Molecular Memory Architect Simulator

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📚 Glossary

DNA Data Storage

The process of encoding digital information (binary data) into sequences of the four DNA nucleotide bases (A, T, G, C) for long-term, ultra-dense data archival.

DNA Fountain

An encoding method developed by Yaniv Erlich and Dina Zielinski (2017) that approaches the theoretical maximum information capacity of DNA at 1.98 bits per nucleotide.

Oligonucleotide

A short, synthetic DNA strand typically 100-200 nucleotides long, used as the basic unit of data storage in DNA memory systems.

DNA Synthesis

The chemical or enzymatic process of constructing DNA strands from individual nucleotides; the 'write' operation in DNA data storage.

DNA Sequencing

The process of reading the order of nucleotides in a DNA strand; the 'read' operation in DNA data storage, using technologies like Illumina or nanopore sequencing.

Error-Correcting Code

Mathematical algorithms (like Reed-Solomon or fountain codes) added to DNA-stored data to detect and correct errors introduced during synthesis, storage, or sequencing.

Silica Encapsulation

A preservation method developed by Robert Grass at ETH Zurich where DNA is sealed inside nanometer silica beads, enabling data survival for thousands of years.

DNA-of-Things (DoT)

A storage architecture by Erlich and Grass (2019) that embeds DNA data into physical objects -- like a 3D-printed rabbit containing its own digital blueprint.

Random Access

The ability to retrieve specific data from a DNA storage system without reading all stored data, achieved using PCR primers as 'file addresses'.

Homopolymer Run

A sequence of identical consecutive DNA bases (e.g., AAAA) that increases synthesis and sequencing errors, requiring encoding constraints.

GC Content

The proportion of guanine (G) and cytosine (C) bases in a DNA sequence; optimal storage requires balanced GC content (around 50%) for stability.

Information Density

The amount of data that can be stored per unit of physical space; DNA achieves approximately 10^17 bytes per cubic millimeter, millions of times denser than flash memory.

Enzymatic Synthesis

A newer DNA synthesis approach using enzymes instead of chemicals, potentially faster and cheaper for data storage applications.

🏆 Key Figures

George M. Church (2012)

Harvard geneticist who demonstrated the first high-capacity DNA data storage by encoding a 650 KB book into synthetic DNA, proving the concept at scale

Yaniv Erlich (2017-2019)

Developed DNA Fountain, achieving near-theoretical-maximum storage density of 1.98 bits/nucleotide, and co-invented DNA-of-Things (DoT) for embedding data in physical objects

Dina Zielinski (2017)

Co-developed the DNA Fountain encoding method at the New York Genome Center, storing an OS, movie, and other files perfectly in DNA

Robert N. Grass (2015-2019)

Developed silica encapsulation at ETH Zurich for preserving DNA data for millennia, and co-invented DNA-of-Things with Erlich

Nick Goldman (2013)

Led the EMBL-EBI team that encoded 739 KB of data in DNA using a ternary encoding scheme with redundancy, published in Nature (2013)

Richard Feynman (1959)

First proposed the idea of using molecules for data storage in his famous 1959 lecture 'There's Plenty of Room at the Bottom'

Luis Ceze & Karin Strauss (2018)

Led the Microsoft/University of Washington collaboration on random-access DNA storage and automated end-to-end DNA data storage systems

💬 Message to Learners

Every living cell on Earth already uses molecular memory -- DNA stores the complete instructions for building and running a human body in a space smaller than the head of a pin. What's remarkable about molecular memory research is that scientists are now repurposing nature's own storage medium for our digital world. A single gram of DNA could replace an entire data center. While we're still working on making it fast and cheap enough for everyday use, the fundamental breakthrough has already been made: we know how to write, store, and perfectly read back digital data using the same molecule that has reliably preserved the story of life for 3.8 billion years.