Distributed Computing with Engineered Bacteria and Its Application in Solving Chemically Generated 2 × 2 Maze Problems.

  title={Distributed Computing with Engineered Bacteria and Its Application in Solving Chemically Generated 2 × 2 Maze Problems.},
  author={Kathakali Sarkar and Saswata Chakraborty and Deepro Bonnerjee and Sangram Bagh},
  journal={ACS synthetic biology},
This work presented an application of genetic distributed computing, where an abstract computational problem was mapped on a complex truth table and solved using simple genetic circuits distributed among various cell populations. Maze generating and solving are challenging problems in mathematics and computing. Here, we mapped all the input-output matrices of a 2 × 2 mathematical maze on a 4-input-4-output truth table. The logic values of four chemical inputs determined the 16 different 2 × 2… 
4 Citations

Synthetic Genetic Reversible Feynman Gate in a Single E. coli Cell and Its Application in Bacterial to Mammalian Cell Information Transfer.

A synthetic genetic reversible Feynman gate is constructed in single E. coli cells, and the input-output relations were measured in a clonal population and the behavior of the circuit was ultrasensitive and predictive.

A Logically Reversible Double Feynman Gate with Molecular Engineered Bacteria Arranged in an Artificial Neural Network-Type Architecture.

To the authors' knowledge, this is the first reversible double Feynman gate realization with living cells and may have significance in development of biocomputer technology, reversible computation, ANN wetware, and synthetic biology.

Deep Learning Concepts and Applications for Synthetic Biology

This review presents an overview of synthetic biology-relevant classes of data and deep learning architectures and highlights emerging studies in synthetic biology that capitalize on deep learning to enable novel understanding and design, and discusses challenges and future opportunities.



Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between cells.

Distributed implementation of Boolean functions by transcriptional synthetic circuits.

This work proposes a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and theNumber of orthogonal DSMs, based on an exact synthesis algorithm to find the minimal circuit per cell, which allows for an extensive database of Boolean functions up to a given number of inputs.

Genetic programs constructed from layered logic gates in single cells

This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.

A single layer artificial neural network type architecture with molecular engineered bacteria for complex conventional and reversible computing

This work created molecular-devices, which worked as artificial neuro-synapses in bacteria, where input chemical signals were linearly combined and processed through a non-linear activation function to produce fluorescent protein outputs and is believed to be the first adaptation of ANN type architecture with engineered cells.

Design, fabrication and device chemistry of a 3-input-3-output synthetic genetic combinatorial logic circuit with a 3 input AND gate in a single bacterial cell.

By adapting circuit minimization and conjugated promoter engineering approach, this work created the first 3-input-3-output logic function in a single bacterial cell and demonstrated the integration of a 3- input AND gate in a larger circuit and a 2- input-2-output synthetic genetic circuit, both for the first time.

Seeing around corners: Cells solve mazes and respond at a distance using attractant breakdown

This work predicted the pathfinding of cells in mazes using computational and mathematical modeling of self-generated gradients and tested the outcomes with real cells in microfluidic mazes, implying that the underlying conceptual model is an effective explanation of general cell behavior.

Layering genetic circuits to build a single cell, bacterial half adder

This work describes a representative case study for the debugging of genetic context-dependent effects through principles elucidated herein, thereby providing a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.

Cellular checkpoint control using programmable sequential logic

A quantitative method to design regulatory circuits that encode sequential logic using NOT gates as the core unit of regulation, in which an input promoter drives the expression of a repressor protein that turns off an output promoter.

Synthetic biology: new engineering rules for an emerging discipline

The basic features of synthetic biology as a new engineering discipline are outlined, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields.

Complex cellular logic computation using ribocomputing devices

It is demonstrated that ribocomputing devices in Escherichia coli can evaluate two-input logic with a dynamic range up to 900-fold and scale them to four-input AND, six-input OR, and a complex 12-input expression.