Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Previous approaches are not highthroughput, are not generalizable or scalable, or lack sufficient data to be effective. We describe single mechanistic reactions as concerted electron movements from an electron orbital source to an electron orbital sink. We use an ex...

Whereas most branches of neuroscience are thought to provide mechanistic explanations, systems neuroscience is not. Two reasons are traditionally cited in support of this conclusion. First, systems neuroscientists rarely, if ever, rely on the dual strategies of decomposition and localization. Second, they typically emphasize organizational properties over the properties of individual components...

Two-component signal transduction systems (TCSs) are commonly used by bacteria to couple environmental stimuli to adaptive responses. Targeting the highly conserved kinase domain in these systems represents a promising strategy for the design of a broad-spectrum antibiotic; however, development of such compounds has been marred by an incomplete understanding of the conserved binding features wi...

If you heat a protein up, the tertiary contacts that secure its three-dimensional shape weaken until eventually the protein unfolds, or ‘‘melts.’’ Not surprisingly, proteins from thermophilic organisms, such as the bacteria that live in hot springs, tend to have higher melting temperatures than their homologs from mesophiles like humans or the bacteria that live within them. The increased melti...

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are ...

This research applies cognitive science to the development and study of computer-based scientific inquiry learning. A scientific inquiry software program designed in the domain of elementary hydrology was adapted for mental model reasoning research, and tested in two middle school science classes. The study explores how qualitative mechanistic cues about system factors influence mental animatio...