Physics and Biology

The following sections are included:

• Coordinators and contributors
• Table of contents
• Preface

The following sections are included:

• Introduction
• At the cellular level
• At the molecular scale
• Bibliography

The following sections are included:

• Introduction
• Fluorescence
• Fluorescence microscopy
• Single molecule imaging
• Conclusion and perspectives
• Bibliography

The following sections are included:

• Elements of molecular biology
• Advantages and drawbacks of single molecule studies
• Order of magnitude of the relevant parameters at the single molecule level
• Single molecule manipulation techniques
• Comparison of the different techniques
• DNA mechanical properties
• Conclusion
• Bibliography

How do we move? More precisely, what are the molecular mechanisms that can explain that our muscles, made of very small components can move at a macrosopic scale? To answer these questions we must introduce molecular motors. Those motors are proteins, or small protein assemblies that, in our cells, transform chemical energy into mechanical work. Then, like we could do for a macroscopic motor, used in a car or in a fan, we are going to study the basic behavior of these molecular machines, present what are their energy sources, calculate their power, their yield. If molecular motors are crucial for our macroscopic movements, we are going to see that they are also essential to cellular transport and that considering the activity of some enzymes as molecular motors bring some interesting new insights on their activity.

The term motility defines the movement of a living organism. One widely known example is the motility of sperm cells, or the one of flagellar bacteria. The propulsive element of such organisms is a cilium(or flagellum) that beats. Although cells in our tissues do not have a flagellum in general, they are still able to move, as we will discover in this chapter. In fact, in both cases of movement, with or without a flagellum, cell motility is due to a dynamic re-arrangement of polymers inside the cell. Let us first have a closer look at the propulsion mechanism in the case of a flagellum or a cilium, which is the best known, but also the simplest, and which will help us to define the hydrodynamic general conditions of cell movement. A flagellum is sustained by cellular polymers arranged in semi-flexible bundles and flagellar beating generates cell displacement. These polymers or filaments are part of the cellular skeleton, or “cytoskeleton”, which is, in this case, external to the cellular main body of the organism. In fact, bacteria move in a hydrodynamic regime in which viscosity dominates over inertia. The system is thus in a hydrodynamic regime of low Reynolds number (Box 5.1), which is nearly exclusively the case in all cell movements. Bacteria and their propulsion mode by flagella beating are our unicellular ancestors 3.5 billion years ago. Since then, we have evolved to form pluricellular organisms. However, to keep the ability of displacement, to heal our wounds for example, our cells lost their flagellum, since it was not optimal in a dense cell environment: cells are too close to each other to leave enough space for the flagella to accomplish propulsion. The cytoskeleton thus developed inside the cell body to ensure cell shape changes and movement, and also mechanical strength within a tissue. The cytoskeleton of our cells, like the polymers or filaments that sustain the flagellum, is also composed of semi-flexible filaments arranged in bundles, and also in cross-linked or branched networks. It is a highly dynamical system in which filaments are able to elongate or slide one on the other with the contribution of very active cellular proteins like molecular motors. The versatile properties of this cytoskeleton ensure the diversity of mechanical behaviors to explain cell rigidity as well as cell motility.

The following sections are included:

• Introduction
• Information coding
• Optical recordings of neuronal activity
• Functional organization of the cortex at the level of a cortical column
• Microarchitecture of a cortical column
• Dynamics of neuronal populations
• Outlook
• Bibliography

The following sections are included:

• Psychophysical properties of hearing
• The cochlear amplifier
• Mechanosensory hair cells
• The “critical” oscillator as a general principle of auditory detection
• Bibliography

Rodents and primates possess an exquisite tactile sensitivity, which allows them to extract a wealth of information about their immediate environment. They can distinguish subtle differences in surface roughness through tactile exploration in a much more precise way than they can do visually. In both sensory systems, tactile information is contained in the sequence of deformation of the tactile organ—the facial hair for rodents (the whiskers), the digital skin for primates — elicited by active rubbing on the probed surface (Figure 8.1). These deformations, registered by mechanosensitive neurons located in inner tissues, are processed by the central nervous system to produce a sensory representation of the surface…

The following sections are included:

• Introduction
• Animals looking for food
• Model of intermittent search
• Minimizing the search time
• Should animals really perform Lévy strategies?
• How does a protein find its target sequence on DNA?
• Active intermittent transport in cells
• Optimizing the kinetic rate constant
• Robustness of the results
• Conclusion
• Bibliography

The following section is included:

• Index