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Molecular Design of Biological and Nano-Materials 231

Figure 8.1 Two distinctive and complementary fabrication technologies: Top-down vs. bottom-up. In the top-
down approach, the boat is limited by the size of the tree. On the other hand, the bottom-up approach, the boat is
built with smaller parts of the tree. There is no size limit to the boat for which parts are used to build it.

8.2 NANOBIOTECHNOLOGY THROUGH MOLECULAR
SELF-ASSEMBLY AS A FABRICATION TOOL

Design of molecular biological materials requires detailed structural knowledge to build advanced
materials and complex systems. Using basic biological building blocks and a large number of
diverse peptide structural motifs (Branden and Tooze, 1999; Petsko and Ringe, 2003), it is possible
to build new materials from bottom-up.
One of the approaches is through molecular self-assembly using these construction units (Bran-
den and Tooze, 1999; Petsko and Ringe, 2003). Molecular self-assembly is ubiquitous in nature,
from lipids (that form oil droplets in water) and surfactants (that form micelles and other complex
structures in water) to sophisticated multiunit ribosome and virus assemblies. Molecular self-
assembly has recently emerged as a new approach in chemical synthesis and materials
fabrication in polymer science, nanotechnology, nanobiotechnology, and various other engineering
pursuits. Molecular self-assembly systems lie at the interface of molecular and structural biology,
protein science, chemistry, polymer science, materials science, and engineering. Many self-assem-
bling systems have been developed. These systems range from organic supramolecular systems, bi-,
tri-block copolymers (Lehn, 1995), and complex DNA structures (Seeman, 2003, 2004), simple and
complex proteins (Petka et al., 1998; Nowak et al., 2002; Schneider et al., 2002) to peptides (Aggeli
et al., 2001; Hartgerink et al., 2001; Zhang et al., 1993, 1995, 2002; Zhang, 2003). Molecular self-
assembly systems represent a significant advance in the molecular engineering of simple molecular
building blocks for a wide range of material and device applications.

8.3 BASIC ENGINEERING PRINCIPLES FOR MICRO- AND NANO-FABRICATION
BASED ON MOLECULAR SELF-ASSEMBLY PHENOMENA

Programmed assembly and self-assembly are ubiquitous in nature at both macroscopic and micro-
scopic scales. The ancient Great Wall of China, the Pyramids of Egypt, the schools of fish in the
ocean, flocks of birds in the sky, herds of wild animals on land, protein folding and oil droplets on
water are all such examples. Programmed assembly describes predetermined planned structures. On
the other hand, self-assembly describes the spontaneous association of numerous individual entities
into a coherent organization and well-defined structures to maximize the benefit of the individual
without external instruction (Figure 8.2).
Just like the construction of a wall, a house, or a building, many other parts of structures can
be prefabricated and program assembled according to architectural plans (Figure 8.3). If we shrink