With the violence in Gaza and Israel subsiding at least for a while, U.S.-Israeli conversations will likely soon return to the much more significant issue of Iran.

The Obama administration and the Netanyahu government were largely on the same page during the Gaza crisis, and the two country’s leaders seemed to be able to set aside their mutual animosity and distrust, working together to defuse the crisis. But much greater turbulence in their relations can be expected by the middle of next year when the issues associated with Iran’s nuclear project will likely reach another crescendo.

Around that time, a number of important developments will converge. First, Iran will have made further progress with its nuclear program, reducing the time that would be required to convert its “nuclear weapon capability” into actual weapons. On current trajectories, by next summer, Iran could have enough 20 percent enriched uranium to reenrich into material for one bomb in three months. Since Israel will understandably feel more immediately threatened by such developments, its leaders will react more nervously than their American counterparts.

Meanwhile, the Obama administration will likely make an effort to resolve the issue diplomatically by engaging Iran for the first time in direct negotiations. Leading a war-weary nation, Obama will undoubtedly attempt to launch a heroic effort to resolve the nuclear dispute with Iran through diplomacy. At a minimum, the talks will be necessary to demonstrate that the United States has made every effort to avoid war.

Unconfirmed reports have recently surfaced that the two governments have already agreed to hold such talks. But it remains unclear whether the Iranian interlocutors in these pre-discussions were authorized by their Supreme Leader to set a negotiations agenda. With sanctions having increasingly devastating effects on the Iranian economy, Ali Khamenei may be more willing to negotiate in the hope of easing them before they spur disaffection and protests that could threaten his regime.

Given these two trajectories, the Obama administration can be expected to continue pressuring Israel to refrain from attacking Iran’s nuclear installations as long as the diplomatic option holds some hope of success. But Netanyahu has already expressed his fear that Iran will just use negotiations to buy time, until its nuclear program is too far advanced to be stopped even by the United States. Israel also worries that Washington’s eagerness to cut a deal may result in an agreement that would include acceptance of some Iranian uranium-enrichment activities—a possibility that Netanyahu regards as extremely dangerous.

Such turbulence will be compounded by the January 22 elections in Israel. The announced alliance between Netanyahu’s Likud and the even more right-wing party of foreign minister Avigdor Lieberman has already indicated that its campaign for the January elections will focus on the promise to end Iran’s nuclear program. If the alliance wins as anticipated, its leaders will likely feel that they have a public mandate to do whatever it takes to meet this objective.

As a result, substantive differences on Iran between the United States and Israel may be exacerbated by style. If the bellicose approach that Lieberman has displayed in his past references to Egypt, Turkey and the Palestinian Authority is reflected in relations with Washington, U.S.-Israeli differences could quickly become acrimonious. Possibly even more important, it is far from clear whether the more moderate Likud leaders who have resisted a military attack against Iran’s nuclear installations during the past year will be asked to join the next government. A number of them, notably Dan Meridor and Benny Begin, have lost their seats in the recent Likud party primaries.

With this expected convergence of divergences, what could be done to avoid a U.S.-Israeli rupture over the Iran issue?

First, the United States and Israel should further enhance their cooperation in a broad array of non-military measures to slow Iran’s nuclear program. The success of such cooperative measures would postpone the convergence of these sources of U.S.-Israeli tension both by delaying Iranian progress but also by strengthening the trust between Washington and Jerusalem.

Second, Obama and Netanyahu should agree on “rules of engagement” for conducting their future dialogue about Iran. Specifically, they should agree to avoid the kind of public squabble on Iran in which they were engaged before the U.S. elections. Instead, their discussions of this issue should follow the quiet manner in which Prime Minister Ehud Olmert and President George W. Bush dealt with Syria’s nuclear reactor, destroyed in 2007.

Third, in order to avoid misunderstandings, Washington should speak with one voice and use every back channel—especially through the multi-layered relations between the U.S. and Israeli defense and intelligence communities—to articulate U.S. national interests clearly, consistently and repeatedly.

Finally, leaders of the two countries should make every effort to reach a common, private and detailed understanding on key issues in U.S.-Iranian talks: What levels of enrichment and what quantities of enriched uranium would Iran be allowed to maintain? Which nuclear facilities would Iran be permitted to continue operating? What verification and monitoring measures would be sufficient to assure that Iran has not begun a dash to a bomb? How will we judge progress in negotiations to ensure that Iran is not using this simply as a cover to continue its nuclear pursuits?

Despite the depth and breadth of the U.S.-Israeli alliance, each is a separate national state with its own national interests. Each has a democratically-elected government that is responsible for protecting its nation’s vital interests as it sees them. And neither can be expected to subcontract its survival to the other.

But if they wish to avoid the turbulence that Iran can be expected to generate in 2013, U.S. and Israeli leaders must work together. By adopting the measures recommended here, their two countries can address the Iranian nuclear buildup while minimizing its negative effects.

Graham Allison is Director of the Harvard Kennedy School’s Belfer Center for Science and International Affairs. Shai Feldman is Director of the Crown Center for Middle East Studies at Brandeis University.