Exploring conformational energy landscape of glassy disaccharides by CPMAS 13C NMR and DFT/GIAO simulations. I. Methodological aspects

The aim of this article is to assess the ability of chemical shift surfaces to provide structural information on conformational distributions of disaccharides in glassy solid state. The validity of the general method leading to a simulation of inhomogeneous 13C chemical shift distributions is discussed in detail. In particular, a proper consideration of extrema and saddle points of the chemical shift map correctly accounts for the observed discontinuities in the experimental CPMAS spectra. Provided that these basic requirements are met, DFT/GIAO chemical shift maps calculated on relaxed conformations lead to a very satisfactory description of the experimental lineshapes. On solid-state trehalose as a model of amorphous disaccharide, this simulation approach defines unambiguously the most populated sugar conformation in the glass, and can help in discriminating the validity of different models of intramolecular energy landscape. Application to other molecular systems with broad conformational populations is foreseen to produce a larger dependence of the calculated chemical shift distribution on the conformational map

Distributed Formal Concept Analysis Algorithms Based on an Iterative MapReduce Framework

While many existing formal concept analysis algorithms are efficient, they are typically unsuitable for distributed implementation. Taking the MapReduce (MR) framework as our inspiration we introduce a distributed approach for performing formal concept mining. Our method has its novelty in that we use a light-weight MapReduce runtime called Twister which is better suited to iterative algorithms than recent distributed approaches. First, we describe the theoretical foundations underpinning our distributed formal concept analysis approach. Second, we provide a representative exemplar of how a classic centralized algorithm can be implemented in a distributed fashion using our methodology: we modify Ganter's classic algorithm by introducing a family of MR* algorithms, namely MRGanter and MRGanter+ where the prefix denotes the algorithm's lineage. To evaluate the factors that impact distributed algorithm performance, we compare our MR* algorithms with the state-of-the-art. Experiments conducted on real datasets demonstrate that MRGanter+ is efficient, scalable and an appealing algorithm for distributed problems.Comment: 17 pages, ICFCA 201, Formal Concept Analysis 201

Investigation of molecular dimers by ensemble and single molecule spectroscopy

We have investigated molecular dimers with different electronic coupling strengths by bulk and single molecule spectroscopy. In one of the dimers the two monomers (perylene-monoimide) are directly connected via a single bond while in the other one they are separated by the benzil motif. The close proximity of the monomers in the first case gives rise to excitonic band splitting which is clearly observable in the bulk absorption spectra. For the benzil structure the electronic interactions are governed by Förster-type energy hopping between the monomers. Fluorescence intensity trajectories at the single molecule level show one-step and two-step bleaching behaviour which appears to be very similar for both dimers. However, emission spectra recorded simultaneously with the trajectories indicate spectral changes which allow to distinguish between weakly and strongly coupled dimers. In the latter case the spectral shape changes significantly when excitonic coupling has been lifted because of photochemical transformation of one of the monomers

Critical fluctuations and breakdown of Stokes-Einstein relation in the Mode-Coupling Theory of glasses

We argue that the critical dynamical fluctuations predicted by the mode-coupling theory (MCT) of glasses provide a natural mechanism to explain the breakdown of the Stokes-Einstein relation. This breakdown, observed numerically and experimentally in a region where MCT should hold, is one of the major difficulty of the theory, for which we propose a natural resolution based on the recent interpretation of the MCT transition as a bona fide critical point with a diverging length scale. We also show that the upper critical dimension of MCT is d_c=8.Comment: Proceedings of the workshop on non-equilibrium phenomena in supercooled fluids, glasses and amorphous materials (17-22 September, 2006, Pisa

Multiple glass transitions in star polymer mixtures: Insights from theory and simulations

The glass transition in binary mixtures of star polymers is studied by mode coupling theory and extensive molecular dynamics computer simulations. In particular, we have explored vitrification in the parameter space of size asymmetry $\delta$ and concentration $\rho_2$ of the small star polymers at fixed concentration of the large ones. Depending on the choice of parameters, three different glassy states are identified: a single glass of big polymers at low $\delta$ and low $\rho_2$, a double glass at high $\delta$ and low $\rho_2$, and a novel double glass at high $\rho_2$ and high $\delta$ which is characterized by a strong localization of the small particles. At low $\delta$ and high $\rho_2$ there is a competition between vitrification and phase separation. Centered in the $(\delta, \rho_2)$-plane, a liquid lake shows up revealing reentrant glass formation. We compare the behavior of the dynamical density correlators with the predictions of the theory and find remarkable agreement between the two.Comment: 15 figures, to be published in Macromolecule

An integrated approach using M. truncatula to identify loci/genes controlling nutritional and physiological quality of legume seeds

An integrated approach using M. truncatula to identify loci/genes controlling nutritional and physiological quality of legume seeds