Pondering With Pegg

From Oscar:Carbon sulfideHot Club de Pari

Nanomechatronics

I like nanomechatronics a lot. Add a single letter to a phrase and come up with an arrangement of a topic or person in the news

Letter Banks

Letter banks use and reuse the letters of a given set (the bank). Here are some nice examples

Picture-Hanging Puzzles

We show how to hang a picture by wrapping rope around n nails, making a polynomial number of twists, such that the picture falls whenever any k out of the n nails get removed, and the picture remains hanging when fewer than k nails get removed. This construction makes for some fun mathematical magic performances. More generally, we characterize the possible Boolean functions characterizing when the picture falls in terms of which nails get removed as all monotone Boolean functions. This construction requires an exponential number of twists in the worst case, but exponential complexity is almost always necessary for general functions.Comment: 18 pages, 8 figures, 11 puzzles. Journal version of FUN 2012 pape

Mathematical modelling of polyamine metabolism in bloodstream-form trypanosoma brucei: An application to drug target identification

© 2013 Gu et al. 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 creditedThis article has been made available through the Brunel Open Access Publishing Fund.We present the first computational kinetic model of polyamine metabolism in bloodstream-form Trypanosoma brucei, the causative agent of human African trypanosomiasis. We systematically extracted the polyamine pathway from the complete metabolic network while still maintaining the predictive capability of the pathway. The kinetic model is constructed on the basis of information gleaned from the experimental biology literature and defined as a set of ordinary differential equations. We applied Michaelis-Menten kinetics featuring regulatory factors to describe enzymatic activities that are well defined. Uncharacterised enzyme kinetics were approximated and justified with available physiological properties of the system. Optimisation-based dynamic simulations were performed to train the model with experimental data and inconsistent predictions prompted an iterative procedure of model refinement. Good agreement between simulation results and measured data reported in various experimental conditions shows that the model has good applicability in spite of there being gaps in the required data. With this kinetic model, the relative importance of the individual pathway enzymes was assessed. We observed that, at low-to-moderate levels of inhibition, enzymes catalysing reactions of de novo AdoMet (MAT) and ornithine production (OrnPt) have more efficient inhibitory effect on total trypanothione content in comparison to other enzymes in the pathway. In our model, prozyme and TSHSyn (the production catalyst of total trypanothione) were also found to exhibit potent control on total trypanothione content but only when they were strongly inhibited. Different chemotherapeutic strategies against T. brucei were investigated using this model and interruption of polyamine synthesis via joint inhibition of MAT or OrnPt together with other polyamine enzymes was identified as an optimal therapeutic strategy.The work was carried out under a PhD programme partly funded by Prof. Ray Welland, School of Computing Science, University of Glasgo

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%–63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with “overprediction” of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation

Krypto, or 24-game

With the numbers (3 3 7 7), can you use arithmetic to reach a goal number of 24? There are many puzzles of this type, such as the four fours puzzle. Some games based on this kind of puzzle include Krypto and the 24-game. Move the sliders to change the given values and goal numberComponente Curricular::Ensino Fundamental::Séries Finais::Matemátic

LU Decomposition

In Mathematica, the function LUDecomposition factors a matrix m into the form P L U, where P is a permutation matrix, L is a lower triangular matrix, and U is an upper triangular matrixComponente Curricular::Educação Superior::Ciências Exatas e da Terra::Matemátic

The stains cellular automaton

Knowledge about growth processes and simple computational systemsThe Stains cellular automata (rule 260320) has the rare property that for almost all initial conditions it will grow irregularly, then stop. A variety of initial conditions with interesting behavior are shown hereComponente Curricular::Educação Superior::Ciências Exatas e da Terra::Matemátic