A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry

The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions. By implicitly transforming the spectral data into an NC-spectrum graph G=(V,E) where |V|=2k+2, we can solve this problem in O(|V|+|E|) time and O(|V|) space using dynamic programming. Our approach can be further used to discover a modified amino acid in O(|V||E|) time and to analyze data with other types of noise in O(|V||E|) time. Our algorithms have been implemented and tested on actual experimental data.Comment: A preliminary version appeared in Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 389--398, 200

Characterization of stochastic processes which stabilize linear companion form systems

AbstractThe class of stochastic processes is characterized which, as multiplicative noise with large intensity, stabilizes a linear system with companion form d×d-matrix. This includes the characterization of parametric noise which stabilizes the damped inverse pendulum. The proof yields also an expansion of the top Lyapunov exponent in terms of the noise intensity as well as a criterion for a stationary diffusion process permitting a stationary integral and it shows that stabilizing noise averages the Lyapunov spectrum

Oxygen-vacancy-mediated Negative Differential Resistance in La and Mg co-substituted BiFeO3 Thin Film

The conductive characteristics of Bi0.9La0.1Fe0.96Mg0.04O3(BLFM) thin film are investigated at various temperatures and a negative differential resistance (NDR) is observed in the thin film, where a leakage current peak occurs upon application of a downward electric field above 80 oC. The origin of the NDR behavior is shown to be related to the ionic defect of oxygen vacancies (VO..) present in the film. On the basis of analyzing the leakage mechanism and surface potential behavior, the NDR behavior can be understood by considering the competition between the polarized distribution and neutralization of VO..

Water and Sediment Discharge from Small Mountainous Rivers, Taiwan: The Roles of Lithology, Episodic Events, and Human Activities

Taiwan’s natural setting creates highly vulnerable watersheds whose rivers discharge disproportionately large quantities of sediment to the coastal ocean. The 16 Taiwanese rivers analyzed in this article discharge ∼180 Mt yr-1 of sediment to the coastal ocean, although totals over the past 20 years have varied between 16 and 440 Mt yr-1. The mean annual sediment yield of 9500 t km-2 yr-1 for the 16 rivers is 60-fold greater than the global yield of 150 t km-2 yr-1, but mean yields for the individual rivers vary by more than 2 orders of magnitude, from 500 to 71,000 t km-2 yr-1. Most sediment erosion and delivery occur in response to typhoon-generated floods, as evidenced by the fact that \u3e75% of the long-term flux occurs in \u3c 1% of the time, about one-third of which reaches hyperpycnal concentrations. Detailed analysis of the 16 watersheds reveals little evidence of any single environmental factor that controls sediment load. The Erren, the highest-yield river on Taiwan, drains an erodible but low-gradient watershed with relatively low runoff. In contrast, three east coast rivers, the Hoping, the Hualien, and the Beinan, have high sediment yields that may be explained by relatively frequent earthquakes coupled with high runoff. Farming and urbanization also have elevated sediment yields in eastern watersheds, whereas Holocene sediments buried in the Taiwan Strait suggest that present-day sediment loads of the western rivers may be no higher than prehuman levels

Hyperpycnal Discharge of Fluvial Sediment to the Ocean: Impact of Super‐Typhoon Herb (1996) on Taiwanese Rivers

Hyperpycnal events (when suspended sediment concentrations exceed 40 g/L) occur in small‐ and medium‐sized rivers throughout the world but are particularly common in Taiwan; they are often related to landslides or debris flows initiated and transported by typhoon floods. Super‐Typhoon Herb, which swept across Taiwan on July 31–August 2, 1996, triggered floods and landslides throughout the southern part of the island. Sediment concentrations in at least seven rivers (Taan, Choshui, Pachang, Erhjen, Tsengwen, Kaoping, and Peinan) approached or exceeded 40 g/L. Calculated sediment discharged from nine rivers (these seven as well as the Wu and Houlung, neither of which apparently reached hyperpycnal concentrations) during these 3 d was 217 million tons (MT)—most of it on August 1—of which ∼80% was discharged at hyperpycnal concentrations. Presumably, most of the sediments discharged by the Peinan River (to the southeast) and the Kaoping, Erhjen, Tsengwen, and Pachang rivers (to the southwest) were transported directly to the Huatong Basin and the South China Sea (via the Penghu Canyon system), respectively. The bulk of the typhoon‐derived sediment (142 MT), however, was discharged to the northwest (primarily by the Choshui River), and its fate remains unknown. It may have ultimately reached the Penghu Canyon system and thereby the South China Sea, but more probably it was transported northward (via the Taiwan Warm Current) toward China, the East China Sea, or (perhaps) the Okinawa Trough

Absorption coefficients in light oil scrubbers

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1941.Includes bibliographical references (leaf 91).by Edward Colin Forbes, John Yü-Ling Kao.M.S

Arginine, a Key Residue for the Enhancing Ability of an Antifreeze Protein of the Beetle Dendroides canadensis

Antifreeze proteins (AFPs) can produce a difference between the nonequilibrium freezing point and the melting point, termed thermal hysteresis (TH). The TH activity of an antifreeze protein (AFP) depends on the specific AFP and its concentration as well as the presence of cosolutes including low molecular mass solutes and/or proteins. We recently identified series of carboxylates and polyols as efficient enhancers for an AFP from the beetle Dendroides canadensis. In this study, we chemically modified DAFP-1 using the arginine-specific reagent 1,2-cyclohexanedione. We demonstrated that 1,2-cyclohexanedione specifically modifies one arginine residue and the modified DAFP-1 loses its enhancing ability completely or partially in the presence of previously identified enhancers. The stronger the enhancement ability of the enhancer on the native DAFP-1, the stronger the enhancement effect of the enhancer on the modified DAFP-1. The weaker enhancers (e.g., glycerol) completely lose their enhancement effect on the modified DAFP-1 due to their inability to compete with 1,2-cyclohexanedione for the arginine residue. Regeneration of the arginine residue using hydroxylamine fully restored the enhancing ability of DAFP-1. These studies indicated that an arginine residue is critical for the enhancing ability of DAFP-1 and the guanidinium group of the arginine residue is important for its interaction with the enhancers, where the general mechanism of arginine−ligand interaction is borne. This work may initiate a complete mechanistic study of the enhancement effect in AFPs