The effect of encapsulation on molecular computing efficiency

Abstract

Summary Form Only Given. Research into molecular computation offers exciting possibilities for interfacing computation with biological systems. This could be achieved using light to switch photochromic molecules between states. For example, 6-Nitro-BIPS can be switched from a Spiropyran (SP) state to a Trans- Merocyanine (MC) state using UV photons while visible light switches from MC to SP. The MC state is also fluorescent. Modified spiropyrans targeted to proteins can improve imaging contrast, alter enzyme activity, alter protein interactions and switch vesicle permeability. We have used NBIPS to produce data registers and logic gates. NBIPS was encapsulated in silicone rubber (4mM NBIPS in methanol mixed 1:5 with PDMS). Molecules were switched with LEDs while detecting fluorescence with a photodiode. Integer data is stored as the relative concentration of MC molecules in a sample. The register value is determined from the fluorescence and its capacity is limited by the dynamic range. Using ~0. lmW/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> illumination we have implemented a 6-bit register. In the same sample we have also implemented several universal logic gate sets; using light-pulse sequences as inputs and the fluorescent signal as output. The switching quantum efficiency (Φ) is strongly dependent on the immediate chemical environment of the NBIPS molecules. For example, in ethanol Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SP→MC</sub> ~0.17 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> , however, when NBIPS was encapsulated in PDMS we measured the Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SP→MC</sub> to be ~0.017. Although this proof-of-concept system demonstrates the possibility of embedding computation into biological systems, it highlights the importance of controlling the chemical environment to achieve high computational speeds.