Samuel Ellis: PhD Final Oral

Samuel Ellis
Friday, November 17, 2017 - 12:00pm
1312 Gilman Hall
Event Type: 

First Name: Samuel
Last Name: Ellis
Major Professor:  Lathrop, Jim & Lutz, Robyn
Committee Member 1: Gilbert, Stephen
Committee Member 2: Henderson, Eric
Committee Member 3:  Lutz, Jack

Status:  PhD Final Oral
Date: Fri, 2017-11-17
Time: 12:00 pm
Location: Gilman 1312

Title: Devices for safety-critical molecular programmed systems
Abstract: The behavior of matter at the molecular level can be programmed to
create nanoscale molecular components that accomplish desired tasks. Many
molecular components are developed with intended uses that are
safety-critical, such as medical applications. Ensuring the correctness and
fault tolerance of such devices is paramount. Techniques to develop robustly
correct programs have been widely studied in software systems and many
devices have been constructed to aid in the safe operation of systems. We
seek to demonstrate the effectiveness of software and safety engineering
techniques in the molecular programming domain.

In this thesis, we present the design of five new devices to aid in the
development of safety-critical molecular programmed systems. We introduce a
Runtime Fault Detection device (RFD) to robustly detect faults and initiate
recovery actions in response to a failed system. We present the Concentration
Monitor, a device that can detect changes, major and minor, in concentrations
in real-time and demonstrate its utility. We also describe methods for
constructing chemical reaction networks that can robustly simulate any
combinatorial logic gate. Finally, we present two devices to log the state of
a molecular program, where the first device logs a state upon receiving a
request, and the second device ensures that the current state meets a defined
validity property before allowing a log to be taken. All devices have been
formally verified using model checking, simulations, or formal proof
techniques. The methods used to construct and verify these devices can be
adapted to the design of future molecular systems to assist in ensuring their