The Use of Molecular Dynamics to Predict the Stability of Squaraine Rotaxanes

Squaraine rotaxanes are fluorescent molecules comprised of two parts—a dumbbell-shaped squaraine dye threaded through a ring-shaped macrocycle—that are held together by hydrogen bonding, hydrophobic effects, and the size of the opening in the macrocycle1. Since the squaraine is an extremely electrophilic species3, nucleophilic attack by water is possible when it slips out of the macrocycle. This results in a loss of fluorescence. These near-IR dyes have many applications, including effective labeling of bacterial cells4. Previous studies have shown that the unprotected squaraine dye is unstable, and the adamantyl rotaxane degrades over time while the isophthalamidyl and pyridinyl rotaxanes remain stable2(Fig. 2). In this study, we aim to determine if molecular dynamics (MD) is an effective method of ascertaining the relative stabilities of squaraine rotaxanes in solution

Efficient Identification of Overlapping Communities

In this paper, we present an e#cient algorithm for finding overlapping communities in social networks. Our algorithm does not rely on the contents of the messages and uses the communication graph only

Arbor: Comparative Analysis Workflows For The Tree Of Life

We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive visual interface. Arbor\u27s user-defined workflows will be exported and shared so that entire analyses can be quickly replicated with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to illustrate the software\u27s key functionality

A new Gödelian argument for hypercomputing minds based on the busy beaver problem

9.9.05 1245am NY time Do human persons hypercompute? Or, as the doctrine of computationalism holds, are they information processors at or below the Turing Limit? If the former, given the essence of hypercomputation, persons must in some real way be capable of infinitary information processing. Using as a springboard Gödel’s little-known assertion that the human mind has a power “converging to infinity, ” and as an anchoring problem Rado’s (1963) Turing-uncomputable “busy beaver ” (or Σ) function, we present in this short paper a new argument that, in fact, human persons can hypercompute. The argument is intended to be formidable, not conclusive: it brings Gödel’s intuition to a greater level of precision, and places it within a sensible case against computationalism.

Abstract

Bridging and bonding are concepts that come from social capital discourse. In this paper, we describe a novel multi-agent model of social evolution, called Statistical Evolution of Social Groups (SESG). We use the model to simulate and monitor the generation and evolution of social communities that exhibit bridging, bonding, or a mix of both. CONTACT