40 research outputs found
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
Time--delay autosynchronization of the spatio-temporal dynamics in resonant tunneling diodes
The double barrier resonant tunneling diode exhibits complex spatio-temporal
patterns including low-dimensional chaos when operated in an active external
circuit. We demonstrate how autosynchronization by time--delayed feedback
control can be used to select and stabilize specific current density patterns
in a noninvasive way. We compare the efficiency of different control schemes
involving feedback in either local spatial or global degrees of freedom. The
numerically obtained Floquet exponents are explained by analytical results from
linear stability analysis.Comment: 10 pages, 16 figure
Accumulation of potentially toxic elements in road deposited sediments in residential and light industrial neighborhoods of Singapore
10.1016/j.jenvman.2011.11.017Journal of Environmental Management101151-163JEVM
Turbidity-based sediment monitoring in northern Thailand: Hysteresis, variability, and uncertainty
10.1016/j.jhydrol.2014.09.010Journal of Hydrology519PB2020-203
Phase equilibria in the system Fe-Zn-O at intermediate conditions between metallic-iron saturation and air
The phase equilibria in the FeO-Fe2O3-ZnO system have been experimentally investigated at oxygen partial pressures between metallic iron saturation and air using a specially developed quenching technique, followed by electron probe X-ray microanalysis (EPMA) and then wet chemistry for determination of ferrous and ferric iron concentrations. Gas mixtures of H-2, N-2, and CO2 or CO and CO2 controlled the atmosphere in the furnace. The determined metal cation ratios in phases at equilibrium were used for the construction of the 1200 degrees C isothermal section of the Fe-Zn-O system. The univariant equilibria between the gas phase, spinel, wustite, and zincite was found to be close to pO(2) = 1 center dot 10(-8) atm at 1200 degrees C. The ferric and ferrous iron concentrations in zincite and spinel at equilibrium were also determined at temperatures from 1200 degrees C to 1400 degrees C at pO(2) = 1 center dot 10(-6) atm and at 1200 degrees C at pO(2) values ranging from 1 center dot 10(-4) to 1 center dot 10(-8) atm. Implications of the phase equilibria in the Fe-Zn-O system for the formation of the platelike zincite, especially important for the Imperial Smelting Process (ISP), are discussed