Vapor Pressure of Ionic Liquids

We argue that the extremely low vapor pressures of room temperature ionic liquids near their triple points are due to the combination of strong ionic characters and of low melting temperatures.Comment: Initially submitted manuscript of article M. Bier and S. Dietrich, Mol. Phys. 108, 211 (2010) [Corrigendum: Mol. Phys. 108, 1413 (2010)

Surface Structures Determined by Kinetic Processes: Adsorption and Diffusion of Oxygen on Pd(100)

Atomic oxygen forms a metastable c(2×2) phase on Pd(100) under conditions of rapid adsorption (high pressure) and slow diffusion (low sample temperature). One possible explanation is that oxygen molecules require an 8-fold ensemble of empty sites for dissociative chemisorption, and that subsequent adatom motion is limited and creates no neighboring pairs of filled sites. We describe the properties of the adlayer predicted by such a model

Surface Chemistry of Perfluoropolyethers and Hydrogenated Analogs: Are Studies of Model Compounds Useful?

We have studied adsorption, desorption, and decomposition of ethers on Ru(001), an atomically-smooth metal surface. We have compared diethers with monoethers, and fluorinated ethers with hydrogenated ethers. The number of ether linkages does not strongly influence adsorption bond strength, nor the extent of decomposition. Fluorination does weaken the adsorption bond strength and prevents decomposition. These studies suggest that the surface properties of monomeric ethers can be used to predict properties of oligomeric, and perhaps even polymeric, ethers

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm

<p>Abstract</p> <p>Background</p> <p>Motif discovery aims to detect short, highly conserved patterns in a collection of unaligned DNA or protein sequences. Discriminative motif finding algorithms aim to increase the sensitivity and selectivity of motif discovery by utilizing a second set of sequences, and searching only for patterns that can differentiate the two sets of sequences. Potential applications of discriminative motif discovery include discovering transcription factor binding site motifs in ChIP-chip data and finding protein motifs involved in thermal stability using sets of orthologous proteins from thermophilic and mesophilic organisms.</p> <p>Results</p> <p>We describe DEME, a discriminative motif discovery algorithm for use with protein and DNA sequences. Input to DEME is two sets of sequences; a "positive" set and a "negative" set. DEME represents motifs using a probabilistic model, and uses a novel combination of global and local search to find the motif that optimally discriminates between the two sets of sequences. DEME is unique among discriminative motif finders in that it uses an informative Bayesian prior on protein motif columns, allowing it to incorporate prior knowledge of residue characteristics. We also introduce four, synthetic, discriminative motif discovery problems that are designed for evaluating discriminative motif finders in various biologically motivated contexts. We test DEME using these synthetic problems and on two biological problems: finding yeast transcription factor binding motifs in ChIP-chip data, and finding motifs that discriminate between groups of thermophilic and mesophilic orthologous proteins.</p> <p>Conclusion</p> <p>Using artificial data, we show that DEME is more effective than a non-discriminative approach when there are "decoy" motifs or when a variant of the motif is present in the "negative" sequences. With real data, we show that DEME is as good, but not better than non-discriminative algorithms at discovering yeast transcription factor binding motifs. We also show that DEME can find highly informative thermal-stability protein motifs. Binaries for the stand-alone program DEME is free for academic use and is available at <url>http://bioinformatics.org.au/deme/</url></p

AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous

Discrimination Training with Multimodal Stimuli Changes Activity in the Mushroom Body of the Hawkmoth Manduca sexta

The mushroom bodies of the insect brain play an important role in olfactory processing, associative learning and memory. The mushroom bodies show odor-specific spatial patterns of activity and are also influenced by visual stimuli.Functional imaging was used to investigate changes in the in vivo responses of the mushroom body of the hawkmoth Manduca sexta during multimodal discrimination training. A visual and an odour stimulus were presented either together or individually. Initially, mushroom body activation patterns were identical to the odour stimulus and the multimodal stimulus. After training, however, the mushroom body response to the rewarded multimodal stimulus was significantly lower than the response to the unrewarded unimodal odour stimulus, indicating that the coding of the stimuli had changed as a result of training. The opposite pattern was seen when only the unimodal odour stimulus was rewarded. In this case, the mushroom body was more strongly activated by the multimodal stimuli after training. When no stimuli were rewarded, the mushroom body activity decreased for both the multimodal and unimodal odour stimuli. There was no measurable response to the unimodal visual stimulus in any of the experiments. These results can be explained using a connectionist model where the mushroom body is assumed to be excited by olfactory stimulus components, and suppressed by multimodal configurations.Discrimination training with multimodal stimuli consisting of visual and odour cues leads to stimulus specific changes in the in vivo responses of the mushroom body of the hawkmoth