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SYNOPSIS OF
COARSE-GRAINED SIMULATION STUDIES OF
ACTIVE FLUIDS
A THESIS
to be submitted by
SANOOP RAMACHANDRAN
for the award of the degree
of
DOCTOR OF PHILOSOPHY
DEPARTMENT OF PHYSICS
INDIAN INSTITUTE OF TECHNOLOGY MADRAS.
JANUARY 2009
1 Introduction
Active fluids are characterized by their ability to drive themselves mechanically with
the uptake of chemical energy. They thus maintain a state which is far from thermo-
dynamic equilibrium. In the past ten years or so, there have been hectic activities in
this newly emergent field of active fluids. The most easily identifiable examples, with
increasing length scale of active constituents, of active fluids are membranes envelop-
ing the cell and its internal organelles, the cell cytoskeleton, bacterial baths, fish shoals,
flocks of birds etc. The specific details of various processes involved in these systems
are so complicated and often are not even known. A theory which would take all the
microscopic details into account would truly be a massive (and probably futile) under-
taking. The physicist’s approach to understanding such systems is to regard these as
driven dissipative systems, and to adopt a coarse-grained approach which neglects the
microscopic details. Membranes with pumps, flocking behaviour in birds and fish, sus-
pensions of bacteria and pattern formation in motor-microtubule mixtures are some of
the systems which have been studied.
2 Motivation, Objective and Scope
Much of the work done in this area has concentrated on membranes with protein pumps,
self-propelled particles such as bacteria and on motor-microtubule mixtures. Certain
membrane proteins, such as bacteriorhodopsin, act as ion pumps which when acti
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