Funnels in Energy Landscapes

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a "folding funnel" as it is discussed in the protein folding literature.Comment: 6 pages, 3 figures, submitted to European Conference on Complex Systems 200

Electric discharge for treatment of trace contaminants

A radio frequency glow discharge reactor is described for removing trace oxidizable contaminants from an oxygen bearing atmosphere. The reaction chamber is defined by an inner metal electrode facing a dielectric backed by an outer conductive electrode. In one embodiment, a conductive liquid forms the conductor of an outer electrode and cools the dielectric. A resonator coupled to a variable radio frequency source generates the high voltages for creating a glow discharge in the chamber at a predetermined pressure whereby the trace contaminants are oxidized into a few simple non-toxic products that may be easily recovered. The corresponding process for removal of trace contaminants from an oxygen-bearing atmosphere with high efficiency independent of the concentration level is also disclosed

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions

Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the computation of atom-atom mappings, i.e., the atom-wise correspondence between products and educts of all published chemical reactions. This can be phrased as a maximum common edge subgraph problem with the constraint that transition states must have cyclic structure. We describe a search tree method well suited for small edit distance and an integer linear program best suited for general instances and demonstrate that it is feasible to compute atom-atom maps at large scales using a manually curated database of biochemical reactions as an example. In this context we address the network completion problem.Comment: ICGT 2016 : 9th International Conference on Graph Transformation, extended technical repor

Perceptions of Bicycle-Friendly Policy Impacts on Accessibility to Transit Services: The First and Last Mile Bridge, MTI Report 12-10

The coordination of bicycle and transit modes has received close attention from public transit planners and researchers in recent years, as transit agencies around the world have installed bicycle racks on transit vehicles, implemented bicycles-on-trains policies, and made other efforts to facilitate bicycle-transit integration. Many planners presume that the catchment area for transit is enlarged by these efforts, but geographic changes in the size of catchment areas have not been effectively documented. This research project was designed to assess the distances travelled on bicycle by cycle-transit users (CTUs), both those who use bicycles as a means of access to transit stops and stations and those who bicycle to and travel on transit with their bicycles. A mixed-methods approach was employed, using a literature review, a survey of cyclist-transit users in Philadelphia and San Francisco, and telephone interviews with a subset of survey respondents. Responses provided by CTUs in the two cities allow us to define their characteristics and behaviors in detail. What is more, they highlight two intriguing conclusions: that transit catchment areas can be much larger for cycle-transit users than for traditional transit users who access transit buses and rail on foot, and that the very concept of a cycle-transit catchment area is quite complex because of the variety of travel opportunities that cycle-transit coordination policies present transit riders. CTUs take advantage of larger catchment areas to reduce their travel costs, and they use those catchment areas in curious, less predictable and more varied ways

Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows

We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions. Pathways are modelled as integer hyperflows and we expand the network model by detailed routing constraints. In contrast to the more traditional approaches like Flux Balance Analysis or Elementary Mode analysis we insist on integer-valued flows. While this choice makes it necessary to solve possibly hard integer linear programs, it has the advantage that more detailed mechanistic questions can be formulated. It is thus possible to query networks for general transformation motifs, and to automatically enumerate optimal and near-optimal pathways. Similarities and differences between our work and traditional approaches in metabolic network analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest