The Small Business Administration unveiled yesterday the details of a new program to funnel federal research money to small, high-technology firms.

The SBA offered as examples of two small firms that would be ideal candidates for the grants--EMV Associates of Rockville, which is a pioneer company in the development of molecule-sized "biochips" for microelectronic data processing, and Crystal Systems of Salem, Mass., which has grown huge, perfect crystals for use in lasers.

"Most of our new ideas, new products and new technologies in this century have originated with small companies," said SBA Administrator James C. Sanders in outlining the program.

More to the point, SBA officials said funding innovative high-tech firms might give the United States an extra edge to beat the Japanese in the next generation of technological competition.

The program, called the Small Business Innovation Research Program, will turn over $45 million to small businesses this fiscal year, and more money each year until 1987 when up to $400 million will be given in grants to small businesses, the SBA said.

James H. McAlear, a co-founder of EMV Associates, explained that his firm has demonstrated the first steps in a technology that aims at replacing today's silicon microelectronic chips, which now store up to 500,000 units of information in a one-quarter inch space, with "biochips" composed of proteins that can carry more than a billion units of information in the same area.

Scientists are rapidly approaching the limits of microelectronic circuitry that can be squeezed onto silicon chips. The next stage, McAlear said, is to jump down from the level of materials to the level of molecules.

The first advance, expected to be on the market in a few years, will be a chip which has a layer of protein molecules onto which thin threads of a circuit can be laid -- the metallic chemical used for the circuit binds directly to the protein molecules.

Other developments further in the future maybe based on research showing that some molecules can be manipulated to flip from one stable state to another, as a switch in a semiconductor chip. Switches of molecular size -- tens of thousands of times smaller than current switches--might be used on a chip. Also, long string-like molecules appear able to conduct signals as wires conduct electricity.

McAlear said that the jump from silicon chips to molecular chips would be as large as the leap from the vacuum tubes of the 1940s to the chips of today. It has been estimated that a single relatively small chip made with molecular parts could hold all the information so far recorded by mankind.

Both EMV and Crystal Systems have received grants from a prototype small business research program started by the National Science Foundation in 1977. The businessmen said their companies would still have carried out their research developments without a grant program, but probably at a slower pace.

SBA officials said that there are 10 federal agencies which are now required by law to set aside a portion of the research budgets for these small business grants. The set-aside is two-tenths of a percent this year, and rises to 1.25 percent by 1987 when the program ends.

Some 5,800 grants are expected to be made under the program, beginning in the spring of 1983. Small businesses first must apply for $50,000 grants to develop ideas, then reapply for $500,000 grants for development of the idea.

SBA officials said the Defense Department is the biggest contributor, granting $16.7 million under the program this year. Other agencies and their funds to be given out this year include: NASA, $10.2 million; Health and Human Services, $6.3 million; and Department of Energy $5.5 million.