A contact-waiting-time metric and RNA folding rates

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base contacts toward RNA structure formation. We apply the metric to RNA sequences whose folding rates were previously determined experimentally. We find that the metric has good correlation (correlation coefficient: -0.95, p << 0.01) with the logarithmically transformed folding rates of those RNA sequences. This suggests that the metric can be useful for predicting RNA folding rates. We use the metric to predict the folding rates of bacterial and eukaryotic group II introns. Future applications of the metric (e.g., to predict structural RNAs) could prove fruitful.Comment: 15 pages, 1 figure, 3 tables, matlab code. Published in FEBS Letters (June '09

Benjamin Banneker\u27s Original Handwritten Document: Observations and Study of the Cicada

Benjamin Banneker, farmer, mathematician, astronomer, and scientist, is known for his mathematical puzzles, ephemeris calculations, almanacs, his wooden clock, land surveying work, and famous letter on human rights. However, as a naturalist, his scientific and systematic observations of the cicadas are less known. In this paper we publicize Banneker’s naturalistic study of the seventeen-year periodic cycle of the cicada and make available the original handwritten document of his observations. We also introduce the audience of this journal to an intriguing natural problem involving prime numbers

An RNA foldability metric; implications for the design of rapidly foldable RNA sequences

Evidence is presented suggesting, for the first time, that the protein foldability metric sigma=(T_theta - T_f)/T_theta, where T_theta and T_f are, respectively, the collapse and folding transition temperatures, could be used also to measure the foldability of RNA sequences. The importance of sigma is discussed in the context of the in silico design of rapidly foldable RNA sequences.Comment: To appear in Biophysical Chemistr

On some (pseudo) involutions in the Riordan group

In this paper, we address a question posed by L. Shapiro regarding algebraic and/or combinatorial characterizations of the elements of order 2 in the Riordan group. We present two classes of combinatorial matrices having pseudo-order 2. In one class, we find generalizations of Pascal’s triangle and use some special cases to discover and prove interesting identities. In the other class, we find generalizations of Nkwanta’s RNA triangle and show that they are pseudo-involutions.