Computer Sciences Commons^™

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

Group Theory Visualized Through The Rubik's Cube, Ashlyn Okamoto

University Honors Theses

In my thesis, I describe the work done to implement several Group Theory concepts in the context of the Rubik’s cube. A simulation of the cube was constructed using Processing-Java and with help from a YouTube series done by TheCodingTrain. I reflect on the struggles and difficulties that came with creating this program along with the inspiration behind the project. The concepts that are currently implemented at this time are: Identity, Associativity, Order, and Inverses. The functionality of the cube is described as it moves like a regular cube but has extra keypresses that demonstrate the concepts listed. Each concept …

Occam Manual, Martin Zwick

Systems Science Faculty Publications and Presentations

Occam is a Discrete Multivariate Modeling (DMM) tool based on the methodology of Reconstructability Analysis (RA). Its typical usage is for analysis of problems involving large numbers of discrete variables. Models are developed which consist of one or more components, which are then evaluated for their fit and statistical significance. Occam can search the lattice of all possible models, or can do detailed analysis on a specific model.

In Variable-Based Modeling (VBM), model components are collections of variables. In State-Based Modeling (SBM), components identify one or more specific states or substates.

Occam provides a web-based interface, which …