Engineering Commons^™

Coel: A Cloud-Based Reaction Network Simulator, Peter Banda, Christof Teuscher

Electrical and Computer Engineering Faculty Publications and Presentations

Chemical Reaction Networks (CRNs) are a formalism to describe the macroscopic behavior of chemical systems. We introduce COEL, a web- and cloud-based CRN simulation framework, which does not require a local installation, runs simulations on a large computational grid, provides reliable database storage, and offers a visually pleasing and intuitive user interface. We present an overview of the underlying software, the technologies, and the main architectural approaches employed. Some of COEL’s key features include ODE-based simulations of CRNs and multicompartment reaction networks with rich interaction options, a built-in plotting engine, automatic DNA-strand displacement transformation and visualization, SBML/Octave/Matlab export, and a …

Design Of Introspective Circuits For Analysis Of Cell-Level Dis-Orientation In Self-Assembled Cellular Systems, Nicholas J. Macias, Christof Teuscher, Lisa J. K. Durbeck

Electrical and Computer Engineering Faculty Publications and Presentations

This paper discusses a novel approach to managing complexity in a large self-assembled system, by utilizing the self-assembling components themselves to address the complexity. A particular challenge is discussed – namely the question of how to deal with elements that are assembled in different orientations from each other – and a solution based on the idea ofintrospective circuitry is described. A methodology for using a set of cells to determine a nearby cell’s orientation is given, leading to a slow (O(n)) means of orienting a 2D region of cells. A modified algorithm is then describe …

Hardware Architectures And Implementations For Associative Memories : The Building Blocks Of Hierarchically Distributed Memories, Changjian Gao

Dissertations and Theses

During the past several decades, the semiconductor industry has grown into a global industry with revenues around $300 billion. Intel no longer relies on only transistor scaling for higher CPU performance, but instead, focuses more on multiple cores on a single die. It has been projected that in 2016 most CMOS circuits will be manufactured with 22 nm process. The CMOS circuits will have a large number of defects. Especially when the transistor goes below sub-micron, the original deterministic circuits will start having probabilistic characteristics. Hence, it would be challenging to map traditional computational models onto probabilistic circuits, suggesting a …

The Quest For Novel Computational Paradigms And Machines, Christof Teuscher

Electrical and Computer Engineering Faculty Publications and Presentations

The quest for novel and unconventional computing machines is mainly motivated by the man-machine dichotomy and by the belief that meeting tomorrow's complex real world challenges will require new paradigms and new engineering methods to organize, train, and program such machines and to interact with them.

Data Allocation For Distributed Programs, Liono Setiowijoso

Dissertations and Theses

This thesis shows that both data and code must be efficiently distributed to achieve good performance in a distributed system. Most previous research has either tried to distribute code structures to improve parallelism or to distribute data to reduce communication costs. Code distribution (exploiting functional parallelism) is an effort to distribute or to duplicate function codes to optimize parallel performance. On the other hand, data distribution tries to place data structures as close as possible to the function codes that use it, so that communication cost can be reduced.

In particular, dataflow researchers have primarily focused on code partitioning and …