A world-renowned Harvard nanoscientist under federal indictment for allegedly failing to disclose financial ties to the Chinese government’s Thousand Talents Program and for cheating on his federal taxes now wants the university to pay his legal bills.

In a lawsuit and affidavit filed in Middlesex Superior Court, Charles M. Lieber, former chair of Harvard’s Chemistry and Chemical Biology Department, said the university is obligated under its contract with its professors to indemnify him in advance for legal bills linked to his university work.

“I pleaded Not Guilty in the criminal case and expect to assert at trial, among other things, that I lacked criminal intent and that I acted at all relevant times in good faith,” Lieber said in an affidavit.

Moreover, Lieber wrote in an affidavit, the cost of defending himself against federal prosecutors who allege he was a willing participant in the Chinese’s government efforts to transfer Western technology will drain his bank accounts leave him facing tax penalties for unwinding some structured investments.

“Payment of all of the costs of a robust defense would substantially, if not completely, deplete my financial resources,” Lieber wrote in court papers. He said he would face tax consequences if forced to liquidate some investments early, and is hoping to use advance payment of legal fees to “plan for the financial security of my family.”

In court papers, Lieber and his attorney, Marc Mukasey, said he has been battling follicular lymphoma for the past seven years, has generated millions of dollars in grant money to Harvard, and has assigned the rights to Harvard to some 50 patents he has earned during his 30 years at the school.

Yet, Harvard is cooperating with US Attorney Andrew Lelling’s office against its employee who has drawn support from more than 80 of his former student who have praised his humanity and his willingness to help them build their own futures, the lawsuit said.

“It is disturbing that Harvard acted solely in its own self-interest by turning its back on a dedicated faculty member who suffers from a terminal illness and who is presumed innocent,” the lawyer asserted in the lawsuit. More importantly, it is illegal.”

According to federal investigators, a professor at a Chinese university approached Lieber in 2011, leading Lieber to travel to to China’s Wuhan University of Technology where he signed an agreement paying him $50,000 a month and $158,000 in living expenses. He also allegedly received $1.5 million to set up a research lab at the Chinese university.

Lieber allegedly failed to disclose the information to both Harvard and the federal government and also allegedly failed to comply with Internal Revenue Service regulations on overseas payments. Lieber has pleaded not guilty to all charges and is free on $1 million bond.

Lieber has previously asked Harvard to step up and pay his legal fees, but has been denied by the university, which has cited, among other issues, that he allegedly misled the school about his ties to the Wuhan University of Technology for years, according to court papers.

Lieber is asking a Middlesex Superior Court judge to issue a preliminary injunction ordering Harvard to start making payments to his lawyers. Lieber has also promised to repay Harvard if he is convicted which could lead to a 10 year prison term and a $500,000 fine, according to court records.

A Harvard University spokesman declined comment in an email to the Globe. Harvard has not filed any response in Middlesex Superior Court as of Friday afternoon.

John R. Ellement can be reached at [email protected]. Follow him on Twitter @JREbosglobe.

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