153 |
1.2 Brownian kinetics in condensed liquids: Old-time physics |
. . . . . 154 |
1.2.1 Two-state transitions in a liquid . . . . . . . . . . . |
. . . . 155 |
1.2.2 Kinetics of first-order reactions in solution . . . . . . |
. . . . 156 |
1.3 Link between force – time – and bond chemistry . . . . . . |
. . . . 158 |
1.3.1 Dissociation of a simple bond under force . . . . . . |
. . . . 158 |
1.3.2 Dissociation of a complex bond under force: |
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Stationary rate approximation . . . . . . . . . . . . |
. . . . 159 |
1.3.3 Evolution of states in complex bonds . . . . . . . . . |
. . . . 163 |
1.4Testing bond strength and the method of dynamic force
spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . |
. . . . 164 |
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1.4.1 Probe mechanics and bond loading dynamics . . . . |
. . . . 165 |
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1.4.2 |
Stochastic process of bond failure under rising force |
. . . . 168 |
1.4.3 |
Distributions of bond lifetime and rupture force . . . |
. . . . 169 |
1.4.4Crossover from near equilibrium to far from equilibrium
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unbonding . . . . . . . . . . . . . . . . . . . . . |
. . . . . . . 172 |
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1.4.5 E ect of soft-polymer linkages on dynamic strengths |
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of bonds . . . . . . . . . . . . . . . . . . . . . . |
. . . . . . . 175 |
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1.4.6 |
Failure of a complex bond and unexpected |
transitions |
|
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in strength . . . . . . . . . . . . . . . . . . . . |
. . . . . . . 177 |
1.5 |
Summary . . . . . . . . . . . . . . . . . . . . . . . . . |
. . . . . . . 185 |
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Part 2: P. Williams and E. Evans |
186 |
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2 Dynamic force spectroscopy. II. Multiple bonds |
187 |
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2.1 |
Hidden mechanics in detachment of multiple bonds . . |
. . . . . . . 187 |
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2.2 |
Impact of cooperativity . . . . . . . . . . . . . . . . . |
. . . . . . . 188 |
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2.3 |
Uncorrelated failure of bonds loaded in series . . . . . |
. . . . . . . 191 |
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2.3.1 Markov sequence of random failures . . . . . . |
. . . . . . . 191 |
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2.3.2 |
Multiple-complex bonds . . . . . . . . . . . . . |
. . . . . . . 193 |
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xxix |
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2.3.3 |
Multiple-ideal bonds . . . . . . . . . . . . . . . . . . . . . . |
194 |
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2.3.4 |
Equivalent single-bond approximation . . . . . . . . . . . . |
195 |
2.4 |
Uncorrelated failure of bonds loaded in parallel . . . . . . . . . . . |
198 |
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2.4.1 Markov sequence of random failures . . . . . . . . . . . . . |
198 |
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2.4.2 |
Equivalent single-bond approximation . . . . . . . . . . . . |
198 |
2.5 |
Poisson statistics and bond formation . . . . . . . . . . . . . . . . |
199 |
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2.6 |
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
203 |
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Seminar 1. Polymerization Forces |
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by M. Dogterom |
205 |
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Course 5. The Physics of Listeria Propulsion |
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by J. Prost |
215 |
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1 |
Introduction |
217 |
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2 |
A genuine gel |
218 |
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2.1 |
A little chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
218 |
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2.2 |
Elastic behaviour . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
220 |
3 |
Hydrodynamics and mechanics |
220 |
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3.1 |
Motion in the laboratory frame . . . . . . . . . . . . . . . . . . . . |
220 |
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3.2 |
Propulsion and steady velocity regimes . . . . . . . . . . . . . . . . |
221 |
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3.3 |
Gel/bacterium friction and saltatory behaviour . . . . . . . . . . . |
223 |
4 |
Biomimetic approach |
225 |
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4.1 |
A spherical Listeria . . . . . . . . . . . . . . . . . . . . . . . . . . . |
225 |
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4.2 |
Spherical symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . |
226 |
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4.3 |
Steady state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
227 |
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4.4 |
Growth with spherical symmetry . . . . . . . . . . . . . . . . . . . |
229 |
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4.5 |
Symmetry breaking . . . . . . . . . . . . . . . . . . . . . . . . . . . |
229 |
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4.6 |
Limitations of the approach and possible improvements . . . . . . |
231 |
5 |
Conclusion |
234 |
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xxx
Course 6. Physics of Composite Cell Membrane and Actin Based Cytoskeleton
by E. Sackmann, A.R. Bausch and L. Vonna |
237 |
1 Architecture of composite cell membranes |
239 |
1.1The lipid/protein bilayer is a multicomponent smectic phase
with mosaic like architecture . . . . . . . . . . . . . . . . . . . . . |
239 |
1.2The spectrin/actin cytoskeleton as hyperelastic cell stabilizer . . . 242
1.3 The actin cortex: Architecture and function . . . . . . . . . . . . . 245
2 Physics of the actin based cytoskeleton |
249 |
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2.1 |
Actin is a living semiflexible polymer . . . . . . . . . . . . . . . . . |
249 |
2.2 |
Actin network as viscoelastic body . . . . . . . . . . . . . . . . . . |
253 |
2.3Correlation between macroscopic viscoelasticity and molecular
|
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motional processes . . . . . . . . . . . . . . . . . . . . . . . . . . . |
258 |
3 |
Heterogeneous actin gels in cells and biological function |
260 |
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3.1 |
Manipulation of actin gels . . . . . . . . . . . . . . . . . . . . . . . |
