MapScript: A map algebra programming language incorporating neighborhood analysis

Map algebra is a data model and simple functional notation to study the distribution and patterns of spatial phenomena. It uses a uniform representation of space as discrete grids, which are organized into layers. This paper discusses extensions to map algebra to handle neighborhood operations with a new data type called a template. Templates provide general windowing operations on grids to enable spatial models for cellular automata, mathematical morphology, and local spatial statistics. A programming language for map algebra that incorporates templates and special processing constructs is described. The programming language is called MapScript. Example program scripts are presented to perform diverse and interesting neighborhood analysis for descriptive, model-based and processed-based analysis.

Photoinduced electron transfer and electronic energy transfer in naphthyl-appended cyclams

A series of novel macrocyclic tetraaza ligands that incorporate a naphthalene moiety as a photoactive chromophore have been prepared and structurally characterized as their Cu(II) complexes. Variable-temperature photophysical studies have concluded that the luminescence quenching evident in the Cu(H) complexes is due to intramolecular electronic energy transfer (EET). In their free-base forms, these ligands undergo reductive luminescence quenching via photoinduced electron transfer (PET) reactions, with proximate amine lone pairs acting as electron donors. Consequently, the emission behavior can be modulated by variations in pH and/or the presence of other Lewis acids such as Zn(H).

The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms

Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying,that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.

Using clusters of computers for large QU-GENE simulation experiments

The QU-GENE Computing Cluster (QCC) is a hardware and software solution to the automation and speedup of large QU-GENE (QUantitative GENEtics) simulation experiments that are designed to examine the properties of genetic models, particularly those that involve factorial combinations of treatment levels. QCC automates the management of the distribution of components of the simulation experiments among the networked single-processor computers to achieve the speedup.

Single-electron measurements with a micromechanical resonator

A mechanical electroscope based on a change in the resonant frequency of a cantilever one micron in size in the presence of charge has recently been fabricated. We derive the decoherence rate of a charge superposition during measurement with such a device using a master equation theory adapted from quantum optics. We also investigate the information produced by such a measurement, using a quantum trajectory approach. Such instruments could be used in mesoscopic electronic systems, and future solid-state quantum computers, so it is useful to know how they behave when used to measure quantum superpositions of charge.

Intramolecular electronic energy transfer in bichromophoric macrocyclic complexes

Efficient intramolecular electronic energy transfer (EET) has been demonstrated for three novel bichromophoric compounds utilizing a macrocyclic spacer as the bridge between the electronic energy donor and acceptor fragments. As their free base forms, emission from the electronically excited donor is absent and the acceptor emission is reductively quenched via photoinduced oxidation of proximate amine lone pairs. As their Zn(II) complexes, excitation of the donor results in sensitization of the electronic acceptor emission.