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Expertimental setups
A cold fusion experiment usually includes:


 * a metal, such as palladium or nickel, in bulk, thin films or powder;
 * deuterium and/or hydrogen, in the form of water, gas or plasma; and
 * an excitation in the form of electricity, magnetism, temperature, pressure, laser beam(s), or of acoustic waves.

Electrolysis cells can be either open cell or closed cell. In open cell systems, the electrolyis products, which are gaseous, are allowed to leave the cell. In closed cell experiments, the products are captured, for example by catalytically recombining the products in a separate part of the experimental system. These experiments generally strive for a steady state condition, with the electrolyte being replaced periodically. There are also "heat after death" experiements, where the evolution of heat is monitored after the electric current is turned off.

Excess heat observations
An excess heat observation is based on an energy balance. Various sources of energy input and output are continuously measured. Under normal condition, the energy input can be matched to the energy output to within experimental error. In experiments such as those run by Fleischmann and Pons, a cell operating steadily at one temperature transitions to operating at a higher temperature with no increase in applied current. At the higher temperature, the energy balance shows an unaccounted term. In the Fleischmann and Pons experiments, the rate of excess heat generation was in the range of 10-20% of total input. The high temperature condition would last for an extended period, making the total excess heat disproportionate to what might be obtained by ordinary chemical reaction of the material contained within the cell at any one time. These high temperature phases did not last indefinitely and did not occur in every experiment, but in those experiments where they did occur, they would usually reoccur several times. Many others have reported similar results.

In 1993, Fleischmann reported "heat-after-death" experiments: he observed the continuing generation of excess heat after the electric current supplied to the electrolytic cell was turned off. Similar observations have been reported by others as well.

Reports of nuclear products in association with excess heat
In association with excess heat, researchers have reported observing gamma rays, neutrons, and tritium (3H) production. Although these reports do not measure quantities commensurate with a rate of deuterium fusion that would account for the excess heat, the quantities were reported to be in excess of background levels.

Considerable attention has been given to measuring 4He production. In the report presented to the DOE in 2004, 4He was detected in five out of sixteen cases where electrolytic cells were producing excess heat, although the amounts detected were very close to background levels and contamination by trace amounts of helium normally present in the air is difficult to avoid.

Studies of non-nuclear explanations
In the original 1989 DOE review, skepticism towards cold fusion focused on four issues: the precision of calorimetry, the lack of consistently reproducible results, the absence of nuclear products in quantities consistent with the excess heat, and the lack of a mainstream theoretical mechanism. In the subsequent years considerable efforts have been made on these fronts. Today these issues still remain the focus of criticisms.

In the first years after the Fleishmann-Pons announcement various challenges were put forth. The efficacy of the stirring method in the Fleischmann-Pons experiment, and thus the validity of the temperature measurements was disputed by Browne. The experiment has also been criticized by Wilson. The possibility that electrochemically mediated deuterium-oxygen recombination can cause the appearance of excess heat was discussed by Shkedi and Jones.

The 2004 DOE panel noted that "significant progress has been made in the sophistication of calorimeters since ... 1989", and summarized that "Evaluations by the reviewers ranged from: 1) evidence for excess power is compelling, to 2) there is no convincing evidence that excess power is produced when integrated over the life of an experiment. The reviewers were split approximately evenly on this topic."

The panel continued, "Many reviewers noted that poor experiment design, documentation, background control and other similar issues hampered the understanding and interpretation of the results presented". The reviewers who did not find the production of excess power convincing said that excess power in the short term is not the same as net energy production over the entire time of an experiment, that such short-term excess power is only a few percent of the total external power applied and hence calibration and systematic effects could account for the purported effect, that all possible chemical and solid state causes of excess heat had not been investigated and eliminated as an explanation, that the magnitude of the effect had not increased after over a decade of work.

Kirk Shanahan suggested that a calibration constant shift could explain apparent excess heat signals, and that such a shift could occur by a redistribution of heat in a F&P cell. He further speculated that such a redistribution would occur if recombination at the electrode became active, but acknowledged that this is not experimentally proven. Cold fusion proponents say that such speculations are not supported by experimental results (in particular, that the measured volume of recombined output evolved gases does not allow for recombination within the cell) a statement that Shanahan's papers dispute.

It has also been suggested that rejecting experiments that fail to produce excess heat as failing for unknown reasons could create a disorted picture of the data.

Evidence for nuclear transmutations
There have been reports that small amounts of copper and other metals can appear within Pd electrodes used in cold fusion experiments. Iwamura et al. report transmuting Cs to Pr and Sr to Mo, with the mass number increasing by 8, and the atomic number by 4 in either case. . Cs or Sr was applied to the surface of a Pd complex consisting of a thin Pd layer, alternating CaO and Pd layers, and bulk Pd. Deuterium was diffused through this complex. The surface was analyzed periodically with X-ray photoelectron spectroscopy and at the end of the experiment with glow discharge mass spectrometry. Production of such heavy nuclei is so unexpected from current understanding of nuclear reactions that extraordinary experimental proof will be needed to convince the scientific community of these results.

Theoretical work
Cold fusion researchers acknowledge the theoretical issues and have proposed various speculative theories (for a full review, see ) to explain the reported observations. None has received mainstream acceptance.

Analysis of factor affecting reproducibility
Although the review panel was not convinced, the cold fusion researchers who presented their review document to the 2004 DOE panel on cold fusion said that the observation of excess heat has been reproduced, that it can be reproduced at will under the proper conditions, and that many of the reasons for failure to reproduce it have been discovered.