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Full-Text Articles in Engineering
Coel: A Cloud-Based Reaction Network Simulator, Peter Banda, Christof Teuscher
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
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 …