COMPUTATION WITH PHOTOCHROMIC MEMORY Jack Christopher Chaplin, BSc (Hons) Thesis submitted to the University of Nottingham for the degree of Doctor of Philosophy September 2012 Introduction ii Abstract Unconventional computing is an area of research in which novel materials and paradigms are utilised to implement computation and data storage. This includes attempts to embed computation into biological systems, which could allow the observation and modification of living processes. This thesis explores the storage and computational capabilities of a biocompatible light-sensitive (photochromic) molecular switch (NitroBIPS) that has the potential to be embedded into both natural and synthetic biological systems. To achieve this, NitroBIPS was embedded in a (PDMS) polymer matrix and an optomechanical setup was built in order to expose the sample to optical stimulation and record fluorescent emission. NitroBIPS has two stable forms - one fluorescent and one non-fluorescent - and can be switched between the two via illumination with ultraviolet or visible light. By exposing NitroBIPS samples to specific stimulus pulse sequences and recording the intensity of fluorescence emission, data could be stored in registers and logic gates and circuits implemented. In addition, by moving the area of illumination, sub-regions of the sample could be addressed. This enabled parallel registers, Turing machine tapes and elementary cellular automata to be implemented. It has been demonstrated, therefore, that photochromic molecular memory can be used to implement conventional universal computation in an unconventional manner. Furthermore, because registers, Turing machine tapes, logic gates, logic circuits and elementary cellular automata all utilise the same samples and same hardware, it has been shown that photochromic computational devices can be dynamically repurposed. NitroBIPS and related molecules have been shown elsewhere to be capable of modifying many biological processes. This includes inhibiting protein binding, perturbing lipid membranes and binding to DNA in a manner that is dependent on the molecule's form. The implementation of universal computation demonstrated in this thesis could, therefore, be used in combination with these biological manipulations as key components within synthetic biology systems or in order to monitor and control natural biological processes. Introduction iii Acknowledgements I’d like to thank firstly both my supervisors, Natalio Krasnogor and Noah Russell, for their support, guidance and discussions over the course of my PhD. Though working in an interdisciplinary field with two supervisors from different disciplines was a tricky prospect, it was the belief and encouragement of these two that got me through. I’d like to thank everyone in the computer science department, the Automated Scheduling, Optimisation and Planning Research Group and the Interdisciplinary Computing and Complex Systems Research Group, with particular thanks to my officemates Lui and German for keeping me company during the long hours at my desk, to the Technical Services Group and particularly Viktor Huddleston for fixing anything and everything that went wrong, and to Deborah Pitchfork, Nick Poxon and Ebru Tasci for their logistical and secretarial support. I’d like to thank everyone in the Institute of Biophysics, Imaging and Optical Science and the Neurophotonics Lab, with particular thanks to Tim Smith, Kevin Webb and Kelly-Ann Vere for the safety training; basic lessons in chemistry and physics; and simply telling me where things are and what they do. Without the efforts of these three and Noah, I’d have been completely lost in a laboratory. I’d also like to thank those who kept me company in the Biology department, including Alex, Bo, Darren, Katharina, Paul and Solomon. Outside the university, I’d like to thank my parents for their unconditional love and support, and for fostering my fledging interest in computers and all of science. Thanks to all the teachers and lecturers during my education who encouraged me to pursue my passions. I’d like to thank all my friends, housemates, family, loved ones and especially to my gorgeous Anna Glozier, who all helped me along this journey of discovery (both in science and in self), who were there to celebrate when things went well, and to commiserate when they didn’t. Lastly, I’d like to acknowledge the Engineering and Physical Sciences Research Council and the University of Nottingham’s Bridging the Gaps initiative for funding my PhD. Introduction iv For everyone. Introduction v Contents Chapter 1: Introduction ............................................................................................ 1 1.1. Background and Motivation .......................................................................... 1 1.2. Research Goals .............................................................................................. 4 1.3. Publications ................................................................................................... 4 1.4. Structure of the Thesis ................................................................................... 6 Chapter 2: Background Material .............................................................................. 8 2.1. Conventional Computing .............................................................................. 8 2.2. Unconventional Computing ........................................................................ 12 2.3. Unconventional Molecular Computing ....................................................... 14 2.4. Molecular Switches ..................................................................................... 17 2.5. Photochromic Molecular Switches .............................................................. 18 2.6. Fluorescence ................................................................................................ 21 2.7. Spiropyran Photochromic Molecular Switches and NitroBIPS .................. 24 2.8. Systems and Synthetic Biology ................................................................... 26 Chapter 3: Computational Model and Programmability ........................................ 29 3.1. Computational Model .................................................................................. 29 3.1.1 Registers ............................................................................................... 29 3.1.2 Logic Gates .......................................................................................... 32 3.1.3 Logic Circuits ....................................................................................... 34 3.2. Programming the System ............................................................................ 36 3.2.1 Drag and Drop Circuits ........................................................................ 37 3.2.2 Compiled Circuits ................................................................................ 38 Chapter 4: Methods ................................................................................................ 43 4.1. eNBIPS Samples ......................................................................................... 43 4.2. Experimental Setup ..................................................................................... 45 Introduction vi 4.2.1 Illumination .......................................................................................... 45 4.2.2 Fluorescence Detection ........................................................................ 56 4.2.3 System Control ..................................................................................... 57 4.2.4 LabVIEW subVIs. ................................................................................ 58 4.3. Summary ..................................................................................................... 66 Chapter 5: Photochromic Molecular Registers ...................................................... 67 5.1. Introduction ................................................................................................. 67 5.2. Optical Theory ............................................................................................. 69 5.3. Thermal Relaxation ..................................................................................... 73 5.4. Overview of Photochromic Registers .......................................................... 75 5.5. Photochromic Register Implementation ...................................................... 78 5.5.1 Initialisation ......................................................................................... 78 5.5.2 Reading ................................................................................................ 85 5.5.3 Writing ................................................................................................. 89 5.5.4 Parallel Registers .................................................................................. 90 5.6. Discussion ................................................................................................... 93 Chapter 6: Steps Toward Photochromic Molecular Turing Machines .................. 96 6.1. Implementation of Photochromic Tape Turing Machines........................... 96 6.2. Programming Busy Beavers in Photochromic Tape Turing Machines ..... 100 6.3. Execution of Busy Beavers on Photochromic Tape Turing Machines...... 101 6.4. Discussion ................................................................................................. 104 Chapter 7: