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Today this is an arduous process, requiring manual manipulation of molecules using such devices as a scanning tunneling microscope. Eventually it is expected to exploit life-like self-replicating 'helper molecules' that are themselves engineered. Thus the field can be seen as a precision form of chemical engineering that includes protein engineering, the creation of protein molecules, a process that occurs naturally in biochemistry, e.g., prion reproduction. However, it provides far more control than genetic modification of an existing genome, which must rely strictly on existing biochemistry to express genes as proteins, and has little power to produce any non-proteins.

Molecular engineering is an important part of pharmaceutical research and materials science. Emergence of scanning tunneling microscopes and picosecond-burst lasers in the 1990s, plus discovery of new carbon nanotube applications to motivate mass production of these custom molecules, drove the field forward to commercial reality in the 2000s.

As it matures, it is seeming to converge with mechanical engineering, since the molecules being designed often resemble small machines. A general theory of molecular mechanosynthesismechanochemistry In conventional chemical synthesis or chemosynthesis, reactive molecules encounter one another through random thermal motion in a liquid or vapor. In mechanosynthesis reactive molecules are attached to molecular mechanical systems, and th to parallel that of photosynthesisPhotosynthesis is a biochemical process in which plants, green algae, and some bacteria use the energy of light to combine water and carbon dioxide into oxygen and energy. It nourishes nearly all living things directly or indirectly, making it vital to li and chemosynthesisChemosynthesis is the biological conversion of 1-carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules (e. hydrogen gas, hydrogen sulfide) or methane as a source of energy, rather (both used by living things) is the ultimate goal of the field. This may lead to a molecular assemblerA molecular assembler is a molecular machine capable of assembling other molecules given instructions, energy, and a supply of smaller "building block" molecules to work from. They can work individually as tiny stand-alone systems, or potentially be organ, according to some, such as K. Eric DrexlerEric Drexler (born April 25, 1955) is best known for popularizing the potential of molecular nanotechnology. Drexler was strongly influenced by ideas on Limits to Growth in the early '70s. His response in his first year at MIT was to seek out someone who, Ralph MerkleMerkle (born 2 February 1952) is a pioneer in public key cryptography, and more recently a researcher and speaker on nanotechnology and cryonics. Merkle graduated from Livermore High School in 1970 and proceeded to study Computer Science at U. Berkeley, o, and Robert FreitasRobert A. Freitas Jr. is Senior Research Fellow at the Institute for Molecular Manufacturing. He holds degrees in physics, psychology, and law, and has written more than 150 technical papers, book chapters, or popular articles on a diverse set of scientif.

Molecular engineering is sometimes called generically " nanotechnologyNanotechnology as a collective term refers to technological developments on the nanometre scale, usually 0. One nanometre equals one thousandth of a micrometre or one millionth of a millimetre. The term sometimes applies to any microscopic technology.", in reference to the nanometre scale at which its basic processes must operate. That term is considered to be vague, however, due to misappropriation of the word in association with other techniques, such as X-ray lithography, that are not used to create new free-floating ions or molecules.

Future developments in molecular engineering hold out the promise of great benefits, as well as great risks. See the nanotechnology article for an extensive discussion of the more speculative aspects of the technology. Of these, the one that sparks the most controversy is that of the molecular assembler.