Browsing by Subject "Resonance energy transfer"

Resonance energy transfer (RET) logic provides a method for building integrated molecular circuits using self-assembled networks of fluorescent molecules to perform computation. The unique operating principles and materials of these circuits make them suitable candidates for introducing computation to domains that are incompatible with conventional silicon-based systems. To realize the full potential of this technology, however, a variety of technical challenges currently preventing the design of larger, more complex systems must be overcome. Two of these primary challenges are energy loss and exciton loss. Energy loss forces the outputs from RET devices to be red-shifted from their inputs. This prevents most independently designed RET components from being cascaded with one another. Exciton loss weakens the output signals from RET devices, making it difficult to observe the computational results. Together, these forms of signal degradation constrain both the size and topology of RET systems.

This work explores new RET devices and circuit design strategies that address the above limitations. The primary contributions of this dissertation are threefold. First, a RET device capable of restoring energy in these systems is designed and experimentally demonstrated. This device enables cascading and feedback in RET logic, two circuit design concepts commonly used in large-scale digital systems. Second, a new style of RET logic design, called Pre-Charge Logic (PCL), is introduced. PCL addresses both forms of signal loss while simultaneously providing a library of cascadable RET logic gates, many of which cannot be implemented using previous methods of RET logic design. Third, the design methods of PCL are explored and validated by simulation and experimental demonstration. Continuous-time Markov chain modeling confirms that the proposed PCL devices perform their intended Boolean operations, while an experimental demonstration of a PCL PASS gate substantiates the underlying operating principles of these devices. Collectively, these contributions pave the way for developing larger, more complex RET systems in the future.

A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical.

In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications.

We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the distribution of dipoles in a given sample of chromophore constructs. The model can be used to evaluate the feasibility of other potential orientation control techniques.

This dissertation hypothesizes,

"It is possible to design a self-assembled, nanoscale, high-speed, resonance energy transfer device exhibiting non-linear gain with a few molecules."

The report recognizes DNA self-assembly, a relatively inexpensive and a massively parallel fabrication process, as a strong candidate for self-assembled RET systems. It successfully investigates into the design and simulations of a novel sequential self-assembly process employed to realize the goal of creating large, scalable, fully-addressable DNA nanostructure-substrate for future molecular circuitry.

As a pre-cursor to the final device modeling various RET wire designs for interconnecting nanocircuits are presented and their modeling and simulation results are discussed. A chromophore RET system using a biomolecular sensor as a proof-of-concept argument that shows it is possible to model and characterize chromophore systems as a first step towards device modeling is also discussed.

Finally, the thesis report describes in detail the design, modeling, characterization, and fabrication of the Closed-Diffusive Exciton Valve: a self-assembled, nanoscale (area of 17.34 nm2), high-speed (3.5 ps to 6 ps) resonance energy transfer device exhibiting non-linear gain using only 10 molecules, thus confirming the hypothesis. It also recognized improvements that can be made in the future to facilitate better device operation and suggested various applications.