An Algorithm for Group Formation and Maximal Independent Set in an Amorphous Computer

Amorphous computing is the study of programming ultra-scale computing environments of smart sensors and actuators cite{white-paper}. The individual elements are identical, asynchronous, randomly placed, embedded and communicate locally via wireless broadcast. Aggregating the processors into groups is a useful paradigm for programming an amorphous computer because groups can be used for specialization, increased robustness, and efficient resource allocation. This paper presents a new algorithm, called the clubs algorithm, for efficiently aggregating processors into groups in an amorphous computer, in time proportional to the local density of processors. The clubs algorithm is well-suited to the unique characteristics of an amorphous computer. In addition, the algorithm derives two properties from the physical embedding of the amorphous computer: an upper bound on the number of groups formed and a constant upper bound on the density of groups. The clubs algorithm can also be extended to find the maximal independent set (MIS) and $Delta + 1$ vertex coloring in an amorphous computer in $O(log N)$ rounds, where $N$ is the total number of elements and $Delta$ is the maximum degree.

SketchIT: A Sketch Interpretation Tool for Conceptual Mechanical Design

We describe a program called SketchIT capable of producing multiple families of designs from a single sketch. The program is given a rough sketch (drawn using line segments for part faces and icons for springs and kinematic joints) and a description of the desired behavior. The sketch is "rough" in the sense that taken literally, it may not work. From this single, perhaps flawed sketch and the behavior description, the program produces an entire family of working designs. The program also produces design variants, each of which is itself a family of designs. SketchIT represents each family of designs with a "behavior ensuring parametric model" (BEP-Model), a parametric model augmented with a set of constraints that ensure the geometry provides the desired behavior. The construction of the BEP-Model from the sketch and behavior description is the primary task and source of difficulty in this undertaking. SketchIT begins by abstracting the sketch to produce a qualitative configuration space (qc-space) which it then uses as its primary representation of behavior. SketchIT modifies this initial qc-space until qualitative simulation verifies that it produces the desired behavior. SketchIT's task is then to find geometries that implement this qc-space. It does this using a library of qc-space fragments. Each fragment is a piece of parametric geometry with a set of constraints that ensure the geometry implements a specific kind of boundary (qcs-curve) in qc-space. SketchIT assembles the fragments to produce the BEP-Model. SketchIT produces design variants by mapping the qc-space to multiple implementations, and by transforming rotating parts to translating parts and vice versa.

Retargeting of pre-set regions on chromosome for high gene expression in mammalian cells

We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two extraneous DNA fragments. The gene gfp2 makes it possible to screen the high expression regions on the chromosome. The extraneous DNA fragments can help to create the unique loci on the chromosome and increase the gene targeting frequency by increasing the homology. After transfection into Chinese hamster ovary cells (CHO) cells, the linearized pRGFP8 can integrate into the chromosome of the host cells and form the unique sites. With FACS, 90 millions transfected cells were sorted and the cells with strongest GFP expression were isolated, and then 8 stable high expression GFP CHO cell lines were selected as candidates for the new host cell. Taking the unique site created by pRGFP8 on the chromosome in the new host cells as a targeting locus, the gfp2 gene was replaced with the gene of interest, human ifngamma, by transfecting the targeting plasmid pRIH-IFN. Then using FACS, the cells with the dimmest GFP fluorescence were selected. These cells showed they had strong abilities to produce the protein of interest, IFN-gamma. During the gene targeting experiment, we found there is positive correlation between the fluorescence density of the GFP CHO host cells and the specific production rate of IFN-gamma. This result shows that the strategy in our expression system is correct: the production of the interesting protein increases with the increase fluorescence of the GFP host cells. This system, the new host cell lines and the targeting vector, can be utilized for highly expressing the gene of interest. More importantly, by using FACS, we can fully screen all the transfected cells, which can reduce the chances of losing the best cells.