Path-integral virial estimator for reaction rate calculation based on the quantum instanton approximation

The quantum instanton approximation is a type of quantum transition state theory that calculates the chemical reaction rate using the reactive flux correlation function and its low order derivatives at time zero. Here we present several path-integral estimators for the latter quantities, which characterize the initial decay profile of the flux correlation function. As with the internal energy or heat capacity calculation, different estimators yield different variances (and therefore different convergence properties) in a Monte Carlo calculation. Here we obtain a virial-type estimator by using a coordinate scaling procedure rather than integration by parts, which allows more computational benefits. We also consider two different methods for treating the flux operator, i.e., local-path and global-path approaches, in which the latter achieves a smaller variance at the cost of using second-order potential derivatives. Numerical tests are performed for a one-dimensional Eckart barrier and a model proton transfer reaction in a polar solvent, which illustrates the reduced variance of the virial estimator over the corresponding thermodynamic estimator.Comment: 23 pages, 5 figures, 1 tabl

Stimulation of bone growth with thrombin peptide derivatives

Disclosed is a method of stimulating bone growth at a site in a subject in need of osteoinduction. The method comprises the step of administering a therapeutically effective amount of an agonist of the non-proteolytically activated thrombin receptor to the site.Board of Regents, University of Texas Syste

A major index for matchings and set partitions

We introduce a statistic \pmaj on partitions of $[n]=\{1,2,..., n\}$, and show that it is equidistributed with the number of 2-crossings over partitions of $[n]$ with given sets of minimal block elements and maximal block elements. This generalizes the classical result of equidistribution for the permutation statistics inversion number and major index.Comment: 17 pages, 9 figure

Determining the orientations of ocean bottom seismometers using ambient noise correlation

The cross-correlation of multicomponent ambient seismic noise can reveal both the velocity and polarization of surface waves propagating between pairs of stations. We explore this property to develop a novel method for determining the horizontal orientation of ocean bottom seismometers (OBS) by analyzing the polarization of Rayleigh waves retrieved from ambient noise cross-correlation. We demonstrate that the sensor orientations can be estimated through maximizing the correlation between the radial-vertical component and the phase-shifted vertical-vertical component of the empirical Green's tensor. We apply this new method to the ELSC (Eastern Lau Spreading Center) OBS experiment data set and illustrate its robustness by comparing the obtained orientations with results from a conventional method utilizing teleseismic P and Rayleigh wave polarizations. When applied to a large OBS array, the ambient noise method provides a larger number of orientation estimates and better azimuthal coverage than typically is possible with traditional methods

CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences

<p>Abstract</p> <p>Background</p> <p>It has been increasingly appreciated that coding sequences harbor regulatory sequence motifs in addition to encoding for protein. These sequence motifs are expected to be overrepresented in nucleotide sequences bound by a common protein or small RNA. However, detecting overrepresented motifs has been difficult because of interference by constraints at the protein level. Sampling-based approaches to solve this problem based on codon-shuffling have been limited to exploring only an infinitesimal fraction of the sequence space and by their use of parametric approximations.</p> <p>Results</p> <p>We present a novel <it>O</it>(<it>N</it>(log <it>N</it>)²)-time algorithm, CodingMotif, to identify nucleotide-level motifs of unusual copy number in protein-coding regions. Using a new dynamic programming algorithm we are able to exhaustively calculate the distribution of the number of occurrences of a motif over all possible coding sequences that encode the same amino acid sequence, given a background model for codon usage and dinucleotide biases. Our method takes advantage of the sparseness of loci where a given motif can occur, greatly speeding up the required convolution calculations. Knowledge of the distribution allows one to assess the exact non-parametric p-value of whether a given motif is over- or under- represented. We demonstrate that our method identifies known functional motifs more accurately than sampling and parametric-based approaches in a variety of coding datasets of various size, including ChIP-seq data for the transcription factors NRSF and GABP.</p> <p>Conclusions</p> <p>CodingMotif provides a theoretically and empirically-demonstrated advance for the detection of motifs overrepresented in coding sequences. We expect CodingMotif to be useful for identifying motifs in functional genomic datasets such as DNA-protein binding, RNA-protein binding, or microRNA-RNA binding within coding regions. A software implementation is available at <url>http://bioinformatics.bc.edu/chuanglab/codingmotif.tar</url></p

Elementary Students’ Computational Thinking Practice in a Bridge Design and Building Challenge (Fundamental)

The increased focus on computational thinking (CT) has grown in recent years for various reasons, such as a general concern about (a) a lack of global competitiveness among American students and general literacy in science, technology, engineering, and math (STEM) fields (Hsu & Cardella, 2013), (b) maintaining the economic competitiveness of the U.S. (Yadav, Hong, & Stephenson, 2016), and (c) preparing students adequately for a society that is increasingly technological (NRC, 2011). CT can help individuals analyze and understand multiple dimensions of a complex problem and identify and apply appropriate tools or techniques to address a complex problem (Wing, 2010). Furthermore, children can benefit from improved technological literacy, content knowledge, and problem-solving skills (Hsu & Cardella, 2013) while practicing CT