Influences on crystal structure due to hydrogen bonding and other effects

One of the most fundamental pieces of information available about a compound is the molecular structure, and one of the best methods for obtaining structural information for crystalline compound is to study the diffraction pattern obtained when the crystal interacts with an X-ray beam. The diffraction pattern can be analysed to give not only the molecular structure, but also information on the packing arrangements in the crystal, the 3-Dimensional crystal structure. This information on the molecular structure and packing within the crystal allow the study of weak intra and intermolecular interactions such as hydrogen bonds. In this project two different methods will be used to study hydrogen bonds. Firstly using a statistical approach, where one type of intramolecular hydrogen bond (the N-H...π bond between neighbouring residues on a peptide chain) is analysed using crystallographic data obtained from the Cambridge Structural Database. Secondly the diffraction data from a several very different compounds are solved and the resulting structures analysed in terms of molecular and crystal structure; how and why the molecules pack as they do in the crystal lattice, and influences of hydrogen bonds on this packing. The effect of changes in the molecular structure on the molecular packing and crystal structure is also considered by the analysis of diffraction data from several groups of compounds where there are small changes in molecular structure in going across the group. The effects considered are; the effect of changing a methyl group for a butyl group in the 1,3-dimethyl-2-imidazolidinone co-crystallised with methane-diphenol-3,5,3',5'-tetra'butyl, the effect of changing the methyl group for an amino or ethyl group in triphenylmethylphosphonium co-crystallised with p-tert-butylcalix[4]arene and finally the effect of changing the metal in the compounds M-bis(2,6-di(^t)butyl-4-methylphenoxy) bis(triphenylaminophosphonium) and M-bis(trimethylsilylamide) bis(triphenylmethylphosphonium), where M is an alkali earth metal

Warren Ames of Upton (a novel)

Thesis (M.A.)--Boston Universit

Peat decomposition records in three pristine ombrotrophic bogs in southern Patagonia

Ombrotrophic bogs in southern Patagonia have been examined with regard to paleoclimatic and geochemical research questions but knowledge about organic matter decomposition in these bogs is limited. Therefore, we examined peat humification with depth by Fourier Transformed Infrared (FTIR) measurements of solid peat, C/N ratio, and δ<sup>13</sup>C and δ<sup>15</sup>N isotope measurements in three bog sites. Peat decomposition generally increased with depth but distinct small scale variation occurred, reflecting fluctuations in factors controlling decomposition. C/N ratios varied mostly between 40 and 120 and were significantly correlated (<i>R</i><sup>2</sup> > 0.55, <i>p</i> < 0.01) with FTIR-derived humification indices. The degree of decomposition was lowest at a site presently dominated by <i>Sphagnum</i> mosses. The peat was most strongly decomposed at the driest site, where currently peat-forming vegetation produced less refractory organic material, possibly due to fertilizing effects of high sea spray deposition. Decomposition of peat was also advanced near ash layers, suggesting a stimulation of decomposition by ash deposition. Values of δ<sup>13</sup>C were 26.5 ± 2‰ in the peat and partly related to decomposition indices, while δ<sup>15</sup>N in the peat varied around zero and did not consistently relate to any decomposition index. Concentrations of DOM partly related to C/N ratios, partly to FTIR derived indices. They were not conclusively linked to the decomposition degree of the peat. DOM was enriched in <sup>13</sup>C and in <sup>15</sup>N relative to the solid phase probably due to multiple microbial modifications and recycling of N in these N-poor environments. In summary, the depth profiles of C/N ratios, δ<sup>13</sup>C values, and FTIR spectra seemed to reflect changes in environmental conditions affecting decomposition, such as bog wetness, but were dominated by site specific factors, and are further influenced by ash deposition and possibly by sea spray input

Self-organization of structures and networks from merging and small-scale fluctuations

We discuss merging-and-creation as a self-organizing process for scale-free topologies in networks. Three power-law classes characterized by the power-law exponents 3/2, 2 and 5/2 are identified and the process is generalized to networks. In the network context the merging can be viewed as a consequence of optimization related to more efficient signaling.Comment: Physica A: Statistical Mechanics and its Applications, In Pres

Scalable Mining of Common Routes in Mobile Communication Network Traffic Data

A probabilistic method for inferring common routes from mobile communication network traffic data is presented. Besides providing mobility information, valuable in a multitude of application areas, the method has the dual purpose of enabling efficient coarse-graining as well as anonymisation by mapping individual sequences onto common routes. The approach is to represent spatial trajectories by Cell ID sequences that are grouped into routes using locality-sensitive hashing and graph clustering. The method is demonstrated to be scalable, and to accurately group sequences using an evaluation set of GPS tagged data

Fast Locality-Sensitive Hashing Frameworks for Approximate Near Neighbor Search

The Indyk-Motwani Locality-Sensitive Hashing (LSH) framework (STOC 1998) is a general technique for constructing a data structure to answer approximate near neighbor queries by using a distribution $\mathcal{H}$ over locality-sensitive hash functions that partition space. For a collection of $n$ points, after preprocessing, the query time is dominated by $O(n^{\rho} \log n)$ evaluations of hash functions from $\mathcal{H}$ and $O(n^{\rho})$ hash table lookups and distance computations where $\rho \in (0,1)$ is determined by the locality-sensitivity properties of $\mathcal{H}$. It follows from a recent result by Dahlgaard et al. (FOCS 2017) that the number of locality-sensitive hash functions can be reduced to $O(\log^2 n)$, leaving the query time to be dominated by $O(n^{\rho})$ distance computations and $O(n^{\rho} \log n)$ additional word-RAM operations. We state this result as a general framework and provide a simpler analysis showing that the number of lookups and distance computations closely match the Indyk-Motwani framework, making it a viable replacement in practice. Using ideas from another locality-sensitive hashing framework by Andoni and Indyk (SODA 2006) we are able to reduce the number of additional word-RAM operations to $O(n^\rho)$.Comment: 15 pages, 3 figure

Power Law of Customers' Expenditures in Convenience Stores

In a convenience store chain, a tail of the cumulative density function of the expenditure of a person during a single shopping trip follows a power law with an exponent of -2.5. The exponent is independent of the location of the store, the shopper's age, the day of week, and the time of day.Comment: 9 pages, 5 figures. Accepted for publication in Journal of the Physical Society of Japan Vol.77No.

Off the Beaten Path: Let's Replace Term-Based Retrieval with k-NN Search

Retrieval pipelines commonly rely on a term-based search to obtain candidate records, which are subsequently re-ranked. Some candidates are missed by this approach, e.g., due to a vocabulary mismatch. We address this issue by replacing the term-based search with a generic k-NN retrieval algorithm, where a similarity function can take into account subtle term associations. While an exact brute-force k-NN search using this similarity function is slow, we demonstrate that an approximate algorithm can be nearly two orders of magnitude faster at the expense of only a small loss in accuracy. A retrieval pipeline using an approximate k-NN search can be more effective and efficient than the term-based pipeline. This opens up new possibilities for designing effective retrieval pipelines. Our software (including data-generating code) and derivative data based on the Stack Overflow collection is available online

Minimizing energy below the glass thresholds

Focusing on the optimization version of the random K-satisfiability problem, the MAX-K-SAT problem, we study the performance of the finite energy version of the Survey Propagation (SP) algorithm. We show that a simple (linear time) backtrack decimation strategy is sufficient to reach configurations well below the lower bound for the dynamic threshold energy and very close to the analytic prediction for the optimal ground states. A comparative numerical study on one of the most efficient local search procedures is also given.Comment: 12 pages, submitted to Phys. Rev. E, accepted for publicatio