Biological Physics (eBook)

Contents 5
Foreword 9
Constructing Tools for the Description of Cell Dynamics 11
1. Introduction 11
2. Hydrodynamic theory of active gels 12
3. Material science aspects 15
4. Cell motility 19
4.1. Proximal region 22
4.2. Distal region 23
5. Cell oscillations 26
6. Wound healing and cytokinesis 31
7. Conclusion 38
References 40
A Physical Model of Cellular Symmetry Breaking 43
1. Introduction 43
2. The actin cortex and polarization 44
3. Build-up and release of tension in actin cortices grown around beads 46
4. Modeling of actin shell growth and rupture around beads 48
5. Comparison of symmetry breaking in cells and around beads 50
6. Symmetry can break from one point or from multiple points 51
7. Stress-induced polarization in other systems 52
8. Conclusion 53
References 53
Motor Proteins as Nanomachines:The Roles of Thermal Fluctuationsin Generating Force and Motion 57
The force-generation problem 57
Rectified-diffusion model 59
Flashing-ratchet model 61
Huxley 1957 and powerstroke models 62
Hand-over-hand models 65
Open questions 66
References 67
Fluctuation Relations for Molecular Motors 70
1. Introduction 70
2. Stochastic models of molecular motors 72
2.1. The basic principle 73
2.2. The flashing ratchet model 75
2.3. A discrete ratchet model 77
2.4. Application of the model to experiments 78
2.4.1. Modes of operation and efficiency: 78
2.4.2. Violation of Onsager and Einstein relations: 81
2.4.3. Beyond two states model of molecular motors. 82
3. Fluctuation relations in models of molecular motors 83
3.1. Modeling processivity at the single motor level 86
3.2. Mechanochemical coupling for the discrete model 87
3.3. Flashing ratchet model on a continuous space 88
3.3.1. The purely mechanical ratchet. 89
3.3.2. The flashing ratchet. 90
4. Conclusions 93
Acknowledgment 94
References 94
Studies of DNA-Replication at the Single Molecule Level Using Magnetic Tweezers 98
1. Introduction 98
2. Magnetic tweezers 99
2.1. Finding beads tethered by a single molecule 101
3. How stretching and twisting DNA helps to track replication process 102
3.1. Stretching a polymer model: dsDNA 102
3.2. Twisting dsDNA 103
3.3. Stretching ssDNA 104
3.4. Unzipping DNA 105
4. Study of the Replisome 107
4.1. The T4 replisome components 107
4.2. A simple replication fork 108
4.3. Helicase, polymerase and replisome assays 108
5. Characterizing the helicase activity 110
5.1. gp41 unwinding rate measurement 110
5.2. gp41 rezipping rate is equal to its ssDNA translocation rate 112
5.3. ssDNA translocation does not involve cooperative ATP hydrolysis 113
5.4. gp41 a passive helicase 114
6. Behaviour of the primosome: coupling activity of the helicase and the primase 116
6.1. Models of primosome behavior during primer synthesis 117
6.2. Two priming mechanisms 118
6.3. Primosome does not pause but disassembles 119
6.4. Primosome activity by DNA looping 120
6.5. Force does not hamper loop formation 122
7. DNA synthesis 123
7.1. Measuring strand displacement synthesis and chain extension activity on ssDNA 123
7.2. Polymerase and holoenzyme activities 123
7.3. Leading strand synthesis: coupling helicase and polymerase activities 126
8. Conclusions 127
Acknowledgment 128
References 128
Evolution of Biological Complexity 132
1. Introduction 132
2. Volvox and its relatives as model organisms 134
3. The advection-diffusion problem 136
4. Allometric scaling of flagella-driven flows 138
5. Phototactic steering 142
6. Flagellar synchronization 143
7. Conclusions 146
Acknowledgment 146
References 146
Conscious and Nonconscious Processes: Distinct Forms of Evidence Accumulation? 149
An experimental strategy for exploring consciousness 149
How do we measure whether conscious access occurred? 150
Subliminal processing and evidence accumulation models 152
Subliminal perception 153
Subliminal semantic processing 155
Subliminal accumulation of evidence towards a decision 155
Role of instruction and attention in subliminal processing 157
Modulation by instructions 158
Modulation by executive attention 158
Modulation of subliminal priming by temporal attention 158
Modulation by spatial attention 160
Recent evidence for extended subliminal processing 160
Limits to subliminal processing 161
Durable and explicit information maintenance 162
Global access and novel combinations of operations 162
Intentional action 163
Cerebral bases of conscious and nonconscious computations 163
global workspace model of conscious access 165
Accounting for subliminal processing 168
A distinct state of preconscious processing 169
Conclusion: Conscious access as a solution to von Neumann’s problem? 171
References 172