A weak characterization of slow variables in stochastic dynamical systems

We present a novel characterization of slow variables for continuous Markov processes that provably preserve the slow timescales. These slow variables are known as reaction coordinates in molecular dynamical applications, where they play a key role in system analysis and coarse graining. The defining characteristics of these slow variables is that they parametrize a so-called transition manifold, a low-dimensional manifold in a certain density function space that emerges with progressive equilibration of the system's fast variables. The existence of said manifold was previously predicted for certain classes of metastable and slow-fast systems. However, in the original work, the existence of the manifold hinges on the pointwise convergence of the system's transition density functions towards it. We show in this work that a convergence in average with respect to the system's stationary measure is sufficient to yield reaction coordinates with the same key qualities. This allows one to accurately predict the timescale preservation in systems where the old theory is not applicable or would give overly pessimistic results. Moreover, the new characterization is still constructive, in that it allows for the algorithmic identification of a good slow variable. The improved characterization, the error prediction and the variable construction are demonstrated by a small metastable system

Giant Anharmonic Phonon Scattering in PbTe

Understanding the microscopic processes affecting the bulk thermal conductivity is crucial to develop more efficient thermoelectric materials. PbTe is currently one of the leading thermoelectric materials, largely thanks to its low thermal conductivity. However, the origin of this low thermal conductivity in a simple rocksalt structure has so far been elusive. Using a combination of inelastic neutron scattering measurements and first-principles computations of the phonons, we identify a strong anharmonic coupling between the ferroelectric transverse optic (TO) mode and the longitudinal acoustic (LA) modes in PbTe. This interaction extends over a large portion of reciprocal space, and directly affects the heat-carrying LA phonons. The LA-TO anharmonic coupling is likely to play a central role in explaining the low thermal conductivity of PbTe. The present results provide a microscopic picture of why many good thermoelectric materials are found near a lattice instability of the ferroelectric type

Linking magmatism with collision in an accretionary orogen

A compilation of U-Pb age, geochemical and isotopic data for granitoid plutons in the southern Central Asian Orogenic Belt (CAOB), enables evaluation of the interaction between magmatism and orogenesis in the context of Paleo-Asian oceanic closure and continental amalgamation. These constraints, in conjunction with other geological evidence, indicate that following consumption of the ocean, collision-related calc-alkaline granitoid and mafic magmatism occurred from 255 ± 2 Ma to 251 ± 2 Ma along the Solonker-Xar Moron suture zone. The linear or belt distribution of end-Permian magmatism is interpreted to have taken place in a setting of final orogenic contraction and weak crustal thickening, probably as a result of slab break-off. Crustal anatexis slightly post-dated the early phase of collision, producing adakite-like granitoids with some S-type granites during the Early-Middle Triassic (ca. 251-245 Ma). Between 235 and 220 Ma, the local tectonic regime switched from compression to extension, most likely caused by regional lithospheric extension and orogenic collapse. Collision-related magmatism from the southern CAOB is thus a prime example of the minor, yet tell-tale linking of magmatism with orogenic contraction and collision in an archipelago-type accretionary orogen

Simultaneously Hermaphroditic Shrimp Use Lipophilic Cuticular Hydrocarbons as Contact Sex Pheromones

Successful mating is essentially a consequence of making the right choices at the correct time. Animals use specific strategies to gain information about a potential mate, which is then applied to decision-making processes. Amongst the many informative signals, odor cues such as sex pheromones play important ecological roles in coordinating mating behavior, enabling mate and kin recognition, qualifying mate choice, and preventing gene exchange among individuals from different populations and species. Despite overwhelming behavioral evidence, the chemical identity of most cues used in aquatic organisms remains unknown and their impact and omnipresence have not been fully recognized. In many crustaceans, including lobsters and shrimps, reproduction happens through a cascade of events ranging from initial attraction to formation of a mating pair eventually leading to mating. We examined the hypothesis that contact pheromones on the female body surface of the hermaphroditic shrimp Lysmata boggessi are of lipophilic nature, and resemble insect cuticular hydrocarbon contact cues. Via chemical analyses and behavioural assays, we show that newly molted euhermaphrodite-phase shrimp contain a bouquet of odor compounds. Of these, (Z)-9-octadecenamide is the key odor with hexadecanamide and methyl linoleate enhancing the bioactivity of the pheromone blend. Our results show that in aquatic systems lipophilic, cuticular hydrocarbon contact sex pheromones exist; this raises questions on how hydrocarbon contact signals evolved and how widespread these are in the marine environment

Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences

BACKGROUND: The number of k-words shared between two sequences is a simple and effcient alignment-free sequence comparison method. This statistic, D(2), has been used for the clustering of EST sequences. Sequence comparison based on D(2 )is extremely fast, its runtime is proportional to the size of the sequences under scrutiny, whereas alignment-based comparisons have a worst-case run time proportional to the square of the size. Recent studies have tackled the rigorous study of the statistical distribution of D(2), and asymptotic regimes have been derived. The distribution of approximate k-word matches has also been studied. RESULTS: We have computed the D(2 )optimal word size for various sequence lengths, and for both perfect and approximate word matches. Kolmogorov-Smirnov tests show D(2 )to have a compound Poisson distribution at the optimal word size for small sequence lengths (below 400 letters) and a normal distribution at the optimal word size for large sequence lengths (above 1600 letters). We find that the D(2 )statistic outperforms BLAST in the comparison of artificially evolved sequences, and performs similarly to other methods based on exact word matches. These results obtained with randomly generated sequences are also valid for sequences derived from human genomic DNA. CONCLUSION: We have characterized the distribution of the D(2 )statistic at optimal word sizes. We find that the best trade-off between computational efficiency and accuracy is obtained with exact word matches. Given that our numerical tests have not included sequence shuffling, transposition or splicing, the improvements over existing methods reported here underestimate that expected in real sequences. Because of the linear run time and of the known normal asymptotic behavior, D(2)-based methods are most appropriate for large genomic sequences

Risk of death in the long QT syndrome when a sibling has died

BACKGROUND: Sudden death of a sibling is thought to be associated with greater risk of death in long QT syndrome (LQTS). However, there is no evidence of such an association. OBJECTIVE: This study sought to test the hypothesis that sudden death of a sibling is a risk factor for death or aborted cardiac arrest (ACA) in patients with LQTS. METHODS: We examined all probands and first-degree and second-degree relatives in the International Long QT Registry from birth to age 40 years with QTc >/= 0.45 s. Covariates included sibling death, QTc, gender by age, syncope, and implantable cardioverter-defibrillator (ICD) and beta-blocker treatment. End points were (1) severe events (ACA, LQTS-related death) and (2) any cardiac event (syncope, ACA, or LQTS-related death). RESULTS: Of 1915 subjects, 270 had a sibling who died. There were 213 severe events and 829 total cardiac events. More subjects with history of sibling death received beta-blocker therapy. Sibling death was not significantly associated with risk of ACA or LQTS-related death, but was associated with increased risk of syncope. QTc >/= 0.53 s (hazard ratio 2.5, P <.01), history of syncope (hazard ratio 6.1, P <.01), and gender were strongly associated with risk of ACA or LQTS-related death. CONCLUSION: Sudden death of a sibling prompted more aggressive treatment but did not predict risk of death or ACA, whereas QTc >/= 0.53 s, gender, and syncope predicted this risk. All subjects should receive appropriate beta-blocker therapy. The decision to implant an ICD should be based on an individual's own risk characteristics (QTc, gender, and history of syncope)

Algebraic Distribution of Segmental Duplication Lengths in Whole-Genome Sequence Self-Alignments

Distributions of duplicated sequences from genome self-alignment are characterized, including forward and backward alignments in bacteria and eukaryotes. A Markovian process without auto-correlation should generate an exponential distribution expected from local effects of point mutation and selection on localised function; however, the observed distributions show substantial deviation from exponential form – they are roughly algebraic instead – suggesting a novel kind of long-distance correlation that must be non-local in origin

Facile Fabrication of Ultrafine Hollow Silica and Magnetic Hollow Silica Nanoparticles by a Dual-Templating Approach

The development of synthetic process for hollow silica materials is an issue of considerable topical interest. While a number of chemical routes are available and are extensively used, the diameter of hollow silica often large than 50 nm. Here, we report on a facial route to synthesis ultrafine hollow silica nanoparticles (the diameter of ca. 24 nm) with high surface area by using cetyltrimethylammmonium bromide (CTAB) and sodium bis(2-ethylhexyl) sulfosuccinate (AOT) as co-templates and subsequent annealing treatment. When the hollow magnetite nanoparticles were introduced into the reaction, the ultrafine magnetic hollow silica nanoparticles with the diameter of ca. 32 nm were obtained correspondingly. Transmission electron microscopy studies confirm that the nanoparticles are composed of amorphous silica and that the majority of them are hollow

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis and brings more accurate information about compound retention times and mass spectra. Despite these advantages, the retention times of the resolved peaks on the two-dimensional gas chromatographic columns are always shifted due to experimental variations, introducing difficulty in the data processing for metabolomics analysis. Therefore, the retention time variation must be adjusted in order to compare multiple metabolic profiles obtained from different conditions.</p> <p>Results</p> <p>We developed novel peak alignment algorithms for both homogeneous (acquired under the identical experimental conditions) and heterogeneous (acquired under the different experimental conditions) GC × GC-MS data using modified Smith-Waterman local alignment algorithms along with mass spectral similarity. Compared with literature reported algorithms, the proposed algorithms eliminated the detection of landmark peaks and the usage of retention time transformation. Furthermore, an automated peak alignment software package was established by implementing a likelihood function for optimal peak alignment.</p> <p>Conclusions</p> <p>The proposed Smith-Waterman local alignment-based algorithms are capable of aligning both the homogeneous and heterogeneous data of multiple GC × GC-MS experiments without the transformation of retention times and the selection of landmark peaks. An optimal version of the SW-based algorithms was also established based on the associated likelihood function for the automatic peak alignment. The proposed alignment algorithms outperform the literature reported alignment method by analyzing the experiment data of a mixture of compound standards and a metabolite extract of mouse plasma with spiked-in compound standards.</p