Qualitative and Quantitative Knowledge in Classical Mechanics

This thesis investigates what knowledge is necessary to solve mechanics problems. A program NEWTON is described which understands and solves problems in mechanics mini-world of objects moving on surfaces. Facts and equations such as those given in mechanics text need to be represented. However, this is far from sufficient to solve problems. Human problem solvers rely on "common sense" and "qualitative" knowledge which the physics text tacitly assumes to be present. A mechanics problem solver must embody such knowledge. Quantitative knowledge given by equations and more qualitative common sense knowledge are the major research points exposited in this thesis. The major issue in solving problems is planning. Planning involves tentatively outlining a possible path to the solution without actually solving the problem. Such a plan needs to be constructed and debugged in the process of solving the problem. Envisionment, or qualitative simulation of the event, plays a central role in this planning process.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

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 with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.