Tag Archives: George Church

Nucleic acid-based memory storage

We’re running out of memory. To be more specific, there are two problems: the supply of silicon and a limit to how much silicon-based memory can store. An April 27, 2016 news item on Nanowerk announces a nucleic acid-based approach to solving the memory problem,

A group of Boise State [Boise State University in Idaho, US] researchers, led by associate professor of materials science and engineering and associate dean of the College of Innovation and Design Will Hughes, is working toward a better way to store digital information using nucleic acid memory (NAM).

An April 25, 2016 Boise State University news release, which originated the news item, expands on the theme of computer memory and provides more details about the approach,

It’s no secret that as a society we generate vast amounts of data each year. So much so that the 30 billion watts of electricity used annually by server farms today is roughly equivalent to the output of 30 nuclear power plants.

And the demand keeps growing. The global flash memory market is predicted to reach $30.2 billion this year, potentially growing to $80.3 billion by 2025. Experts estimate that by 2040, the demand for global memory will exceed the projected supply of silicon (the raw material used to store flash memory). Furthermore, electronic memory is rapidly approaching its fundamental size limits because of the difficulty in storing electrons in small dimensions.

Hughes, with post-doctoral researcher Reza Zadegan and colleagues Victor Zhirnov (Semiconductor Research Corporation), Gurtej Sandhun (Micron Technology Inc.) and George Church (Harvard University), is looking to DNA molecules to solve the problem. Nucleic acid — the “NA” in “DNA” — far surpasses electronic memory in retention time, according to the researchers, while also providing greater information density and energy of operation.

Their conclusions are outlined in an invited commentary in the prestigious journal Nature Materials published earlier this month.

“DNA is the data storage material of life in general,” said Hughes. “Because of its physical and chemical properties, it also may become the data storage material of our lives.” It may sound like science fiction, but Hughes will participate in an invitation-only workshop this month at the Intelligence Advanced Research Projects Activity (IARPA) Agency to envision a portable DNA hard drive that would have 500 Terabytes of searchable data – that’s about the the size of the Library of Congress Web Archive.

“When information bits are encoded into polymer strings, researchers and manufacturers can manage and manipulate physical, chemical and biological information with standard molecular biology techniques,” the paper [in Nature Materials?] states.

Cost-competitive technologies to read and write DNA could lead to real-world applications ranging from artificial chromosomes, digital hard drives and information-management systems, to a platform for watermarking and tracking genetic content or next-generation encryption tools that necessitate physical rather than electronic embodiment.

Here’s how it works. Current binary code uses 0’s and 1’s to represent bits of information. A computer program then accesses a specific decoder to turn the numbers back into usable data. With nucleic acid memory, 0’s and 1’s are replaced with the nucleotides A, T, C and G. Known as monomers, they are covalently bonded to form longer polymer chains, also known as information strings.

Because of DNA’s superior ability to store data, DNA can contain all the information in the world in a small box measuring 10 x 10 x 10 centimeters cubed. NAM could thus be used as a sustainable time capsule for massive, scientific, financial, governmental, historical, genealogical, personal and genetic records.

Better yet, DNA can store digital information for a very long time – thousands to millions of years. Currently, usable information has been extracted from DNA in bones that are 700,000 years old, making nucleic acid memory a promising archival material. And nucleic acid memory uses 100 million times less energy than storing data electronically in flash, and the data can live on for generations.

At Boise State, Hughes and Zadegan are examining DNA’s stability under extreme conditions. DNA strands are subjected to temperatures varying from negative 20 degrees Celsius to 100 degrees Celsius, and to a variety of UV exposures to see if they can still retain their information. What they’re finding is that much less information is lost with NAM than with the current state of the industry.

Here’s a link to and a citation for the Nature Materials paper,

Nucleic acid memory by Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, & William L. Hughes. Nature Materials 15, 366–370 (2016)  doi:10.1038/nmat4594 Published online 23 March 2016

This paper is behind a paywall.

Toggling atomic switches and other talks at the Foresight Institute’s 2013 technical conference

The correct title for the conference, which took place almost one year ago (Jan. 11-13, 2013 in Palo Alto, California, US, is the 2013 Foresight Technical Conference: Illuminating Atomic Precision, and the organizers, the Foresight Institute in a Dec. 2, 2013 posting by James Lewis have announced a number of conference videos have been made available and have provided a transcript of sorts for one of the videos,

A select set of videos from the 2013 Foresight Technical Conference: Illuminating Atomic Precision, held January 11-13, 2013 in Palo Alto, have been made available on vimeo. Videos have been posted of those presentations for which the speakers have consented. Other presentations contained confidential information and will not be posted.

Here’s a listing of the 2013 conference presentations made available (click to access the videos),

  • Larry Millstein: Introductory comments at Foresight Technical Conference 2013
  • J. Fraser Stoddart: Introductory comments at Foresight Technical Conference 2013
  • Leonhard Grill: “Assembly and Manipulation of Molecules at the Atomic Scale”
  • John Randall: “Atomically Precise Manufacturing”
  • Philip Moriarty: “Mechanical Atom Manipulation: Towards a Matter Compiler?”
  • David Soloveichik: “DNA Displacement Cascades”
  • Alex Wissner-Gross: “Bringing Computational Programmability to Nanostructured Surfaces”
  • Joseph Puglisi: “Deciphering the Molecular Choreography of Translation”
  • Feynman Awards Banquet at Foresight Technical Conference 2013
  • Gerhard Klimeck: “Multi-Million Atom Simulations for Single Atom Transistor Structures”
  • William Goddard: “Nanoscale Materials, Devices, and Processing Predicted from First Principals” [Note: He’s a wearing a jaunty beret adding a note of style not usually found at technical conferences.]
  • Gerhard Klimeck: “Mythbusting Knowledge Transfer Mechanisms through Science Gateways”
  • Art Olson: “New Methods of Exploring, Analyzing, and Predicting Molecular Interactions”
  • George Church: “Regenesis: Bionano”
  • Dean Astumian: “Microscopic Reversibility: The Organizing Principle for Molecular Machines”
  • Larry Millstein: Closing comments at Foresight Technical Conference 2013

In his Foresight Institute blog posting  Lewis goes on to offer a description of Philip Moriarty’s presentation “Mechanical Atom Manipulation: Towards a Matter Compiler?,”

Prof. Moriarty presented his work with the qPlus technique of non-contact AFM of semiconductors, using chemical forces to mechanically move atoms around to structure matter, focusing on the tip of the probe—specifically how to optimize the tip structure, and how to return the tip to a previously known state. He begins with a brief review of how non-contact AFM uses a damped, driven oscillator to measure and manipulate what is happening at the level of single chemical bonds. The tip at the end of the oscillating cantilever measures the frequency shift of the cantilever as it approaches and interacts with the surface, and it maintains a constant amplitude of oscillation by pumping energy into the system. The frequency shift provides information about conservative forces acting on the tip, and the amount of energy pumped in gives a handle on non-conservative, or dissipative, forces. Before diving into the experimental details of his own work, Prof. Moriarty noted that various experimental accomplishments have vindicated Eric Drexler’s assertion that single atom chemistry could be done using purely mechanical force.

I found this description to be a beautiful piece of technical writing although I do have to admit to being distracted by thoughts of Sherlock Holmes on reading “Prof. Moriarty.” One final note, I noted the reference to Eric Drexler in the last sentence of my excerpt as Drexler was a Foresight Institute founder amongst his many other accomplishments.