sources, fast computers, quantum-mechanically based potential functions, and statistical methods for single-molecule analysis.

These tools and technologies reflect a top-down approach to probing living systems: designing and building technologies using macroscale techniques and then using those technologies to examine biological systems. No doubt top-down approaches to designing new tools will continue to be extraordinarily useful, but the scope of what can be accomplished through such tools is limited. Recently, bottom-up technology—whereby self-assembly of nanostructures can be used to create new materials and to perform functions that can probe biological systems—has started to allow collecting much more useful data for understanding these and other complex biological issues (Whitesides and Grzybowski, 2002).

Until recently it was not possible to control the molecules and assemblies of molecules from which the bottom-up-designed devices are composed. However, such control is now becoming possible, and although technological hurdles still must be overcome, not only will this control allow for the design and manipulation of bottom-up technologies, but also a new array of techniques developed from such technologies should provide a substantially different perspective on a given problem. For example, the effect of a controlled-design molecular assembly on the behavior of protein-ligand binding could provide immensely useful information about the mechanisms behind molecular recognition.


Cellular Environment

Moving beyond the fundamentals of molecular recognition, new tools and techniques will be needed to study molecules within cells, the function of cells and assemblies of cells, and larger biological systems. The complexity of the biological milieu of a single cell, and the fundamental challenges it poses for a technology that tries to probe it, cannot be overstated. Several characteristics of the subcellular milieu are particularly relevant:

  • High concentration of macromolecules,

  • Extreme heterogeneity of components,

  • Highly organized components, from the nanoscale and on up,

  • Local protein densities that may approach the densities of closely packed spheres,

  • Dynamic and directed transport of components coupled with diffusion,

  • Two phases of water: one behaves like bulk solvent and the other, presumably water of hydration, has very different physical properties, and

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