Did the California Institute of Technology ignore faculty reports that an Israeli spy might be working at a campus-controlled research facility so as not to jeopardize an $8 billion National Aeronautics and Space Administration contract? That’s the basis of a whistleblower suit filed last week against Caltech by Sandra Troian, a professor of applied physics there who says the university, after dismissing her concerns, tried to retaliate against her for speaking with federal authorities during their own investigation into the matter.

Troian says that a former postdoctoral research scholar in NASA's Jet Propulsion Laboratory, which is managed by Caltech, violated federal law by sharing security-sensitive research information with an Israeli institution and on the internet.

Caltech officials, along with the former Caltech employee in question, deny the claims and accuse Troian of suing due to negative conclusions about her in a recent research misconduct investigation.

According to the suit, Troian hired Amir Gat, a recent Ph.D. in aerospace engineering from Technion-Israel Institute of Technology, in early 2010, to help design a new type of space micropropulsion system. The project, funded by the Defense Advanced Research Projects Agency, allegedly was subject to federal export control laws governing unauthorized sharing of information, and Troian says she and Gat signed agreements saying they would protect security-sensitive research.

Soon after Gat was hired, Troian says, she began to suspect him of security violations. He allegedly stored sensitive information on his personal laptop, not his work computer as required. He is also alleged to have purposely entered erroneous numbers into design software codes. Later in 2010, a computer virus attack on Troian’s work computer resulted in hundreds of files being uploaded to an IP address outside Caltech, and days of interruption to Troian's network.

Troian says that she traced the virus to Gat's computer and confronted him about it. She says Gat refused to disclose websites he visited prior to the attack, but eventually admitted that he had shared details about the micropropulsion system with Daniel Weihs, his doctoral adviser at Technion, without permission. According to the suit, Weihs sits on Israel’s National Steering Committee for Space Infrastructure of the Ministry of Science and holds other federal positions related to space research.

Gat also allegedly made 65 Internet posts about operating principles for the system, also in violation of the security agreement he signed with the lab, and was caught wandering around, alone, in an access-restricted experimental area. He allegedly said he was "looking around," and that he hoped to be hired by Technion when he eventually returned to Israel.

Troian shared her growing concerns about Gat with Caltech administrators on multiple occasions during the summer of 2010. But she says they looked the other way to protect the university’s good name and -- more materially -- the NASA contract, which was up for review at that time. According to the suit, "Caltech was seeking to renew its contract with NASA to manage [the lab] and, as part of the reapplication process, needed to certify that its employees and contractors were not violating U.S. government security regulations," including International Traffic in Arms Regulations.

In August 2010, according to the suit, Troian dismissed Gat from her lab, and he transferred to another research group at Caltech. Troian reported her ongoing concerns to Caltech's vice provost of research, Morteza Gharib, who said allegedly said, "It's not my business." Gat worked in Gharib's lab until July 2012, when he returned to Technion as an assistant professor of mechanical engineering.

Two years after she first reported her concerns to Caltech, Troian says, the Federal Bureau of Investigation approached her about Gat as part of its own investigation into possible security breaches at the lab. Troian said that she had shared her suspicions about Gat with Caltech in 2010, to no avail. But she allegedly refused to sign an affidavit, for fear of retaliation by Caltech.

Soon after her contact with the FBI, Troian says, a small group of Caltech administrators began threatening her job and asking her about what she had told federal investigators. She was allegedly told that Caltech doesn’t “like [its] people calling the authorities.” Troian says that Edward Stolper, the Caltech provost, eventually told her that he would make her “miserable,” and to “wait for the next two years of being confrontational with Caltech. It just won’t be fun.”

She says that Caltech falsely accused her of research misconduct, denied her research funding, and put falsified documents alleging that three postdoctoral fellows had filed “serious complaints” against her in her personnel file, among other forms of retaliation. She also alleges that Caltech copied her entire computer hard drive without her permission, even though it contained security-sensitive and personal information.

Caltech denies Troian’s claims. In a statement, a university spokeswoman said that Caltech “intends to vigorously defend this lawsuit, which is meritless. The institution is confident in its compliance with export control laws and International Traffic in Arms Regulations, and regularly cooperates with government agencies, including the FBI, as appropriate.”

The statement continues: "The plaintiff, who was dissatisfied with the outcome of a recent internal campus investigation into her decision to list her cat as the author of a published abstract and omit recognition of a postdoctoral scholar who performed related research, suffered no retaliation and remains an active faculty member of the institution.”

Gat also denies all the allegations -- including that he ever worked at the Jet Propulsion Lab. In an email, he said "I am not, or ever have been, an 'Israeli spy.' I joined Caltech as an academic researcher and based my work on publicly available research papers. As an academic researcher my research was expected to be published in scientific journals. As a foreign national I did not have any security clearance and thus couldn't work on secret projects."

He said he worked in Troian's research group for about three months in 2010, and "very happily" transferred to a different group after that.

Gat said he never launched a virus from his computer, and that a spy probably wouldn't use his own computer for subterfuge anyway. The best guess he could make regarding the 65 internet posts, he said, was that he posted publicly available research to a website called CiteULike, which Troian asked him to delete. He also denied sharing sensitive information with Weihs after arriving at Caltech. He said he was never knowingly investigated by the FBI, and only heard about the espionage allegations after Troian filed her suit last week.

Caltech declined to provide additional information about the case. Troian says in her suit that she once used her cat’s name -- M. Pucci -- as a placeholder until she could find a new assistant to co-author an abstract for a 10-minute talk at an American Physical Society conference. That was in 2012, following the abrupt departure from Caltech of a second research assistant. She says that the quirky naming practice is common among scientists, and that Andre Geim, a Nobel Prize-winning physicist, even once listed his hamster as paper co-author.

But the university accused Troian of falsifying the record and misrepresenting the research assistant's work as her own, according to the suit. A faculty committee found the professor guilty of research misconduct; she says the investigation was biased against her and ignored evidence in her favor.

Troian said in a statement that she’s committed her “heart and soul to Caltech,” but won’t let administrators involved in her case “ruin my career.” She alleges that Caltech retaliated against her in violation of California labor law and breached key contract obligations in how it treated her. She’s requesting a trial by jury and damages in excess of $25,000.

The plaintiff’s lawyers say that Caltech relies on its contract with NASA to manage the high-profile Jet Propulsion Lab for billions of dollars in funding, and that it couldn't risk a security scandal as the contract was up for renewal.

Lynne Bernabei, who is representing Troian from Washington, said the case was another example of a “large university failing in its management of an important national laboratory." The government, Bernabei said, "should scrutinize Caltech’ s ability to fix security breaches at [the Jet Propulsion Lab].”

There have been several concerns about security at the lab in recent years. In 2012, a laptop containing the personal information of lab employees was stolen from a lab employee’s car in Washington. Also in 2012, a federal investigation revealed that NASA networks had suffered thousands of security breaches between 2010 and 2011, including one in which Chinese hackers gained full access to key lab systems and accounts. That allowed them “to alter files, user accounts from mission-critical [lab] systems and upload tools to steal user credentials,” The Los Angeles Times reported at the time.