Now showing items 1-20 of 139

    • Cellular Gate Technology 

      Knight, Thomas F.; Sussman, Gerald Jay (First International Conference on UNCONVENTIONAL MODELS OF COMPUTATION, Auckland, New Zealand, 1998-01-05)
      We propose a biochemically plausible mechanism for constructing digital logic signals and gates of significant complexity within living cells. These mechanisms rely largely on co-opting existing biochemical machinery and ...
    • Amorphous Computing 

      Abelson, Harold; Allen, Don; Coore, Daniel; Hanson, Chris; Homsy, George; e.a. (1999-08-29)
      Amorphous computing is the development of organizational principles and programming languages for obtaining coherent behaviors from the cooperation of myriads of unreliable parts that are interconnected in unknown, ...
    • A Standard Parts List for Biological Circuitry 

      Arkin, Adam P; Endy, Drew (DARPA White Paper, 1999-10-07)
      One of the hallmarks of biochemical circuits found in nature is analog, asymmetric, asynchronous design. That is, there is little standardization of parts, e.g. all the promoters have different strengths and kinetics, ...
    • Cellular computation and communications using engineered genetic regulatory networks 

      Weiss, Ron, 1970- (Massachusetts Institute of Technology, 2001)
      In this thesis, I present an engineering discipline for obtaining complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish ...
    • DARPA BioComp Plasmid Distribution 1.00 of Standard Biobrick Components 

      Knight, Thomas (MIT Artificial Intelligence Laboratory, 2002-05-22)
      This distribution consists of 300 ng aliquots of plasmid DNA for each of twelve components and compound constructs utilizing our idempotent assembly strategy. The dried DNA should be stable at room temperature for many ...
    • Idempotent Vector Design for Standard Assembly of Biobricks 

      Knight, Thomas (MIT Artificial Intelligence Laboratory; MIT Synthetic Biology Working Group, 2003)
      The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly reaction to be both an experimental tool for addressing the current research topic, and an experiment in and of itself. One ...
    • Fluorescence Assay for Polymerase Arrival Rates 

      Che, Austin (2003-08-31)
      To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a ...
    • Strategy for Biological Risk & Security 

      Endy, Drew (2003-10)
      Why do biological risks exist? Can we develop and implement a strategy for thoughtfully approaching future biological risks? This short, working report provides an abstract introduction to the problem of biological risk ...
    • Fluorescence assay for polymerase arrival rates 

      Che, Austin, 1979- (Massachusetts Institute of Technology, 2004)
      To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a ...
    • BioJADE: A Design and Simulation Tool for Synthetic Biological Systems 

      Goler, Jonathan A. (2004-05-28)
      The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us ...
    • BioBricks++: Simplifying Assembly of Standard DNA Components 

      Che, Austin (2004-06-09)
      Construction of complex biological systems can require assembling many modules together. However, existing assembly schemes are lacking in generality, ease of use, or power to perform some desirable operations. Currently, ...
    • Refactoring Bacteriophage T7 (2004 version) 

      Chan, Leon; Kosuri, Sriram; Endy, Drew (2004-10)
      Natural biological systems are selected by evolution to continue to exist. Evolution might give rise to complicated systems that are difficult to discover, measure, model, and direct. Here, we redesign the genome of a ...
    • Engineering the Interface Between Cellular Chassis and Integrated Biological Systems 

      Canton, Bartholomew (2005-08-08)
      The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help ...
    • Design and Evolution of Engineered Biological Systems 

      Kelly, Jason (2005-08-11)
      To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. Here, I propose to explore how existing forward engineering ...
    • iGEM 2005 Invitation Supplement 

      Endy, Drew (2005-09-29)
      This document provides background material in support of the 2005 intercollegiate Genetically Engineered Machine Competition (aka iGEM). Herein, you can read quick summaries of earlier competitions and courses, obtain a ...
    • Engineering transcription-based digital logic devices 

      Shetty, Reshma P.; Knight, Thomas F. Jr (Sixth International Conference on Systems Biology, 2005-10-20)
      The goal of Synthetic Biology is to engineer systems from biological parts. One class of systems are those whose purpose is to process information. My work seeks to build transcription-based devices for use in combinational ...
    • Design and Evolution of Engineered Biological Systems 

      Kelly, Jason; Michener, Josh; Endy, Drew (Sixth International Conference on Systems Biology, 2005-10-20)
      To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. We are interested in exploring how existing forward ...
    • Engineering the Interface Between Cellular Chassis and Integrated Biological Systems 

      Canton, Bartholomew; Endy, Drew (2005-10-21)
      The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help ...
    • Rapid Characterization of Cellular Pathways Using Time-Varying Signals 

      Thomson, Ty M; Endy, Drew (International Conference on Systems Biology, 2005-10-21)
      The use of traditional tools for the discovery and characterization of biological systems has resulted in a wealth of biological knowledge. Unfortunately, only a small portion of the biological world is well-understood ...
    • Adventures in Synthetic Biology 

      Wadey, Chuck; Deese, Isadora; Endy, Drew (OpenWetWare & Nature Publishing Group, 2005-11-24)