Chemistry Reference
In-Depth Information
Chapter 1
Introduction
The structural hierarchy, functional complexity and, most importantly, the delicate
interplay between the two in complex open systems often lead to intriguing behav-
iour. In particular, quite unexpected collective phenomena are often observed when
many similar units couple with one another, resulting in pattern formation, emer-
gence, broken symmetries, and phase transitions. While some physical systems dis-
play spontaneous collective ordering, such realizations are particularly striking in
situations when the systems are far from thermal equilibrium. The molecular orga-
nization during cell division [
1
], spatio-temporal patterns due to catalytic reactions
at surfaces [
2
,
3
], spontaneous emergence of animal and bird flocks [
4
], turbulence
and cloud formation, cellular growth and organization during morphogenesis [
5
]are
just a few such phenomena spanning various length and time scales.
Indeed, life itself may be viewed as a complex system comprised of interacting
self-organizing hierarchical subunits [
6
,
7
]. Though at first glance, cells are simply
lipid bilayer compartments containing macromolecules, they are capable of many
complex functions such as growth, replication, locomotion and communication (Fig.
1.1
). The interplay between functional units and the resulting complex dynamics
spans multiple length and time hierarchies. This is evident in Fig.
1.1
, which shows
a few exemplary processes in a bacterial cell. While the organization of macromole-
cules within the cell give rise to a set of functions such as growth and replication, the
co-ordination of the motion of multiple cells leads to a fascinating organization of
the individual cells into a seemingly collective entity. A natural question that arises
then is: how is this organization and the emergence of function co-ordinated?
The machinery of life is predominantly comprised of
soft matter
and is maintained
off equilibriumby the supply and consumption of energy via suitable chemical means.
Soft matter
, such as proteins, colloids, emulsions and membranes, is characterized by
typical interaction energies on the thermal scale (
kT
), such that non-trivial opera-
tions are possible preferentially at room temperature, as in biological processes. A
fewmain soft building blocks—lipids, proteins and nucleic acids—constitute biolog-
ical matter. These building blocks have evolved such that they either self-assemble
into a desired structure or function, or can be assembled at the expense of only small
∼
