UNM Rainforest Innovations

Professor and Chair, Department of Computer Science

The University of New Mexico

Dr. Stefanovic has disclosed seven inventions to STC, received two UNM-affiliated issued U. S. patent, and has two pending U. S. patent applications for his molecular computing technologies.

Molecular computing is still in development and was not even in existence until just a decade or so ago. The key to molecular computing is DNA, which is very similar to a computer hard drive in that it stores permanent information about genes. DNA strands can also be programmed to communicate with one another; when given a clear input command, they can respond to other nearby molecules to give logical, predictable outcomes. The programming used on DNA consists of logic gates that rely on DNA code. The logic gates detect fragments of genetic material as input, combine together these fragments and form a single output. While individual molecular gates and small networks have been constructed, these gates are yet to be integrated at higher levels of complexity. In today’s ever-evolving market, the ability to truly integrate molecular components is critical in the construction of next-generation molecular devices.

Dr. Stefanovic’s technology is a solution-phase molecular assembly of over 100 molecular logic gates. The technology is a second generation molecular automaton capable of playing a complete game of tic-tac-toe against a human opponent, and encompasses 76 permissible game plays. In fact, the automaton played complete games according to a perfect strategy, demonstrating high levels of molecular computational ability.

The construction consists of three classes of stem-loop controlled deoxyribozyme-based logic gates that are allosterically modulated by input oligonucleotides to produce fluorescent output signals. By developing particles that are able to effectively communicate with one another, this technology opens the door to more efficient DNA analysis and molecular computing. The signals move in a user-friendly, two-color output system.

The technology has applications for micro-array style diagnostics, analysis of multiple DNA sequences, multiplex single nucleotide polymorphism (SNP) detection, viral lineage attribution, detection and release of small molecules, inhibition of enzymatic activity, and development of autonomous molecular devices.

Dr. Stefanovic’s research is focused on molecular computing, nanotechnology, programming language implementation, and studying the interface of computing, engineering, and biochemistry. He has developed DNA-based molecular networks that can be trained to compute logic functions, classify diagnostic inputs, and even play games.


8,119,782 Medium Scale Integration of Molecular Logic Gates in an Automaton, issued February 12, 2012

9,476,090 Signal Propagation Biomolecules, Devices and Methods, issued October 25, 2016


Signal Propagation Biomolecules, Devices and Methods

Hybrid Architecture System and Method for High-Dimensional Sequence Processing

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