A Lifetime-based Garbage Collector for LISP Systems on General-Purpose Computers

Garbage collector performance in LISP systems on custom hardware has been substantially improved by the adoption of lifetime-based garbage collection techniques. To date, however, successful lifetime-based garbage collectors have required special-purpose hardware, or at least privileged access to data structures maintained by the virtual memory system. I present here a lifetime-based garbage collector requiring no special-purpose hardware or virtual memory system support, and discuss its performance.

Fluorescence Assay for Polymerase Arrival Rates

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 specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.