Biological Physics

We give a survey of the work which we and others have done over the last years on “active gels”. In particular, we show how one can construct a set of equations describing gels in which the cross-links can be moved around by active elements constantly consuming energy. This situation corresponds to the cell cytoskeleton, which is thought to control most of cell dynamics. We illustrate the potential usefulness of the equations, first by giving material science types of applications, second by discussing cell behavior such as motility, oscillations, wound healing and cytokinesis.

Cells can polarize in response to external signals, such as chemical gradients, cell-cell contacts, and electromagnetic fields. However, cells can also polarize in the absence of an external cue. For example, a motile cell that initially has a more or less round shape can lose its symmetry spontaneously even in a homogeneous environment and start moving in random directions. One of the principal determinants of cell polarity is the cortical actin network that underlies the plasma membrane. Tension in this network generated by myosin motors can be relaxed by rupture of the shell, leading to polarization. In this chapter, we discuss how simplified model systems can help us to understand the physics that underlies the mechanics of symmetry breaking.

Motor proteins are enzymes that convert chemical energy derived from the hydrolysis of a small molecule called ATP into mechanical work used to power directed movement along cytoskeletal filaments inside cells. Motor proteins have essential biological functions such as driving the contraction of muscle, the beating of sperm and cilia, and the transport of intracellular cargoes. Motor proteins are also interesting from a physical point of view because they do what no man-made engines do: they transduce chemical energy directly to mechanical work without using heat or electrical energy as an intermediate. A central issue in the mechanism of this chemomechanical transduction by motor proteins concerns the roles played by thermal fluctuations, diffusion and Brownian motion. In this lecture I discuss several molecular models for motor proteins, including so-called ratchet models, and compare predictions of these models to experimental results for the microtubule-based motor protein kinesin. I argue that kinesin, which has two motor domains or “heads,” walks using a “hand-over-hand” mechanism such that at least one head is bound to the microtubule. Diffusion likely plays an essential role by facilitating the search of the unbound head for the next binding site, a distance 8 nm away. During this diffusive phase, the bound head supports the load ensuring that forward motion can still take place even against loads up to several piconewtons.

This review is focused on the application of specific fluctuation relations, such as the Gallavotti-Cohen relation, to ratchet models of a molecular motor. A special emphasis is placed on two-state models such as the flashing ratchet model. We derive the Gallavotti-Cohen fluctuation relation for these models and we discuss some of its implications.

The development of tools to manipulate single biomolecules has opened a new vista on the study of many cellular processes. In this review we will focus on the use of magnetic tweezers to study the behavior of enzymes involved in DNA replication. Depending on the DNA substrate used, magnetic tweezers give access either to the advancement in real time of the so-called replication fork or to the torsional state (the so-called supercoiled density) of the DNA molecule. We will show how the new tools at our disposal can be used to gain an unprecedented description of the kinetic properties of enzymes. The comparison of these results with theoretical models allows us to get insight into the mechanism used by the enzymes under study. This analysis is often out of reach of more classical, bulk techniques.

It is a general rule of nature that larger organisms are more complex, at least as measured by the number of distinct types of cells present. This reflects the fitness advantage conferred by a division of labor among specialized cells over homogeneous totipotency. Yet, increasing size has both costs and benefits, and the search for understanding the driving forces behind the evolution of multicellularity is becoming a very active area of research. This article presents an overview of recent experimental and theoretical work aimed at understanding this biological problem from the perspective of physics. For a class of model organisms, the Volvocine green algae, an emerging hypothesis connects the transition from organisms with totipotent cells to those with terminal germ-soma differentiation to the competition between diffusion and fluid advection created by beating flagella. A number of challenging problems in fluid dynamics, nonlinear dynamics, and control theory emerge when one probes the workings of the simplest multicellular organisms.

Among the many brain events evoked by a visual stimulus, which ones are associated specifically with conscious perception, and which merely reflect nonconscious processing? Understanding the neuronal mechanisms of consciousness is a major challenge for cognitive neuroscience. Recently, progress has been achieved by contrasting behavior and brain activation in minimally different experimental conditions, one of which leads to conscious perception whereas the other does not. This chapter reviews briefly this line of research and speculates on its theoretical interpretation. I propose to draw links between evidence accumulation models, which are highly successful in capturing elementary psychophysical decisions, and the conscious/nonconscious dichotomy. In this framework, conscious access would correspond to the crossing of a threshold in evidence accumulation within a distributed global workspace, a set of recurrently connected neurons with long axons that is able to integrate and broadcast back evidence from multiple brain processors. During nonconscious processing, evidence would be accumulated locally within specialized subcircuits, but would fail to reach the threshold needed for global ignition and, therefore, conscious reportability.