260 |
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3.2 |
Control of organization and function of actin cortex |
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by cell signalling . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
265 |
4 |
Micromechanics and microrheometry of cells |
267 |
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5Activation of endothelial cells: On the possibility
of formation of stress fibers as phase transition of actin-network
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triggered by cell signalling pathways |
271 |
6 |
On cells as adaptive viscoplastic bodies |
274 |
7 |
Controll of cellular protrusions controlled by actin/myosin |
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cortex |
278 |
Course 7. Cell Adhesion as Wetting Transition? |
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by E. Sackmann and R. Bruinsma |
285 |
1 |
Introduction |
287 |
2 |
Mimicking cell adhesion |
292 |
3 |
Microinterferometry: A versatile tool to evaluate adhesion |
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strength and forces |
294 |
4 |
Soft shell adhesion is controlled by a double well interfacial |
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potential |
294 |
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xxxi |
5 |
How is adhesion controlled by membrane elasticity? |
297 |
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6 |
Measurement of adhesion strength by interferometric contour |
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analysis |
299 |
|
7 |
Switching on specific forces: Adhesion as localized |
dewetting |
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process |
300 |
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8 |
Measurement of unbinding forces, receptor-ligand leverage |
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and a new role for stress fibers |
300 |
|
9 |
An application: Modification of cellular adhesion strength |
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by cytoskeletal mutations |
303 |
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10 |
Conclusions |
303 |
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A |
Appendix: Generic interfacial forces |
304 |
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Course 8. Biological Physics in Silico |
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by R.H. Austin |
311 |
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1 |
Why micro/nanofabrication? |
315 |
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Lecture 1a: Hydrodynamic Transport |
319 |
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1 |
Introduction: The need to control flows in 2 1/2 D |
319 |
|
2 |
Somewhat simple hydrodynamics in 2 1/2 D |
321 |
|
3 |
The N-port injector idea |
328 |
|
4 |
Conclusion |
333 |
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Lecture 1b: Dielectrophoresis and Microfabrication |
335 |
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1 |
Introduction |
335 |
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2 |
Methods |
337 |
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2.1 |
Fabrication . . . . . . . . . . . . . . . . . . . . . . . . . |
. . . . . . 337 |
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2.2 |
Viscosity . . . . . . . . . . . . . . . . . . . . . . . . . . . |
. . . . . . 338 |
|
2.3 |
Electronics and imaging . . . . . . . . . . . . . . . . . . |
. . . . . . 338 |
|
2.4 |
DNA samples . . . . . . . . . . . . . . . . . . . . . . . . |
. . . . . . 338 |
3 |
Results |
339 |
|
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3.1 Basic results and dielectrophoretic force extraction . . . |
. . . . . . 339 |
|
4 |
Data and analysis |
343 |
|
xxxii
5 |
Origin of the low frequency dielectrophoretic force in DNA |
347 |
6 |
Conclusion |
353 |
Lecture 2a: Hex Arrays |
356 |
|
1 |
Introduction |
356 |
2 |
Experimental approach |
360 |
3 |
Conclusions |
364 |
Lecture 2b: The DNA Prism |
366 |
|
1 |
Introduction |
366 |
2 |
Design |
366 |
3 |
Results |
367 |
4 |
Conclusions |
372 |
Lecture 2c: Bigger is Better in Rachets |
374 |
|
1 |
The problems with insulators in rachets |
374 |
2 |
An experimental test |
375 |
3 |
Conclusions |
381 |
Lecture 3: Going After Epigenetics |
382 |
|
1 |
Introduction |
382 |
2 |
The nearfield scanner |
383 |
3 |
The chip |
384 |
4 |
Experiments with molecules |
387 |
5 |
Conclusions |
391 |
Lecture 4: Fractionating Cells |
392 |
|
1 |
Introduction |
392 |
2 |
Blood specifics |
392 |
3 |
Magnetic separation |
397 |
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xxxiii |
4 |
Microfabrication |
398 |
|
5 |
Magnetic field gradients |
399 |
|
6 |
Device interface |
401 |
|
7 |
A preliminary blood cell run |
406 |
|
8 |
Conclusions |
409 |
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Lecture 5: Protein Folding on a Chip |
411 |
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1 |
Introduction |
411 |
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2 |
Technology |
412 |
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3 |
Experiments |
415 |
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4 |
Conclusions |
418 |
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Course 9. Some Physical Problems in Bioinformatics |
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by E.D. Siggia |
421 |
|
1 |
Introduction |
423 |
|
2 |
New technologies |
425 |
|
3 |
Sequence comparison |
427 |
|
4 |
Clustering |
430 |
|
5 |
Gene regulation |
432 |
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Course 10. Three Lectures on Biological Networks |
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by M.O. Magnasco |
435 |
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1 |
Enzymatic networks. Proofreading knots: |
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How DNA topoisomerases disentangle DNA |
438 |
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1.1 |
Length scales and energy scales . . . . . . . . . . . . . . . . . . . |
. 439 |
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1.2 |
DNA topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
. 440 |
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1.3 |
Topoisomerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
. 441 |
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1.4 |
Knots and supercoils . . . . . . . . . . . . . . . . . . . . . . . . . |
. 444 |
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1.5 |
Topological equilibrium . . . . . . . . . . . . . . . . . . . . . . . |
. 446 |
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1.6 |
Can topoisomerases recognize topology? . . . . . . . . . . . . . . |
. 447 |
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1.7 |
Proposal: Kinetic proofreading . . . . . . . . . . . . . . . . . . . |
. 448 |