He was 86 and had been in failing health since he fell and broke a hip in February.
When Alpher was in graduate school, some scientists had already proposed that the universe began in a massive explosion nearly 14 billion years ago. But most astrophysicists favored the so-called steady-state theory, which held that the universe had always existed in its current state and would continue to do so forever.
Alpher's calculations supporting the Big Bang and showing how to prove its existence attracted a small flurry of interest, but fell by the wayside in a community that was committed to steady-state.
When experimental proof finally came two decades later, his contributions were overlooked in favor of those from theoreticians who had, in essence, simply repeated his work.
"It's kind of sad and, I think, unfair," physics Nobel laureate Arno Penzias said in a 1999 interview. "This poor guy has been eating himself up for 50 years. You do something great and don't get credit for it -- that shouldn't happen in a fair world. Most of the stuff we now know about the universe stems from their calculations."
It was only many years later that Alpher's contributions began to be acknowledged. In the highly regarded 1993 book, "The First Three Minutes," physics Nobel laureate Steven Weinberg described Alpher's work as "the first thoroughly modern analysis of the early history of the universe."
That recognition peaked last month, when Alpher was awarded a National Medal of Science by President Bush in a ceremony honoring recipients for 2005 and 2006. The award was accepted by Alpher's son Victor because Alpher was too ill to travel for the ceremony.
"This is yet more recognition after the miscarriage of scientific justice," said mechanical engineer Philip G. Kosky, a colleague of Alpher at General Electric and Union College. "His work is the window on the cosmos and to not win the Nobel is truly one of the great black marks on the Nobel committee."
In 1946, Alpher had just finished the research for his original doctoral thesis at George Washington University in Washington, D.C., when his mentor George Gamow showed him an article in a Russian physics journal reporting the same results.
Forced to start over, Alpher accepted a suggestion from Gamow that he study the formation of elements in the early universe, a concept known as primordial synthesis. His goal was to predict the concentrations of various elements in the universe if the Big Bang had occurred.
His calculations showed that immediately after the initial explosion, the universe was filled with radiation and other primitive matter that Alpher dubbed "ylem," a term meaning roughly "what was there before everything."
The ylem decayed to produce protons, electrons, neutrons and other particles, which eventually combined to produce the elements. Alpher calculated that it would form 10 atoms of hydrogen for every one atom of helium, precisely the ratio observed by astronomers.
Other researchers later successfully predicted the concentrations of other elements.
When it came time to publish Alpher's thesis results in the journal Physical Review, Gamow -- a former colonel in the Red army with a puckish sense of humor -- proposed adding the name of eminent physicist Hans Bethe as a coauthor. The authors thus became Alpher, Bethe and Gamow, a play on the first letters of the Greek alphabet and a popular name for a theory that dealt with the beginning of the universe.
Unfortunately, with two such distinguished physicists listed as coauthors, other scientists incorrectly assumed that Alpher had made only a small contribution to the research.
Nonetheless, the paper was published shortly before Alpher was scheduled to defend his thesis and an unprecedented 300 people -- as well as several newspaper reporters -- showed up for the defense.
Asked how long the primordial nucleosynthesis would have taken, Alpher replied 300 seconds, and a story in the next day's Washington Post was headlined: "World Began in 5 Minutes, New Theory."
Alpher quickly followed up with a second paper, written with Robert Herman of the Johns Hopkins University Applied Physics Laboratory, predicting that the radiation from the original explosion was still present in the universe, having cooled to a temperature of about 5 degrees Celsius above absolute zero, or about 450 degrees Fahrenheit below zero.
But astronomers were still committed to the steady-state universe, and most did not think it was technically possible to look for the remnant radiation.
As a consequence, Alpher's contributions faded from memory and, disheartened, he left academia in 1955 to join General Electric's research laboratory in Schenectady, N.Y., where he spent 32 years.
In 1964, radio astronomers Penzias and Robert Wilson of Bell Telephone Laboratories in Holmdel, N.J., were tuning their radio telescope with it pointed toward space when they detected a background hissing that could not be explained. After a year of trying to eliminate the noise, they concluded that they were observing the remnant radiation, which had a temperature of about 3 degrees Celsius above absolute zero.
In solving the mystery, they consulted with Princeton University cosmologists Robert Dicke and P.J. Peebles, who had independently predicted the existence of the background radiation. The two groups published joint papers explaining the discovery -- not citing Alpher and Herman.
Thirteen years later, Penzias and Wilson received the Physics Nobel for their work, and the Nobel citation also did not mention Alpher.
Reflecting on the events in a 1999 issue of Discover magazine, Alpher said "Was I hurt? Yes! How the hell did they think I'd feel? I was miffed at the time that they'd never even invited us down to see the damned radio telescope. It was silly to be annoyed, but I was."
In a 1988 article, Alpher and Herman had presented a more sedate complaint: "Thinking back, we could not help but be struck by the observation that contrary to what is so often presented, science does not necessarily proceed in an orderly and logical fashion."
Penzias cited Alpher's work in his Nobel laureate address, but the damage had already been done. A month later, Alpher suffered a heart attack, possibly brought on by the stress of fighting for recognition, and his recovery was slow and painful.
Ralph Asher Alpher was born in Washington on Feb. 3, 1921, the youngest of four children of building contractor Samuel Alpher and Rose Maleson Alpher.
A prodigy, he graduated from high school at the age of 16 and was offered a full scholarship to the Massachusetts Institute of Technology. In an interview with an alumnus, however, it came out that he was Jewish and the scholarship was withdrawn.
He enrolled instead at George Washington University, but economic circumstances compelled him to work during the day while attending classes at night. During World War II, he was a civilian contract physicist with the U.S. Navy -- while continuing his nighttime classes -- where he worked on degaussing ships to protect them from magnetic mines and on the detection of submarines by airborne magnetometers.
He began working at the Applied Physics Laboratory in 1944 through his work with the Navy and continued there until he joined GE in 1955. He joined Union College in Schenectady and remained there until his retirement in 2004.
In 1943, Alpher married Louise Ellen Simons, who died in 2004.
In addition to Victor, of Austin, he is survived by a daughter, Harriet Lebetkin of Danbury, Conn.; and two granddaughters.